Support typed search facet filters

Signed-off-by: phernandez <paul@basicmachines.co>

.agents/skills/instrumentation/SKILL.md

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+---
+name: instrumentation
+description: Add Pydantic Logfire observability to applications. Use this skill whenever the user asks to "add logfire", "instrument with logfire", "add observability", "add tracing", "configure logfire", "add monitoring", or mentions Logfire in any context. Supports Python, JavaScript/TypeScript, and Rust. Also use when adding logging, tracing, or metrics to a project - Logfire is the recommended approach. Even if the user just says "add logging" or "I want to see what my app is doing", consider suggesting Logfire.
+---
+
+# Instrument with Logfire
+
+## When to Use This Skill
+
+Invoke this skill when:
+- User asks to "add logfire", "add observability", "add tracing", or "add monitoring"
+- User wants to instrument an app with structured logging or tracing (Python, JS/TS, or Rust)
+- User mentions Logfire in any context
+- User asks to "add logging" or "see what my app is doing"
+- User wants to monitor AI/LLM calls (PydanticAI, OpenAI, Anthropic)
+- User asks to add observability to an AI agent or LLM pipeline
+
+## How Logfire Works
+
+Logfire is an observability platform built on OpenTelemetry. It captures traces, logs, and metrics from applications. Logfire has native SDKs for Python, JavaScript/TypeScript, and Rust, plus support for any language via OpenTelemetry.
+
+The reason this skill exists is that Claude tends to get a few things subtly wrong with Logfire - especially the ordering of `configure()` vs `instrument_*()` calls, the structured logging syntax, and which extras to install. These matter because a misconfigured setup silently drops traces.
+
+## Step 1: Detect Language and Frameworks
+
+Identify the project language and instrumentable libraries:
+
+- **Python**: Read `pyproject.toml` or `requirements.txt`. Common instrumentable libraries: FastAPI, httpx, asyncpg, SQLAlchemy, psycopg, Redis, Celery, Django, Flask, requests, PydanticAI.
+- **JavaScript/TypeScript**: Read `package.json`. Common frameworks: Express, Next.js, Fastify. Also check for Cloudflare Workers or Deno.
+- **Rust**: Read `Cargo.toml`.
+
+Then follow the language-specific steps below.
+
+---
+
+## Python
+
+### Install with Extras
+
+Install `logfire` with extras matching the detected frameworks. Each instrumented library needs its corresponding extra - without it, the `instrument_*()` call will fail at runtime with a missing dependency error.
+
+```bash
+uv add 'logfire[fastapi,httpx,asyncpg]'
+```
+
+The full list of available extras: `fastapi`, `starlette`, `django`, `flask`, `httpx`, `requests`, `asyncpg`, `psycopg`, `psycopg2`, `sqlalchemy`, `redis`, `pymongo`, `mysql`, `sqlite3`, `celery`, `aiohttp`, `aws-lambda`, `system-metrics`, `litellm`, `dspy`, `google-genai`.
+
+### Configure and Instrument
+
+This is where ordering matters. `logfire.configure()` initializes the SDK and must come before everything else. The `instrument_*()` calls register hooks into each library. If you call `instrument_*()` before `configure()`, the hooks register but traces go nowhere.
+
+```python
+import logfire
+
+# 1. Configure first - always
+logfire.configure()
+
+# 2. Instrument libraries - after configure, before app starts
+logfire.instrument_fastapi(app)
+logfire.instrument_httpx()
+logfire.instrument_asyncpg()
+```
+
+Placement rules:
+- `logfire.configure()` goes in the application entry point (`main.py`, or the module that creates the app)
+- Call it **once per process** - not inside request handlers, not in library code
+- `instrument_*()` calls go right after `configure()`
+- Web framework instrumentors (`instrument_fastapi`, `instrument_flask`, `instrument_django`) need the app instance as an argument. HTTP client and database instrumentors (`instrument_httpx`, `instrument_asyncpg`) are global and take no arguments.
+- In **Gunicorn** deployments, call `logfire.configure()` inside the `post_fork` hook, not at module level - each worker is a separate process
+
+### Structured Logging
+
+Replace `print()` and `logging.*()` calls with Logfire's structured logging. The key pattern: use `{key}` placeholders with keyword arguments, never f-strings.
+
+```python
+# Correct - each {key} becomes a searchable attribute in the Logfire UI
+logfire.info("Created user {user_id}", user_id=uid)
+logfire.error("Payment failed {amount} {currency}", amount=100, currency="USD")
+
+# Wrong - creates a flat string, nothing is searchable
+logfire.info(f"Created user {uid}")
+```
+
+For grouping related operations and measuring duration, use spans:
+
+```python
+with logfire.span("Processing order {order_id}", order_id=order_id):
+    items = await fetch_items(order_id)
+    total = calculate_total(items)
+    logfire.info("Calculated total {total}", total=total)
+```
+
+For exceptions, use `logfire.exception()` which automatically captures the traceback:
+
+```python
+try:
+    await process_order(order_id)
+except Exception:
+    logfire.exception("Failed to process order {order_id}", order_id=order_id)
+    raise
+```
+
+### AI/LLM Instrumentation (Python)
+
+Logfire auto-instruments AI libraries to capture LLM calls, token usage, tool invocations, and agent runs.
+
+```bash
+uv add 'logfire[pydantic-ai]'
+# or: uv add 'logfire[openai]' / uv add 'logfire[anthropic]'
+```
+
+Available AI extras: `pydantic-ai`, `openai`, `anthropic`, `litellm`, `dspy`, `google-genai`.
+
+```python
+logfire.configure()
+logfire.instrument_pydantic_ai()  # captures agent runs, tool calls, LLM request/response
+# or:
+logfire.instrument_openai()       # captures chat completions, embeddings, token counts
+logfire.instrument_anthropic()    # captures messages, token usage
+```
+
+For PydanticAI, each agent run becomes a parent span containing child spans for every tool call and LLM request.
+
+---
+
+## JavaScript / TypeScript
+
+### Install
+
+```bash
+# Node.js
+npm install @pydantic/logfire-node
+
+# Cloudflare Workers
+npm install @pydantic/logfire-cf-workers logfire
+
+# Next.js / generic
+npm install logfire
+```
+
+### Configure
+
+**Node.js (Express, Fastify, etc.)** - create an `instrumentation.ts` loaded before your app:
+
+```typescript
+import * as logfire from '@pydantic/logfire-node'
+logfire.configure()
+```
+
+Launch with: `node --require ./instrumentation.js app.js`
+
+The SDK auto-instruments common libraries when loaded before the app. Set `LOGFIRE_TOKEN` in your environment or pass `token` to `configure()`.
+
+**Cloudflare Workers** - wrap your handler with `instrument()`:
+
+```typescript
+import { instrument } from '@pydantic/logfire-cf-workers'
+
+export default instrument(handler, {
+  service: { name: 'my-worker', version: '1.0.0' }
+})
+```
+
+**Next.js** - set environment variables for OpenTelemetry export:
+
+```
+OTEL_EXPORTER_OTLP_TRACES_ENDPOINT=https://logfire-api.pydantic.dev/v1/traces
+OTEL_EXPORTER_OTLP_HEADERS=Authorization=<your-write-token>
+```
+
+### Structured Logging (JS/TS)
+
+```typescript
+// Structured attributes as second argument
+logfire.info('Created user', { user_id: uid })
+logfire.error('Payment failed', { amount: 100, currency: 'USD' })
+
+// Spans
+logfire.span('Processing order', { order_id }, {}, async () => {
+  logfire.info('Processing step completed')
+})
+
+// Error reporting
+logfire.reportError('order processing', error)
+```
+
+Log levels: `trace`, `debug`, `info`, `notice`, `warn`, `error`, `fatal`.
+
+---
+
+## Rust
+
+### Install
+
+```toml
+[dependencies]
+logfire = "0.6"
+```
+
+### Configure
+
+```rust
+let shutdown_handler = logfire::configure()
+    .install_panic_handler()
+    .finish()?;
+```
+
+Set `LOGFIRE_TOKEN` in your environment or use the Logfire CLI to select a project.
+
+### Structured Logging (Rust)
+
+The Rust SDK is built on `tracing` and `opentelemetry` - existing `tracing` macros work automatically.
+
+```rust
+// Spans
+logfire::span!("processing order", order_id = order_id).in_scope(|| {
+    // traced code
+});
+
+// Events
+logfire::info!("Created user {user_id}", user_id = uid);
+```
+
+Always call `shutdown_handler.shutdown()` before program exit to flush data.
+
+---
+
+## Verify
+
+After instrumentation, verify the setup works:
+
+1. Run `logfire auth` to check authentication (or set `LOGFIRE_TOKEN`)
+2. Start the app and trigger a request
+3. Check https://logfire.pydantic.dev/ for traces
+
+If traces aren't appearing: check that `configure()` is called before `instrument_*()` (Python), check that `LOGFIRE_TOKEN` is set, and check that the correct packages/extras are installed.
+
+## References
+
+Detailed patterns and integration tables, organized by language:
+
+- **Python**: `${CLAUDE_PLUGIN_ROOT}/skills/instrumentation/references/python/logging-patterns.md` (log levels, spans, stdlib integration, metrics, capfire testing) and `${CLAUDE_PLUGIN_ROOT}/skills/instrumentation/references/python/integrations.md` (full instrumentor table with extras)
+- **JavaScript/TypeScript**: `${CLAUDE_PLUGIN_ROOT}/skills/instrumentation/references/javascript/patterns.md` (log levels, spans, error handling, config) and `${CLAUDE_PLUGIN_ROOT}/skills/instrumentation/references/javascript/frameworks.md` (Node.js, Cloudflare Workers, Next.js, Deno setup)
+- **Rust**: `${CLAUDE_PLUGIN_ROOT}/skills/instrumentation/references/rust/patterns.md` (macros, spans, tracing/log crate integration, async, shutdown)

.agents/skills/instrumentation/references/javascript/frameworks.md

@@ -0,0 +1,78 @@
+# JavaScript Framework Setup
+
+## Node.js (Express, Fastify, etc.)
+
+Create `instrumentation.ts` and load it before your app:
+
+```typescript
+// instrumentation.ts
+import * as logfire from '@pydantic/logfire-node'
+import 'dotenv/config'
+
+logfire.configure()
+```
+
+Launch:
+
+```bash
+node --require ./instrumentation.js app.js
+# or with ts-node:
+npx ts-node --require ./instrumentation.ts app.ts
+```
+
+The SDK auto-instruments common libraries (http, fetch, express, etc.) when loaded before the app via `--require`.
+
+## Cloudflare Workers
+
+```typescript
+import { instrument } from '@pydantic/logfire-cf-workers'
+
+const handler = {
+    async fetch(request: Request, env: Env, ctx: ExecutionContext) {
+        return new Response('Hello')
+    },
+}
+
+export default instrument(handler, {
+    service: { name: 'my-worker', version: '1.0.0' },
+})
+```
+
+Add `LOGFIRE_TOKEN` to `.dev.vars` and enable `nodejs_compat` in `wrangler.toml`:
+
+```toml
+compatibility_flags = ["nodejs_compat"]
+```
+
+## Next.js / Vercel
+
+Set environment variables in `.env.local` or Vercel dashboard:
+
+```bash
+OTEL_EXPORTER_OTLP_TRACES_ENDPOINT=https://logfire-api.pydantic.dev/v1/traces
+OTEL_EXPORTER_OTLP_METRICS_ENDPOINT=https://logfire-api.pydantic.dev/v1/metrics
+OTEL_EXPORTER_OTLP_HEADERS=Authorization=<your-write-token>
+```
+
+Optionally use the `logfire` package for manual spans in server components and API routes:
+
+```typescript
+import * as logfire from 'logfire'
+
+logfire.info('Server action executed', { action: 'createUser' })
+```
+
+## Deno
+
+Deno has built-in OpenTelemetry support. Set environment variables:
+
+```bash
+OTEL_EXPORTER_OTLP_TRACES_ENDPOINT=https://logfire-api.pydantic.dev/v1/traces
+OTEL_EXPORTER_OTLP_HEADERS=Authorization=<your-write-token>
+```
+
+Run with telemetry enabled:
+
+```bash
+deno run --allow-env --unstable-otel app.ts
+```

.agents/skills/instrumentation/references/javascript/patterns.md

@@ -0,0 +1,75 @@
+# JavaScript / TypeScript Patterns
+
+## Log Levels
+
+From lowest to highest severity:
+
+```typescript
+logfire.trace('Detailed trace', { detail: x })
+logfire.debug('Debug info', { state: s })
+logfire.info('Normal operation', { event: e })
+logfire.notice('Notable event', { event: e })
+logfire.warn('Warning', { issue: i })
+logfire.error('Error occurred', { error: err })
+logfire.fatal('Fatal error', { error: err })
+```
+
+All methods accept `(message, attributes?, options?)`. Options can include `{ tags: ['tag1'] }`.
+
+## Spans
+
+### Callback-based (auto-closes)
+
+```typescript
+await logfire.span('Processing order', { order_id }, {}, async () => {
+    const items = await fetchItems(order_id)
+    logfire.info('Fetched items', { count: items.length })
+    return processItems(items)
+})
+```
+
+### Manual control
+
+```typescript
+const span = logfire.startSpan('Long operation', { job_id })
+try {
+    await doWork()
+} finally {
+    span.end()
+}
+```
+
+Child spans reference their parent via the `parentSpan` option.
+
+## Error Handling
+
+```typescript
+try {
+    await processOrder(orderId)
+} catch (error) {
+    logfire.reportError('order processing', error)
+    throw error
+}
+```
+
+`reportError` automatically extracts stack traces and error details into structured span attributes.
+
+## Configuration
+
+### Environment variables
+
+```bash
+LOGFIRE_TOKEN=your-write-token
+LOGFIRE_SERVICE_NAME=my-service
+LOGFIRE_SERVICE_VERSION=1.0.0
+```
+
+### Programmatic
+
+```typescript
+logfire.configure({
+    token: process.env.LOGFIRE_TOKEN,
+    serviceName: 'my-service',
+    serviceVersion: '1.0.0',
+})
+```

.agents/skills/instrumentation/references/python/integrations.md

@@ -0,0 +1,67 @@
+# Python Integration Reference
+
+## Web Frameworks
+
+| Framework | Instrumentor | Needs app instance | Extra |
+|-----------|-------------|-------------------|-------|
+| FastAPI | `logfire.instrument_fastapi(app)` | Yes | `fastapi` |
+| Django | `logfire.instrument_django(app)` | Yes | `django` |
+| Flask | `logfire.instrument_flask(app)` | Yes | `flask` |
+| Starlette | `logfire.instrument_starlette(app)` | Yes | `starlette` |
+| AIOHTTP | `logfire.instrument_aiohttp_client()` | No | `aiohttp` |
+
+## HTTP Clients
+
+| Library | Instrumentor | Extra |
+|---------|-------------|-------|
+| httpx | `logfire.instrument_httpx()` | `httpx` |
+| requests | `logfire.instrument_requests()` | `requests` |
+
+## Databases
+
+| Library | Instrumentor | Extra |
+|---------|-------------|-------|
+| asyncpg | `logfire.instrument_asyncpg()` | `asyncpg` |
+| psycopg | `logfire.instrument_psycopg()` | `psycopg` |
+| psycopg2 | `logfire.instrument_psycopg2()` | `psycopg2` |
+| SQLAlchemy | `logfire.instrument_sqlalchemy()` | `sqlalchemy` |
+| PyMongo | `logfire.instrument_pymongo()` | `pymongo` |
+| MySQL | `logfire.instrument_mysql()` | `mysql` |
+| SQLite3 | `logfire.instrument_sqlite3()` | `sqlite3` |
+| Redis | `logfire.instrument_redis()` | `redis` |
+
+## AI/LLM Frameworks
+
+| Framework | Instrumentor | Extra |
+|-----------|-------------|-------|
+| PydanticAI | `logfire.instrument_pydantic_ai()` | `pydantic-ai` |
+| OpenAI | `logfire.instrument_openai()` | `openai` |
+| Anthropic | `logfire.instrument_anthropic()` | `anthropic` |
+| LiteLLM | `logfire.instrument_litellm()` | `litellm` |
+| DSPy | `logfire.instrument_dspy()` | `dspy` |
+| Google GenAI | `logfire.instrument_google_genai()` | `google-genai` |
+
+## Task Queues
+
+| Framework | Instrumentor | Extra |
+|-----------|-------------|-------|
+| Celery | `logfire.instrument_celery()` | `celery` |
+
+## Other
+
+| Feature | Instrumentor | Extra |
+|---------|-------------|-------|
+| System Metrics | `logfire.instrument_system_metrics()` | `system-metrics` |
+| Pydantic Models | `logfire.instrument_pydantic()` | - (built-in) |
+| AWS Lambda | handler wrapper | `aws-lambda` |
+
+## Gunicorn Configuration
+
+```python
+# gunicorn.conf.py
+import logfire
+
+def post_fork(server, worker):
+    logfire.configure()
+    logfire.instrument_fastapi(app)
+```

.agents/skills/instrumentation/references/python/logging-patterns.md

@@ -0,0 +1,101 @@
+# Python Logging Patterns
+
+## Log Levels
+
+From lowest to highest severity:
+
+```python
+logfire.trace("Detailed trace {detail}", detail=x)
+logfire.debug("Debug info {state}", state=s)
+logfire.info("Normal operation {event}", event=e)
+logfire.notice("Notable event {event}", event=e)
+logfire.warn("Warning {issue}", issue=i)
+logfire.error("Error occurred {error}", error=err)
+logfire.fatal("Fatal error {error}", error=err)
+```
+
+## Nested Spans
+
+Spans nest to create a tree visible in the Logfire UI. Use them to show the structure of an operation, not just that it happened:
+
+```python
+with logfire.span("HTTP request {method} {url}", method="POST", url=url):
+    with logfire.span("Serialize payload"):
+        payload = model.model_dump_json()
+    with logfire.span("Send request"):
+        response = await client.post(url, content=payload)
+    logfire.info("Response {status}", status=response.status_code)
+```
+
+## Standard Library Logging Integration
+
+For projects that already use Python's `logging` module, route existing log calls through Logfire rather than rewriting them all:
+
+```python
+from logging import basicConfig
+import logfire
+
+logfire.configure()
+basicConfig(handlers=[logfire.LogfireLoggingHandler()])
+```
+
+Or with `dictConfig`:
+
+```python
+from logging.config import dictConfig
+import logfire
+
+logfire.configure()
+dictConfig({
+    'version': 1,
+    'handlers': {
+        'logfire': {'class': 'logfire.LogfireLoggingHandler'},
+    },
+    'root': {'handlers': ['logfire']},
+})
+```
+
+## Suppressing Noisy Libraries
+
+Some libraries emit excessive debug logs. Silence them at the `logging` level:
+
+```python
+import logging
+
+logging.getLogger('httpcore').setLevel(logging.WARNING)
+logging.getLogger('httpx').setLevel(logging.WARNING)
+```
+
+## Custom Metrics
+
+For dashboards and alerting, create metrics:
+
+```python
+counter = logfire.metric_counter("orders_processed", unit="1")
+counter.add(1, {"status": "success"})
+
+histogram = logfire.metric_histogram("request_duration", unit="s")
+histogram.record(0.123, {"endpoint": "/api/users"})
+
+gauge = logfire.metric_gauge("active_connections")
+gauge.set(42)
+```
+
+## Testing with capfire
+
+Use the `capfire` pytest fixture to assert on emitted spans without sending data to production:
+
+```python
+from logfire.testing import CaptureLogfire
+
+def test_order_processing(capfire: CaptureLogfire) -> None:
+    process_order(order_id=123)
+
+    spans = capfire.exporter.exported_spans_as_dict()
+    assert any(
+        span['attributes'].get('order_id') == 123
+        for span in spans
+    )
+```
+
+Configure logfire with `send_to_logfire=False` in test fixtures to prevent production data leakage.

.agents/skills/instrumentation/references/rust/patterns.md

@@ -0,0 +1,106 @@
+# Rust Patterns
+
+## Core Macros
+
+The Rust SDK is built on `tracing` and `opentelemetry`. All `tracing` macros work automatically with Logfire.
+
+### Events (log points)
+
+```rust
+logfire::trace!("Detailed trace {detail}", detail = x);
+logfire::debug!("Debug info {state}", state = s);
+logfire::info!("Normal operation {event}", event = e);
+logfire::warn!("Warning {issue}", issue = i);
+logfire::error!("Error occurred {err}", err = e);
+```
+
+### Spans
+
+```rust
+// Scoped - span closes when closure completes
+logfire::span!("Processing order {order_id}", order_id = id).in_scope(|| {
+    let items = fetch_items(id);
+    logfire::info!("Fetched {count} items", count = items.len());
+    process_items(items)
+});
+
+// Guard-based - span closes when guard is dropped
+let _guard = logfire::span!("Long operation {job_id}", job_id = id).entered();
+do_work();
+// span ends when _guard goes out of scope
+```
+
+## Configuration
+
+```rust
+use logfire;
+
+fn main() -> Result<(), Box<dyn std::error::Error>> {
+    let shutdown_handler = logfire::configure()
+        .install_panic_handler()  // captures panics as error spans
+        .finish()?;
+
+    // application code...
+
+    shutdown_handler.shutdown()?;  // flush all pending spans
+    Ok(())
+}
+```
+
+Set `LOGFIRE_TOKEN` in your environment or use the Logfire CLI (`logfire auth`).
+
+## Tracing Crate Compatibility
+
+Any library using `tracing` macros automatically sends data through Logfire:
+
+```rust
+use tracing;
+
+tracing::info!("This also appears in Logfire");
+
+#[tracing::instrument]
+fn my_function(param: &str) {
+    // automatically creates a span with param as an attribute
+}
+```
+
+## Log Crate Integration
+
+The `log` crate is automatically captured and forwarded to Logfire. Libraries using `log::info!()`, `log::error!()`, etc. will appear in your Logfire dashboard without any additional configuration.
+
+## Async Spans
+
+```rust
+use tracing::Instrument;
+
+async fn process_order(order_id: u64) {
+    let span = logfire::span!("process order {order_id}", order_id = order_id);
+    async {
+        fetch_items(order_id).await;
+        logfire::info!("Order processed");
+    }
+    .instrument(span)
+    .await;
+}
+```
+
+## Shutdown
+
+Always call `shutdown()` before program exit to flush pending data:
+
+```rust
+// In main()
+let shutdown_handler = logfire::configure().finish()?;
+
+// ... app runs ...
+
+// Before exit
+shutdown_handler.shutdown()?;
+```
+
+For web servers using `tokio`, handle shutdown via signal:
+
+```rust
+tokio::signal::ctrl_c().await?;
+shutdown_handler.shutdown()?;
+```

.claude/settings.json

@@ -1,3 +1,21 @@
 {
-  "enabledPlugins": {}
+  "$schema": "https://json.schemastore.org/claude-code-settings.json",
+  "env": {
+    "CLAUDE_BASH_MAINTAIN_PROJECT_WORKING_DIR": "1",
+    "CLAUDE_CODE_DISABLE_FEEDBACK_SURVEY": "1",
+    "CLAUDE_CODE_NO_FLICKER": "1",
+    "CLAUDE_CODE_DISABLE_ADAPTIVE_THINKING": "1"
+  },
+  "permissions": {
+    "allow": [
+      "Bash(just fast-check)",
+      "Bash(just check)",
+      "Bash(just fix)",
+      "Bash(just typecheck)",
+      "Bash(just lint)",
+      "Bash(just test)"
+    ],
+    "deny": []
+  },
+  "enableAllProjectMcpServers": true
 }

.claude/skills/instrumentation

@@ -0,0 +1 @@
+../../.agents/skills/instrumentation

.github/workflows/test.yml

@@ -5,10 +5,11 @@ concurrency:
   cancel-in-progress: true
 
 on:
+  # Trigger: PR branch pushes already publish commit statuses that show up on the PR.
+  # Why: running the full matrix on both push and pull_request doubles CI time for the
+  #      exact same branch head commit.
+  # Outcome: each branch push runs the test suite once, including PR updates.
   push:
-    branches: [ "main" ]
-  pull_request:
-    branches: [ "main" ]
 
 jobs:
   static-checks:
@@ -52,7 +53,6 @@ jobs:
   test-sqlite-unit:
     name: Test SQLite Unit (${{ matrix.os }}, Python ${{ matrix.python-version }})
     timeout-minutes: 30
-    needs: [static-checks]
     strategy:
       fail-fast: false
       matrix:
@@ -92,14 +92,13 @@ jobs:
         run: |
           uv pip install -e ".[dev]"
 
-      - name: Run tests (SQLite Unit)
+      - name: Run tests
         run: |
           just test-unit-sqlite
 
   test-sqlite-integration:
     name: Test SQLite Integration (${{ matrix.os }}, Python ${{ matrix.python-version }})
     timeout-minutes: 45
-    needs: [static-checks]
     strategy:
       fail-fast: false
       matrix:
@@ -139,21 +138,37 @@ jobs:
         run: |
           uv pip install -e ".[dev]"
 
-      - name: Run tests (SQLite Integration)
+      - name: Run tests
         run: |
           just test-int-sqlite
 
   test-postgres-unit:
     name: Test Postgres Unit (Python ${{ matrix.python-version }})
     timeout-minutes: 30
-    needs: [static-checks]
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ "3.12", "3.13", "3.14" ]
+        include:
+          - python-version: "3.12"
+          - python-version: "3.13"
+          - python-version: "3.14"
     runs-on: ubuntu-latest
-
-    # Note: No services section needed - testcontainers handles Postgres in Docker
+    services:
+      postgres:
+        image: pgvector/pgvector:pg16
+        env:
+          POSTGRES_USER: basic_memory_user
+          POSTGRES_PASSWORD: dev_password
+          POSTGRES_DB: basic_memory_test
+        ports:
+          - 5432:5432
+        options: >-
+          --health-cmd "pg_isready -U basic_memory_user -d basic_memory_test"
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+    env:
+      BASIC_MEMORY_TEST_POSTGRES_URL: postgresql://basic_memory_user:dev_password@127.0.0.1:5432/basic_memory_test
 
     steps:
       - uses: actions/checkout@v4
@@ -180,21 +195,37 @@ jobs:
         run: |
           uv pip install -e ".[dev]"
 
-      - name: Run tests (Postgres Unit)
+      - name: Run tests
         run: |
           just test-unit-postgres
 
   test-postgres-integration:
     name: Test Postgres Integration (Python ${{ matrix.python-version }})
     timeout-minutes: 45
-    needs: [static-checks]
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ "3.12", "3.13", "3.14" ]
+        include:
+          - python-version: "3.12"
+          - python-version: "3.13"
+          - python-version: "3.14"
     runs-on: ubuntu-latest
-
-    # Note: No services section needed - testcontainers handles Postgres in Docker
+    services:
+      postgres:
+        image: pgvector/pgvector:pg16
+        env:
+          POSTGRES_USER: basic_memory_user
+          POSTGRES_PASSWORD: dev_password
+          POSTGRES_DB: basic_memory_test
+        ports:
+          - 5432:5432
+        options: >-
+          --health-cmd "pg_isready -U basic_memory_user -d basic_memory_test"
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+    env:
+      BASIC_MEMORY_TEST_POSTGRES_URL: postgresql://basic_memory_user:dev_password@127.0.0.1:5432/basic_memory_test
 
     steps:
       - uses: actions/checkout@v4
@@ -221,14 +252,13 @@ jobs:
         run: |
           uv pip install -e ".[dev]"
 
-      - name: Run tests (Postgres Integration)
+      - name: Run tests
         run: |
           just test-int-postgres
 
   test-semantic:
     name: Test Semantic (Python 3.12)
     timeout-minutes: 45
-    needs: [static-checks]
     runs-on: ubuntu-latest
 
     steps:
@@ -254,68 +284,8 @@ jobs:
 
       - name: Install dependencies
         run: |
-          uv pip install -e ".[dev,semantic]"
+          uv pip install -e ".[dev]"
 
-      - name: Run tests (Semantic)
+      - name: Run tests
         run: |
           just test-semantic
-
-  coverage:
-    name: Coverage Summary (combined, Python 3.12)
-    timeout-minutes: 60
-    needs:
-      - static-checks
-      - test-sqlite-unit
-      - test-sqlite-integration
-      - test-postgres-unit
-      - test-postgres-integration
-      - test-semantic
-    if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
-    runs-on: ubuntu-latest
-
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          submodules: true
-
-      - name: Set up Python 3.12
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.12"
-          cache: "pip"
-
-      - name: Install uv
-        run: |
-          pip install uv
-
-      - uses: extractions/setup-just@v3
-
-      - name: Create virtual env
-        run: |
-          uv venv
-
-      - name: Install dependencies
-        run: |
-          uv pip install -e ".[dev,semantic]"
-
-      - name: Run combined coverage (SQLite + Postgres)
-        run: |
-          just coverage
-
-      - name: Add coverage report to job summary
-        if: always()
-        run: |
-          {
-            echo "## Coverage"
-            echo ""
-            echo '```'
-            uv run coverage report -m
-            echo '```'
-          } >> "$GITHUB_STEP_SUMMARY"
-
-      - name: Upload HTML coverage report
-        if: always()
-        uses: actions/upload-artifact@v4
-        with:
-          name: htmlcov
-          path: htmlcov/

AGENTS.md

@@ -22,15 +22,16 @@ See the [README.md](README.md) file for a project overview.
 - Run unit tests (Postgres): `just test-unit-postgres`
 - Run integration tests (SQLite): `just test-int-sqlite`
 - Run integration tests (Postgres): `just test-int-postgres`
-- Run impacted tests: `just testmon` (pytest-testmon)
+- Run impacted tests: `just testmon` (pytest-testmon; only tests affected by changed code)
 - Run MCP smoke test: `just test-smoke`
-- Fast local loop: `just fast-check`
+- Fast local loop: `just fast-check` (default iteration flow)
 - Local consistency check: `just doctor`
 - Generate HTML coverage: `just coverage`
 - Single test: `pytest tests/path/to/test_file.py::test_function_name`
 - Run benchmarks: `pytest test-int/test_sync_performance_benchmark.py -v -m "benchmark and not slow"`
 - Lint: `just lint` or `ruff check . --fix`
-- Type check: `just typecheck` or `uv run pyright`
+- Type check: `just typecheck` or `uv run ty check src tests test-int`
+- Type check (pyright): `just typecheck-pyright` or `uv run pyright`
 - Format: `just format` or `uv run ruff format .`
 - Run all code checks: `just check` (runs lint, format, typecheck, test)
 - Create db migration: `just migration "Your migration message"`
@@ -47,10 +48,12 @@ See the [README.md](README.md) file for a project overview.
 ### Code/Test/Verify Loop (fast path)
 
 1) **Code:** make changes.
-2) **Test:** `just fast-check` (lint/format/typecheck + impacted tests + MCP smoke).
+2) **Test:** `just fast-check` (lint/format/typecheck + pytest-testmon impacted tests for changed code).
 3) **Verify:** `just doctor` (end-to-end file ↔ DB loop in a temp project).
 4) **Full gate (when needed):** `just test` or `just check` for SQLite + Postgres.
 
+Run `just test-smoke` when you specifically need the MCP smoke flow.
+
 If testmon is “cold,” the first run may be long. Subsequent runs get much faster.
 
 ### Test Structure
@@ -441,5 +444,9 @@ With GitHub integration, the development workflow includes:
 3. **Branch management** - Claude can create feature branches for implementations
 4. **Documentation maintenance** - Claude can keep documentation updated as the code evolves
 5. **Code Commits**: ALWAYS sign off commits with `git commit -s`
+6. **Pull Request Titles**: PR titles must follow the semantic format enforced by `.github/workflows/pr-title.yml`: `type(scope): summary`
+   - Allowed types: `feat`, `fix`, `chore`, `docs`, `style`, `refactor`, `perf`, `test`, `build`, `ci`
+   - Allowed scopes: `core`, `cli`, `api`, `mcp`, `sync`, `ui`, `deps`, `installer`
+   - Example: `fix(cli): propagate cloud workspace routing`
 
 This level of integration represents a new paradigm in AI-human collaboration, where the AI assistant becomes a full-fledged team member rather than just a tool for generating code snippets.

CHANGELOG.md

@@ -2,20 +2,225 @@
 
 ## Unreleased
 
+## v0.20.3 (2026-03-26)
+
+### Bug Fixes
+
+- **#698**: CLI cloud commands now use API key when configured
+  - `get_authenticated_headers()` only checked OAuth tokens, ignoring `config.cloud_api_key`
+  - All CLI cloud commands (`upload`, `status`, `snapshot`, `restore`, etc.) failed for API-key-only users while MCP tools worked fine
+  - Now mirrors the same credential priority as MCP: API key first, OAuth fallback
+  - Fixes `bm cloud upload --project` returning "project does not exist" when authenticated with `bmc_*` API key
+
+## v0.20.2 (2026-03-10)
+
+### Bug Fixes
+
+- Fix auto-update Homebrew detection: `brew outdated` exits 1 when a formula is outdated, not on error
+  - Previously treated exit code 1 as a failure, causing "Automatic update check failed" instead of detecting the available update
+
+## v0.20.1 (2026-03-10)
+
+### Bug Fixes
+
+- **#661**: Fix `bm project list` MCP column to show transport type (stdio/https) instead of DB presence
+  - Renamed "MCP (stdio)" column to "MCP"
+  - Shows actual routing mode: `stdio` for local, `https` for cloud projects
+  - Clears local path display for cloud-mode projects
+- **#662**: Invalidate config cache when file is modified by another process
+  - Adds mtime-based cache validation to `ConfigManager.load_config()`
+  - Long-lived processes (MCP stdio server) now detect external config changes
+  - Fixes `bm project set-cloud` having no effect on running MCP server
+
+## v0.20.0 (2026-03-10)
+
 ### Features
 
-- Add `--strip-frontmatter` to `basic-memory tool read-note`
-  - Default behavior is unchanged: `content` still includes raw markdown with frontmatter.
-  - With `--strip-frontmatter`, both text and JSON modes return body-only markdown content.
-  - JSON output now includes an additive `frontmatter` field with parsed YAML metadata (or `null`
-    when no valid opening frontmatter block exists).
+- **#643**: Default-on auto-update system and `bm update` command
+  - Automatic background update checks for CLI installs (uv tool, Homebrew)
+  - Install-source detection (homebrew, uv_tool, uvx, unknown) with uvx skip behavior
+  - Periodic check gating via `auto_update_last_checked_at` + `update_check_interval` config
+  - Manager-specific update flows: Homebrew (`brew upgrade`) and uv tool (`uv tool upgrade`)
+  - Silent, non-blocking MCP behavior via daemon thread before server run
+  - Manual commands: `bm update` (force check + apply) and `bm update --check` (check only)
+  - New config fields: `auto_update`, `update_check_interval`, `auto_update_last_checked_at`
 
-## v0.18.3 (2026-02-12)
+## v0.19.2 (2026-03-09)
+
+### Bug Fixes
+
+- **#657**: Coerce string params to list/dict in MCP tools
+  - MCP clients that serialize `list`/`dict` arguments as JSON strings no longer fail Pydantic validation
+  - Adds `BeforeValidator` coercion to `search_notes` (`entity_types`, `note_types`, `tags`, `metadata_filters`), `write_note` (`metadata`), and `canvas` (`nodes`, `edges`)
+- **#655**: Handle SQLite and Windows semantic search regressions
+  - Fix embedding status query for non-semantic SQLite databases
+  - Windows-safe log file rotation with per-process log filenames
+  - Robust `setup_logging` that handles all environments cleanly
+
+## v0.19.1 (2026-03-08)
+
+### Bug Fixes
+
+- **#649**: Enforce strict entity resolution in destructive MCP tools (`edit_note`, `move_note`, `delete_note`)
+  - Prevents fuzzy-match fallback from silently editing/moving/deleting the wrong note
+  - DST-related timeframe validation fix (round instead of truncate days)
+
+### Features
+
+- **#648**: Add `insert_before_section` and `insert_after_section` edit operations
+- Add `GET /knowledge/graph` endpoint for full graph visualization
+
+### Dependencies
+
+- Bump authlib from 1.6.6 to 1.6.7
+
+## v0.19.0 (2026-03-07)
+
+### Highlights
+
+- **Semantic vector search** for SQLite and Postgres with FastEmbed embeddings
+- **Schema system** for validating and inferring knowledge base structure
+- **Per-project cloud routing** with API key authentication
+- **Upgraded to FastMCP 3.0** with tool annotations
+- **CLI overhaul** with JSON output, workspace awareness, and project dashboard
+
+### Features
+
+- **#550**: Add semantic vector search for SQLite and Postgres
+  - FastEmbed-based embeddings with automatic backfill
+  - Hybrid search combining full-text and vector similarity
+  - Score-based fusion replacing RRF for better ranking
+  - `min_similarity` override for tuning search precision
+  - Semantic dependencies are now default, with optional extras fallback
+
+- **#549**: Schema system for Basic Memory
+  - `schema_infer` — infer schema from existing notes
+  - `schema_validate` — validate notes against a schema definition
+  - `schema_diff` — compare schemas across projects
+  - Frontmatter validation support (#597)
+  - Read schema definitions from file instead of stale DB metadata (#635)
+
+- **#555**: Per-project local/cloud routing with API key auth
+  - Individual projects route through cloud while others stay local
+  - `basic-memory cloud set-key` and `basic-memory project set-cloud/set-local`
+  - Stdio MCP honors per-project cloud routing (#590)
+
+- **#598**: Upgrade FastMCP 2.12.3 to 3.0.1 with tool annotations
+
+- **#585**: Add JSON output mode for MCP tools (default text)
+  - `--json` output for CLI commands for scripting and CI
+
+- **#576**: Add workspace selection flow for MCP and CLI
+  - Workspace-aware cloud project listing
+  - CLI refactoring for workspace support
+
+- **#544**: Project-prefixed permalinks and memory URL routing
+
+- **#632**: Add overwrite guard to `write_note` tool
+
+- **#614**: `edit_note` append/prepend auto-creates note if not found
+
+- **#609**: Richer content context in search results
+  - Return matched chunk text in search results (#601)
+  - Improved content hit rate
+
+- **#602**: Add `created_by` and `last_updated_by` user tracking to Entity
+
+- **#600**: Rename `entity_type` to `note_type` across codebase
+
+- **#574**: Add `display_name` and `is_private` to ProjectItem
+
+- **#569**: Expose `external_id` in EntityResponse and link resolver
+
+- **#567**: Isolate default SQLite DB by config dir
+
+- **#560**: Enable `default_project_mode` by default
+
+- **#559**: Add `basic-memory watch` CLI command
+
+- **#546**: Add cloud discovery touchpoints to CLI and MCP
+
+- **#572**: CLI analytics via Umami event collector
+
+- Replace project info with htop-inspired dashboard
+
+- Merge `search_by_metadata` into `search_notes` with optional query
+
+- Add `--strip-frontmatter` to `basic-memory tool read-note`
+
+- Add `destination_folder` parameter to `move_note` tool
+
+### Bug Fixes
+
+- **#644**: Fix default project resolution in cloud mode
+  - ChatGPT search/fetch tools broken in cloud mode
+  - `resolve_project_parameter` falls back to projects API
+
+- **#638**: Restore API backward compatibility for v0.18.x clients
+
+- **#637**: Create backup before config migration overwrites old format
+
+- **#636**: `list_workspaces` bypasses factory pattern on cloud MCP server
+
+- **#631**: `build_context` related_results schema validation failure
+
+- **#613**: Reduce excessive log volume by demoting per-request noise to DEBUG
+
+- **#612**: Handle quoted picoschema enum strings in YAML frontmatter
+
+- **#607**: Guard against closed streams in promo and missing vector tables
+
+- **#606**: Accept null for `expected_replacements` in `edit_note`
+
+- **#595**: `recent_activity` dedup and pagination across MCP tools
+
+- **#593**: Backend-specific distance-to-similarity conversion
+
+- **#582**: Use LinkResolver fallback in `build_context` for flexible identifier matching
+
+- **#577**: Replace RRF with score-based fusion in hybrid search
+
+- **#575**: Remove hardcoded "main" default from `default_project`
+
+- **#534**: Speed up `bm --version` startup
+
+- Fix semantic embeddings not generated on fresh DB or upgrade
+
+- Clarify `search_notes` parameter naming and fix `note_types` case sensitivity
+
+- Parse `tag:` prefix at MCP tool level to avoid hybrid search failure
+
+- Cap sqlite-vec knn k parameter at 4096 limit
+
+- Parameterize SQL queries in search repository type filters
+
+- Coerce list frontmatter values to strings for title and type fields
+
+- Avoid `Post(**metadata)` crash when frontmatter contains 'content' or 'handler' keys
+
+- Upgrade cryptography and python-multipart for security advisories
+
+### Internal
+
+- **#594**: Add `ty` as supplemental type checker
+- Batched vector sync orchestration across repositories
+- FastEmbed parallel guardrails and provider caching
+- Improved cloud CLI status and error messages
+- CI coverage and Postgres test fixes
+
+## v0.18.5 (2026-02-13)
+
+### Bug Fixes
+
+- Strip NUL bytes from content before PostgreSQL search indexing
+  ([`ec9b2c4`](https://github.com/basicmachines-co/basic-memory/commit/ec9b2c4))
+
+## v0.18.4 (2026-02-12)
 
 ### Bug Fixes
 
 - Use global `--header` flag for Tigris consistency on all rclone transactions
-  ([`7fcf587`](https://github.com/basicmachines-co/basic-memory/commit/7fcf587))
+  ([`0eae0e1`](https://github.com/basicmachines-co/basic-memory/commit/0eae0e1))
   - `--header-download` / `--header-upload` only apply to GET/PUT requests, missing S3
     ListObjectsV2 calls that bisync issues first. Non-US users saw stale edge-cached metadata.
   - `--header` applies to ALL HTTP transactions (list, download, upload), fixing bisync for
@@ -1920,12 +2125,12 @@ Signed-off-by: phernandez <paul@basicmachines.co>
 - Update CLAUDE.md ([#33](https://github.com/basicmachines-co/basic-memory/pull/33),
   [`dfaf0fe`](https://github.com/basicmachines-co/basic-memory/commit/dfaf0fea9cf5b97d169d51a6276ec70162c21a7e))
 
-fix spelling in CLAUDE.md: enviroment -> environment Signed-off-by: Ikko Eltociear Ashimine
+fix spelling in CLAUDE.md: environment typo Signed-off-by: Ikko Eltociear Ashimine
   <eltociear@gmail.com>
 
 ### Refactoring
 
-- Move project stats into projct subcommand
+- Move project stats into project subcommand
   ([`2a881b1`](https://github.com/basicmachines-co/basic-memory/commit/2a881b1425c73947f037fbe7ac5539c015b62526))
 
 Signed-off-by: phernandez <paul@basicmachines.co>
@@ -2354,7 +2559,7 @@ Co-authored-by: phernandez <phernandez@basicmachines.co>
 
 ### Bug Fixes
 
-- Refix vitual env in installer build
+- Refix virtual env in installer build
   ([`052f491`](https://github.com/basicmachines-co/basic-memory/commit/052f491fff629e8ead629c9259f8cb46c608d584))
 
 
@@ -2373,7 +2578,7 @@ Co-authored-by: phernandez <phernandez@basicmachines.co>
 
 ### Bug Fixes
 
-- Fix path to intaller app artifact
+- Fix path to installer app artifact
   ([`53d220d`](https://github.com/basicmachines-co/basic-memory/commit/53d220df585561f9edd0d49a9e88f1d4055059cf))
 
 
@@ -2381,7 +2586,7 @@ Co-authored-by: phernandez <phernandez@basicmachines.co>
 
 ### Bug Fixes
 
-- Activate vitualenv in installer build
+- Activate virtualenv in installer build
   ([`d4c8293`](https://github.com/basicmachines-co/basic-memory/commit/d4c8293687a52eaf3337fe02e2f7b80e4cc9a1bb))
 
 - Trigger installer build on release

README.md

@@ -11,9 +11,9 @@
 
 - **Cross-device and multi-platform support is here.** Your knowledge graph now works on desktop, web, and mobile.
 - **Cloud is optional.** The local-first open-source workflow continues as always.
-- **OSS discount:** use code `{{OSS_DISCOUNT_CODE}}` for 20% off for 3 months.
+- **OSS discount:** use code `BMFOSS` for 20% off for 3 months.
 
-[Sign up now →](https://basicmemory.com)
+[Sign up now →](https://basicmemory.com?utm_source=github&utm_medium=referral&utm_campaign=readme)
 
 with a 7 day free trial
 
@@ -23,8 +23,21 @@ Basic Memory lets you build persistent knowledge through natural conversations w
 Claude, while keeping everything in simple Markdown files on your computer. It uses the Model Context Protocol (MCP) to
 enable any compatible LLM to read and write to your local knowledge base.
 
-- Website: https://basicmemory.com
-- Documentation: https://docs.basicmemory.com
+## What's New in v0.19.0
+
+- **Semantic Vector Search** — find notes by meaning, not just keywords. Combines full-text and vector similarity for hybrid search with FastEmbed embeddings.
+- **Schema System** — infer, validate, and diff the structure of your knowledge base with `schema_infer`, `schema_validate`, and `schema_diff` tools.
+- **Per-Project Cloud Routing** — route individual projects through the cloud while others stay local, using API key authentication (`basic-memory project set-cloud`).
+- **FastMCP 3.0** — upgraded to FastMCP 3.0 with tool annotations for better client integration.
+- **CLI Overhaul** — JSON output mode (`--json`) for scripting, workspace-aware commands, and an htop-inspired project dashboard.
+- **Smarter Editing** — `edit_note` append/prepend auto-creates notes if they don't exist; `write_note` has an overwrite guard to prevent accidental data loss.
+- **Richer Search Results** — matched chunk text returned in search results for better context.
+
+See the full [CHANGELOG](CHANGELOG.md) for details.
+
+- Website: [basicmemory.com](https://basicmemory.com?utm_source=github&utm_medium=referral&utm_campaign=readme)
+- Documentation: [docs.basicmemory.com](https://docs.basicmemory.com?utm_source=github&utm_medium=referral&utm_campaign=readme)
+- Community: [Discord](https://discord.gg/tyvKNccgqN?utm_source=github&utm_medium=referral&utm_campaign=readme)
 
 ## Pick up your conversation right where you left off
 
@@ -62,6 +75,36 @@ uv tool install basic-memory
 
 You can view shared context via files in `~/basic-memory` (default directory location).
 
+## Automatic Updates
+
+Basic Memory includes a default-on auto-update flow for CLI installs.
+
+- **Auto-install supported:** `uv tool` and Homebrew installs
+- **Default check interval:** every 24 hours (`86400` seconds)
+- **MCP-safe behavior:** update checks run silently in `basic-memory mcp` mode
+- **`uvx` behavior:** skipped (runtime is ephemeral and managed by `uvx`)
+
+Manual update commands:
+
+```bash
+# Check now and install if supported
+bm update
+
+# Check only, do not install
+bm update --check
+```
+
+Config options in `~/.basic-memory/config.json`:
+
+```json
+{
+  "auto_update": true,
+  "update_check_interval": 86400
+}
+```
+
+To disable automatic updates, set `"auto_update": false`.
+
 ## Why Basic Memory?
 
 Most LLM interactions are ephemeral - you ask a question, get an answer, and everything is forgotten. Each conversation
@@ -396,7 +439,8 @@ basic-memory project ls --name main --cloud
 
 No-flag behavior defaults to local when no project context is present.
 
-The local MCP server (`basic-memory mcp`) always uses local routing (including `--transport stdio`).
+The local MCP server routes per transport: `--transport stdio` honors per-project routing
+(local or cloud), while `--transport streamable-http` and `--transport sse` always route locally.
 
 **CLI Note Editing (`tool edit-note`):**
 
@@ -437,8 +481,7 @@ list_directory(dir_name, depth) - Browse directory contents with filtering
 **Search & Discovery:**
 ```
 search(query, page, page_size) - Search across your knowledge base
-search_notes(query, page, page_size, search_type, types, entity_types, after_date, metadata_filters, tags, status, project) - Search with filters
-search_by_metadata(filters, limit, offset, project) - Structured frontmatter search
+search_notes(query, page, page_size, search_type, types, entity_types, after_date, metadata_filters, tags, status, project) - Search with filters (query is optional for filter-only searches)
 ```
 
 **Project Management:**
@@ -473,15 +516,40 @@ canvas(nodes, edges, title, folder) - Generate knowledge visualizations
 "What have I been working on in the past week?"
 ```
 
-## Futher info
+## Further info
 
-See the [Documentation](https://docs.basicmemory.com) for more info, including:
+See the [Documentation](https://docs.basicmemory.com?utm_source=github&utm_medium=referral&utm_campaign=readme) for more info, including:
 
-- [Complete User Guide](https://docs.basicmemory.com/user-guide/)
-- [CLI tools](https://docs.basicmemory.com/guides/cli-reference/)
-- [Cloud CLI and Sync](https://docs.basicmemory.com/guides/cloud-cli/)
-- [Managing multiple Projects](https://docs.basicmemory.com/guides/cli-reference/#project)
-- [Importing data from OpenAI/Claude Projects](https://docs.basicmemory.com/guides/cli-reference/#import)
+- [Complete User Guide](https://docs.basicmemory.com/user-guide/?utm_source=github&utm_medium=referral&utm_campaign=readme)
+- [CLI tools](https://docs.basicmemory.com/guides/cli-reference/?utm_source=github&utm_medium=referral&utm_campaign=readme)
+- [Cloud CLI and Sync](https://docs.basicmemory.com/guides/cloud-cli/?utm_source=github&utm_medium=referral&utm_campaign=readme)
+- [Managing multiple Projects](https://docs.basicmemory.com/guides/cli-reference/?utm_source=github&utm_medium=referral&utm_campaign=readme#project)
+- [Importing data from OpenAI/Claude Projects](https://docs.basicmemory.com/guides/cli-reference/?utm_source=github&utm_medium=referral&utm_campaign=readme#import)
+
+## Telemetry
+
+Basic Memory collects anonymous, minimal usage events to understand how the CLI-to-cloud conversion funnel performs. This helps us prioritize features and improve the product.
+
+**What we collect:**
+- Cloud promo impressions (when the promo banner is shown)
+- Cloud login attempts and outcomes
+- Promo opt-out events
+
+**What we do NOT collect:**
+- No file contents, note titles, or knowledge base data
+- No personally identifiable information (PII)
+- No IP address tracking or fingerprinting
+- No per-command or per-tool-call tracking
+
+Events are sent to our [Umami Cloud](https://umami.is) instance, an open-source, privacy-focused analytics platform. Events are fire-and-forget on a background thread — analytics never blocks or slows the CLI.
+
+**Opt out** by setting the environment variable:
+
+```bash
+export BASIC_MEMORY_NO_PROMOS=1
+```
+
+This disables both promo messages and all telemetry events.
 
 ## Logging
 
@@ -505,6 +573,7 @@ Basic Memory uses [Loguru](https://github.com/Delgan/loguru) for logging. The lo
 | `BASIC_MEMORY_FORCE_CLOUD` | `false` | When `true`, forces cloud API routing |
 | `BASIC_MEMORY_EXPLICIT_ROUTING` | `false` | When `true`, marks route selection as explicit (`--local`/`--cloud`) |
 | `BASIC_MEMORY_ENV` | `dev` | Set to `test` for test mode (stderr only) |
+| `BASIC_MEMORY_NO_PROMOS` | `false` | When `true`, disables cloud promo messages and telemetry |
 
 ### Examples
 
@@ -571,6 +640,7 @@ Tests use pytest markers for selective execution:
 just install          # Install with dev dependencies
 just lint             # Run linting checks
 just typecheck        # Run type checking
+just typecheck-ty     # Run ty type checking (incremental supplement to pyright)
 just format           # Format code with ruff
 just fast-check       # Fast local loop (fix/format/typecheck + testmon + smoke)
 just doctor           # Local consistency check (temp config)
@@ -578,6 +648,11 @@ just check            # Run all quality checks
 just migration "msg"  # Create database migration
 ```
 
+**Type Checking Strategy:**
+- `just typecheck` (Pyright) remains the primary, blocking type checker.
+- `just typecheck-ty` (Astral `ty`) is available as a supplemental checker while rules are adopted incrementally.
+- We recommend running both locally while reducing `ty` diagnostics over time.
+
 **Local Consistency Check:**
 ```bash
 basic-memory doctor   # Verifies file <-> database sync in a temp project
@@ -602,4 +677,4 @@ and submitting PRs.
  </picture>
 </a>
 
-Built with ♥️ by Basic Machines
+Built with ♥️ by [Basic Machines](https://basicmachines.co?utm_source=github&utm_medium=referral&utm_campaign=readme)

docker-compose.yml

@@ -17,7 +17,9 @@ services:
     volumes:
 
       # Persistent storage for configuration and database
-      - basic-memory-config:/root/.basic-memory:rw
+      # Container runs as `appuser` (Dockerfile USER directive), so the CLI
+      # config dir lives under /home/appuser, not /root.
+      - basic-memory-config:/home/appuser/.basic-memory:rw
 
       # Mount your knowledge directory (required)
       # Change './knowledge' to your actual Obsidian vault or knowledge directory

docs/SPEC-PER-PROJECT-ROUTING.md

@@ -10,7 +10,7 @@ This document is the canonical contract for local/cloud routing behavior in CLI,
 ## Goals
 
 1. Remove global `cloud_mode` from runtime/routing semantics.
-2. Keep MCP stdio local-only and predictable.
+2. Keep MCP HTTP/SSE local-only; let stdio honor per-project routing.
 3. Make CLI routing explicit and easy to reason about.
 4. Support projects that exist in both local and cloud without ambiguity.
 
@@ -45,14 +45,14 @@ When explicit routing is active, project mode does not override the selected rou
     "main": {
       "path": "/Users/me/basic-memory",
       "mode": "local",
-      "cloud_sync_path": null,
+      "local_sync_path": null,
       "bisync_initialized": false,
       "last_sync": null
     },
     "specs": {
       "path": "specs",
       "mode": "cloud",
-      "cloud_sync_path": "/Users/me/dev/specs",
+      "local_sync_path": "/Users/me/dev/specs",
       "bisync_initialized": true,
       "last_sync": "2026-02-06T17:36:38.544153"
     }
@@ -79,13 +79,25 @@ When explicit routing is active, project mode does not override the selected rou
   - reports auth state (API key, OAuth token validity)
   - runs health checks only when credentials are available
 
-## MCP Stdio Local Guarantee
+## MCP Transport Routing
 
-`bm mcp --transport stdio` always routes locally.
+### Stdio (default)
 
-The command sets explicit local routing (`BASIC_MEMORY_FORCE_LOCAL=true` and
-`BASIC_MEMORY_EXPLICIT_ROUTING=true`) before starting the server. This prevents cloud routing for stdio MCP,
-even if the selected project has `mode: cloud`.
+`bm mcp --transport stdio` uses natural per-project routing.
+
+- Local-mode projects route through the in-process ASGI transport.
+- Cloud-mode projects route to the cloud proxy with Bearer auth (API key).
+- No explicit routing env vars are injected by the CLI command.
+- Externally-set env vars are honored (e.g. `BASIC_MEMORY_FORCE_CLOUD=true` for cloud deployments).
+- Users who need all projects forced local can set `BASIC_MEMORY_FORCE_LOCAL=true` externally.
+
+### HTTP and SSE Transports
+
+`bm mcp --transport streamable-http` and `bm mcp --transport sse` always route locally.
+
+These transports set explicit local routing (`BASIC_MEMORY_FORCE_LOCAL=true` and
+`BASIC_MEMORY_EXPLICIT_ROUTING=true`) before starting the server. This prevents cloud
+routing regardless of project mode, since HTTP/SSE serve as local API endpoints.
 
 ## Project List UX for Dual Presence
 
@@ -130,6 +142,6 @@ Runtime mode is no longer a cloud/local routing switch for local app flows.
 3. `--local/--cloud` always override per-project mode for that command.
 4. No-project + no-flags commands route local by default.
 5. `bm cloud login/logout` do not toggle routing behavior.
-6. `bm mcp` remains local-only in stdio mode.
+6. `bm mcp` stdio routes per-project mode; HTTP/SSE remain local-forced.
 7. `bm project list` communicates dual local/cloud presence without ambiguity.
 8. `bm project ls` output identifies route target explicitly.

docs/ai-assistant-guide-extended.md

@@ -91,10 +91,11 @@ SQLite Database (Index)
 # List all projects
 projects = await list_memory_projects()
 
-# Response structure:
+# Response structure (each entry includes external_id you can pass as project_id):
 # [
 #   {
 #     "name": "main",
+#     "external_id": "550e8400-e29b-41d4-a716-446655440000",
 #     "path": "/Users/name/notes",
 #     "is_default": True,
 #     "note_count": 156,
@@ -102,6 +103,7 @@ projects = await list_memory_projects()
 #   },
 #   {
 #     "name": "work",
+#     "external_id": "9f86d081-884c-42a3-b5e3-1c0c5b4c8e52",
 #     "path": "/Users/name/work-notes",
 #     "is_default": False,
 #     "note_count": 89,
@@ -164,6 +166,44 @@ active_project = "main"
 results = await search_notes(query="topic", project=active_project)
 ```
 
+### `project` vs `project_id`
+
+Every project has two identifiers:
+
+- **`project`** — human-readable name (e.g., `"main"`). Easy to use, but can collide across cloud workspaces.
+- **`project_id`** — stable `external_id` UUID. Always unambiguous; takes precedence over `project` when both are passed.
+
+**When to prefer `project_id`:**
+
+1. **Cloud multi-workspace setups.** If the user belongs to more than one workspace (personal + organization, or several organizations) and the same project name might exist in more than one of them, pass `project_id` to route to the exact project. Without it, name resolution falls back to the default workspace, which may not be the one the user means.
+2. **After `list_memory_projects()`.** Once you have the `external_id`, prefer using it — it's the same number of characters in JSON and saves a name-resolution round-trip.
+3. **When persisting a project choice across a long session.** UUIDs are stable; names can be renamed.
+
+**When `project` (name) is fine:**
+
+- Local single-workspace setups (no collision risk).
+- One-off operations where the name is clearly visible to the user (e.g., quick `search_notes(project="main", ...)`).
+- The user explicitly references a project by name in their message.
+
+**Example — cloud multi-workspace pattern:**
+
+```python
+# Discover and pick the right project for this user
+projects = await list_memory_projects()
+target = next(p for p in projects if p["name"] == "research" and p["workspace"]["slug"] == "acme")
+
+# Use the UUID for all subsequent operations — no ambiguity
+await write_note(
+    title="Meeting Notes",
+    content="...",
+    folder="meetings",
+    project_id=target["external_id"],
+)
+results = await search_notes(query="kickoff", project_id=target["external_id"])
+```
+
+**Precedence rule:** When both are passed, `project_id` wins. This lets you safely supply `project="main"` for backward compatibility while still routing precisely with `project_id`.
+
 ### Cross-Project Operations
 
 **Some tools work across all projects when project parameter omitted:**
@@ -427,6 +467,8 @@ await write_note(
 )
 ```
 
+> **Important**: `write_note` errors if the note already exists. Use `edit_note` for incremental changes, or pass `overwrite=True` to replace.
+
 **Well-structured note**:
 
 ```python
@@ -760,6 +802,9 @@ notes = await read_note(
     identifier="memory://specs/*",
     project="main"
 )
+
+# Cross-project URL (auto-routes to the correct project)
+note = await read_note(identifier="memory://research/specs/api-design")
 ```
 
 ```python
@@ -1060,16 +1105,19 @@ results = await search_notes(
     project="main"
 )
 
-# Metadata-only search
-results = await search_by_metadata(
-    filters={"type": "spec", "status": "in-progress"},
+# Metadata-only search (no query needed)
+results = await search_notes(
+    metadata_filters={"type": "spec", "status": "in-progress"},
     project="main"
 )
 ```
 
 ### Search Types
 
-**Text search (default)**:
+Available types: `"text"`, `"title"`, `"permalink"`, `"vector"`/`"semantic"`, `"hybrid"`.
+Default is `"hybrid"` when semantic search is enabled, `"text"` otherwise.
+
+**Text search**:
 
 ```python
 # Full-text search across all content
@@ -1080,15 +1128,50 @@ results = await search_notes(
 )
 ```
 
-**Semantic search**:
+**Title and permalink search**:
+
+```python
+# Search by title only
+results = await search_notes(query="API Design", search_type="title", project="main")
+
+# Search by permalink
+results = await search_notes(query="specs/api-design", search_type="permalink", project="main")
+```
+
+**Semantic/vector search**:
 
 ```python
 # Semantic/vector search (if enabled)
 results = await search_notes(
     query="user login security",
-    search_type="semantic",
+    search_type="semantic",  # or "vector"
     project="main"
 )
+
+# Override similarity threshold
+results = await search_notes(
+    query="user login security",
+    search_type="semantic",
+    min_similarity=0.5,
+    project="main"
+)
+```
+
+**Hybrid search** (combines text + semantic):
+
+```python
+results = await search_notes(
+    query="authentication best practices",
+    search_type="hybrid",
+    project="main"
+)
+```
+
+**Tag shorthand in query**:
+
+```python
+# Use tag: prefix as shorthand
+results = await search_notes(query="tag:security", project="main")
 ```
 
 ### Search Response
@@ -2161,6 +2244,31 @@ active_project = projects[0]["name"]
 results = await search_notes(query="test", project=active_project)
 ```
 
+### Note Already Exists
+
+**Error**: `write_note` called for a note that already exists
+
+**Solution**:
+
+```python
+# Preferred: use edit_note for incremental updates
+await edit_note(
+    identifier="Existing Topic",
+    operation="append",
+    content="\n- [update] new information",
+    project="main"
+)
+
+# Alternative: replace the entire note
+await write_note(
+    title="Existing Topic",
+    content="# Existing Topic\n...",
+    folder="notes",
+    overwrite=True,
+    project="main"
+)
+```
+
 ### Entity Not Found
 
 **Error**: Note doesn't exist
@@ -2716,14 +2824,15 @@ await write_note(
 
 ### Content Management
 
-**write_note(title, content, folder, tags, note_type, project)**
-- Create or update markdown notes
+**write_note(title, content, folder, tags, note_type, overwrite, project)**
+- Create new markdown notes (errors if note already exists unless overwrite=True)
 - Parameters:
   - `title` (required): Note title
   - `content` (required): Markdown content
   - `folder` (required): Destination folder
   - `tags` (optional): List of tags
   - `note_type` (optional): Type of note (stored in frontmatter). Can be "note", "person", "meeting", "guide", etc.
+  - `overwrite` (optional): Set to True to replace an existing note (default: error if exists)
   - `project` (required unless default_project_mode): Target project
 - Returns: Created/updated entity with permalink
 - Example:
@@ -2890,19 +2999,20 @@ contents = await list_directory(
 
 ### Search & Discovery
 
-**search_notes(query, page, page_size, search_type, types, entity_types, after_date, metadata_filters, tags, status, project)**
+**search_notes(query, page, page_size, search_type, types, entity_types, after_date, metadata_filters, tags, status, min_similarity, project)**
 - Search across knowledge base
 - Parameters:
-  - `query` (required): Search query
+  - `query` (optional): Search query (not required for filter-only searches)
   - `page` (optional): Page number (default: 1)
   - `page_size` (optional): Results per page (default: 10)
-  - `search_type` (optional): "text" or "semantic"
+  - `search_type` (optional): "text", "title", "permalink", "vector"/"semantic", "hybrid" (default: "hybrid" when semantic enabled, "text" otherwise)
   - `types` (optional): Entity type filter
   - `entity_types` (optional): Observation category filter
   - `after_date` (optional): Date filter (ISO format)
-  - `metadata_filters` (optional): Structured frontmatter filters (dict)
-  - `tags` (optional): Frontmatter tags filter (list)
+  - `metadata_filters` (optional): Structured frontmatter filters (dict, supports `$in`, `$gt`, `$gte`, `$lt`, `$lte`, `$between` operators)
+  - `tags` (optional): Frontmatter tags filter (list); also available via `tag:` query shorthand
   - `status` (optional): Frontmatter status filter (string)
+  - `min_similarity` (optional): Override similarity threshold for vector/hybrid search
   - `project` (required unless default_project_mode): Target project
 - Returns: Matching entities with scores
 - Example:
@@ -2915,18 +3025,11 @@ results = await search_notes(
 )
 ```
 
-**search_by_metadata(filters, limit, offset, project)**
-- Metadata-only search using structured frontmatter
-- Parameters:
-  - `filters` (required): Dict of field -> value (supports $in, $gt/$gte/$lt/$lte, $between)
-  - `limit` (optional): Max results (default: 20)
-  - `offset` (optional): Pagination offset (default: 0)
-  - `project` (required unless default_project_mode): Target project
-- Returns: Matching entities
-- Example:
+**Metadata-only search (via search_notes)**
+- Use `search_notes` with `metadata_filters` and no `query` for metadata-only searches:
 ```python
-results = await search_by_metadata(
-    filters={"type": "spec", "status": "in-progress"},
+results = await search_notes(
+    metadata_filters={"type": "spec", "status": "in-progress"},
     project="main"
 )
 ```
@@ -2978,6 +3081,15 @@ await delete_project(project_name="old-project")
 status = await sync_status(project="main")
 ```
 
+**list_workspaces()**
+- List available workspaces (cloud)
+- Parameters: None
+- Returns: List of workspaces with metadata
+- Example:
+```python
+workspaces = await list_workspaces()
+```
+
 ### Visualization
 
 **canvas(nodes, edges, title, folder, project)**
@@ -3246,8 +3358,8 @@ await edit_note(
     project="main"
 )
 
-# Avoid: Complete rewrite
-# (unless necessary for major restructuring)
+# When full rewrite is needed, use overwrite=True
+await write_note(title="Note", content="...", folder="notes", overwrite=True)
 ```
 
 ### 14. Tagging Strategy

docs/cloud-cli.md

@@ -113,14 +113,14 @@ bm project add research --cloud
 bm project add research --cloud --local-path ~/Documents/research
 
 # Or configure sync for existing project
-bm project sync-setup research ~/Documents/research
+bm cloud sync-setup research ~/Documents/research
 ```
 
 **What happens under the covers:**
 
 When you add a project with `--local-path`:
 1. Project created on cloud at `/app/data/research`
-2. Local path stored in config for that project (`cloud_sync_path`)
+2. Local path stored in config for that project (`local_sync_path`)
 3. Local directory created if it doesn't exist
 4. Bisync state directory created at `~/.basic-memory/bisync-state/research/`
 
@@ -236,7 +236,7 @@ bm project add research --cloud --local-path ~/Documents/research
 
 ```bash
 # Project already exists on cloud
-bm project sync-setup research ~/Documents/research
+bm cloud sync-setup research ~/Documents/research
 ```
 
 **What this does:**
@@ -739,7 +739,7 @@ bm project sync --name research
 **Solution:**
 
 ```bash
-bm project sync-setup research ~/Documents/research
+bm cloud sync-setup research ~/Documents/research
 bm project bisync --name research --resync
 ```
 
@@ -795,7 +795,7 @@ bm project list --local                   # Local project list
 bm project list --cloud                   # Cloud project list
 bm project add <name> --cloud             # Create cloud project (no sync)
 bm project add <name> --cloud --local-path <path> # Create with local sync
-bm project sync-setup <name> <path>       # Add sync to existing project
+bm cloud sync-setup <name> <path>       # Add sync to existing project
 bm project rm <name>                      # Delete project
 ```
 

docs/logfire-instrumentation-strategy.md

@@ -0,0 +1,499 @@
+# Logfire Instrumentation Strategy
+
+## Why
+
+We want Logfire in Basic Memory for two specific use cases:
+
+1. Local development and performance investigation
+2. Cloud deployments where Basic Memory runs inside Basic Memory Cloud
+
+This instrumentation must be:
+
+- Disabled by default
+- Useful when enabled
+- Safe for local-first users
+- Searchable in Logfire over time
+
+The previous integration added telemetry, but it leaned too much on generic framework instrumentation. That created noisy spans with weak names and made the trace view harder to navigate. This strategy favors manual instrumentation around Basic Memory's real units of work.
+
+## Core Principles
+
+### 1. Default-off
+
+Basic Memory should ship with Logfire disabled unless the operator explicitly enables it.
+
+That means:
+
+- no required token for normal local usage
+- no surprise outbound telemetry
+- no behavior change for existing users
+
+### 2. Manual spans over automatic framework spans
+
+We should not rely on broad auto-instrumentation for FastAPI, MCP, SQLAlchemy, or HTTP as the primary experience.
+
+Why:
+
+- auto-generated span names are often generic
+- routes and middleware produce too many low-signal spans
+- it becomes harder to answer product questions like "why was `write_note` slow?" or "where did sync time go?"
+
+The preferred model is:
+
+- one meaningful root span per high-level operation
+- a small number of child spans for important phases
+- optional targeted instrumentation only where it adds clear value
+
+### 3. Logs must live inside traces
+
+Basic Memory already uses `loguru` pervasively. The Logfire integration should preserve that and make those logs visible inside the active trace/span context.
+
+If traces exist but the logs are detached from them, the integration is not doing its job.
+
+### 4. Stable names, selective attributes
+
+Span names should describe the operation class, not the specific input.
+
+Good:
+
+- `mcp.tool.write_note`
+- `sync.project.scan`
+- `search.execute`
+- `routing.resolve_project`
+
+Bad:
+
+- `Searching for "foo bar baz"`
+- `POST /v2/projects/123/search/`
+- `write note to /specs/api.md`
+
+Dynamic values belong in attributes, not in the span name.
+
+## What We Should Not Do
+
+### Avoid broad FastAPI auto-instrumentation
+
+We should not turn on `instrument_fastapi()` and treat that as the main telemetry story.
+
+It may still be useful in narrowly scoped debugging, but it should not define the production trace shape. The meaningful root spans should come from Basic Memory's own entrypoints and service boundaries.
+
+### Avoid per-file spans by default
+
+`sync` can process many files. A span per file will explode trace cardinality and make performance views noisy.
+
+Default behavior should be:
+
+- one span for the project sync
+- child spans for scan, move handling, delete handling, markdown sync batch, relation resolution, embedding sync, watermark update
+- per-file spans only for failures or very slow outliers
+
+### Avoid high-cardinality attributes on every span
+
+Do not attach large or highly variable values everywhere:
+
+- raw note content
+- file bodies
+- long search text
+- arbitrary metadata blobs
+- unique IDs that make every span shape distinct
+
+Prefer compact, queryable attributes:
+
+- `project_name`
+- `workspace_id`
+- `route_mode`
+- `scan_type`
+- `file_count`
+- `result_count`
+- `search_type`
+- `retrieval_mode`
+- `duration_ms`
+
+## Proposed Architecture
+
+Add a dedicated telemetry module in core Basic Memory, separate from logging setup.
+
+Suggested shape:
+
+```python
+# basic_memory/telemetry.py
+
+def configure_telemetry(service_name: str, *, enable_logfire: bool) -> None: ...
+def telemetry_enabled() -> bool: ...
+def span(name: str, **attrs): ...
+def bind_telemetry_context(**attrs): ...
+```
+
+This module should:
+
+- configure Logfire only when explicitly enabled
+- set up the Logfire `loguru` handler
+- expose lightweight helpers so application code does not import `logfire` directly everywhere
+- degrade cleanly to no-op behavior when disabled
+
+This keeps the rest of the codebase readable and makes it easy to reason about what telemetry is doing.
+
+## Logging Integration Strategy
+
+### Goal
+
+When a span is active, logs emitted through `loguru` during that operation should show up in the same trace.
+
+### Preferred design
+
+1. Configure Logfire once in the telemetry bootstrap
+2. Add the Logfire `loguru` handler to the existing `loguru` configuration
+3. At operation boundaries, bind stable contextual fields with `loguru`
+4. Let logs emitted inside the span inherit the active trace context
+
+### Context to bind
+
+Bind only the fields that help correlate work across the system:
+
+- `service_name`
+- `entrypoint`
+- `project_name`
+- `workspace_id`
+- `route_mode`
+- `tool_name`
+- `command_name`
+
+This binding should happen at the root of an operation, not deep in leaf functions.
+
+### Important nuance
+
+We should not try to encode the entire trace model into logger extras. The logger context should be a human-meaningful slice of the active operation. Trace linkage comes from the active Logfire/OpenTelemetry context; logger extras are there to improve searchability and readability.
+
+## Span Model
+
+### Root spans
+
+Each user-visible or system-visible operation should get one root span.
+
+Examples:
+
+- `cli.command.status`
+- `cli.command.project_sync`
+- `api.request.search`
+- `mcp.tool.write_note`
+- `mcp.tool.read_note`
+- `mcp.tool.search_notes`
+- `sync.project.run`
+- `db.semantic_backfill`
+
+### Child spans
+
+Child spans should represent real phases whose duration we care about.
+
+Examples:
+
+- `routing.client_session`
+- `routing.resolve_project`
+- `routing.resolve_workspace`
+- `api.search.execute`
+- `sync.project.scan`
+- `sync.project.detect_moves`
+- `sync.project.apply_changes`
+- `sync.project.resolve_relations`
+- `sync.project.sync_embeddings`
+- `sync.file.markdown`
+- `sync.file.regular`
+- `search.execute`
+- `search.relaxed_fts_retry`
+- `db.init`
+- `db.migrate`
+
+### Span naming rules
+
+- Use dot-separated names
+- Start with subsystem
+- Keep the verb at the end
+- Keep names stable across runs
+- Never include request-specific text in the span name
+
+## Attribute Taxonomy
+
+### Required attributes on root spans
+
+Every root span should have a small common set:
+
+- `service_name`
+- `entrypoint`
+- `project_name` when applicable
+- `workspace_id` when applicable
+- `route_mode` with values like `local_asgi`, `cloud_proxy`, `factory`
+
+### Operation-specific attributes
+
+Examples:
+
+For search:
+
+- `search_type`
+- `retrieval_mode`
+- `page`
+- `page_size`
+- `result_count`
+- `fallback_used`
+
+For sync:
+
+- `scan_type`
+- `force_full`
+- `new_count`
+- `modified_count`
+- `deleted_count`
+- `move_count`
+- `skipped_count`
+- `embeddings_enabled`
+
+For note operations:
+
+- `tool_name`
+- `note_type`
+- `directory`
+- `overwrite`
+- `output_format`
+
+### Attributes to avoid by default
+
+- full `query.text`
+- full note titles if they create privacy or cardinality issues
+- file content
+- raw frontmatter
+- raw HTTP bodies
+
+If we need richer payloads for a local debugging session, that should be an explicit temporary mode, not the default telemetry shape.
+
+## Instrumentation Plan By Layer
+
+### 1. Entrypoints
+
+Instrument these first:
+
+- `cli.app` callback and major commands
+- API lifespan and selected routers
+- MCP server lifespan
+- MCP tool entrypoints
+
+Why:
+
+- this establishes clean root spans
+- it gives us trace boundaries that match how users think about the product
+
+### 2. Routing and context resolution
+
+Instrument:
+
+- client routing decisions
+- workspace resolution
+- project resolution
+- default-project fallback
+
+Why:
+
+- Basic Memory has local/cloud/per-project routing logic
+- when something is slow or surprising, we need to know which path was taken
+
+### 3. Sync and indexing
+
+This is the highest-value area to instrument deeply.
+
+Instrument:
+
+- sync root
+- scan strategy decision
+- filesystem scan
+- move detection
+- delete handling
+- markdown sync phase
+- relation resolution
+- vector embedding sync
+- scan watermark update
+
+Why:
+
+- this is where performance work will happen
+- cloud and local both benefit from this visibility
+
+### 4. Search
+
+Instrument:
+
+- search execution
+- retrieval mode
+- relaxed FTS fallback
+- result shaping
+
+Why:
+
+- search is user-facing and latency-sensitive
+- hybrid/vector/FTS paths need to be distinguishable
+
+### 5. Database and initialization
+
+Instrument selectively:
+
+- DB init
+- migrations
+- semantic backfill
+- connection mode selection
+
+Avoid full automatic SQL span firehose by default.
+
+## Recommended Rollout Phases
+
+## Task List
+
+- [x] Phase 1: Bootstrap and config gating
+- [x] Phase 2: Root spans for entrypoints and primary operations
+- [x] Phase 3: Child spans for sync, search, and routing
+- [x] Phase 4: Failure-focused detail and final verification
+- [x] Phase 5: Loguru context binding and scoped context inheritance
+
+## Recommended Rollout Phases
+
+### Phase 1: Bootstrap and config gating
+
+Add:
+
+- telemetry bootstrap module
+- config/env gating
+- `loguru` + Logfire handler integration
+
+This gives immediate value with low noise.
+
+### Phase 2: Root spans for entrypoints and primary operations
+
+Add:
+
+- root spans for CLI, API, MCP, and main MCP tools
+- stable root attributes for project, workspace, route mode, and operation type
+
+This gives us clean top-level traces that match how users think about the product.
+
+### Phase 3: Child spans for sync, search, and routing
+
+Add child spans to:
+
+- sync
+- search
+- routing
+
+This is the main performance-investigation layer.
+
+### Phase 4: Failure-focused detail
+
+Add selective deeper spans/log enrichment for:
+
+- sync failures
+- relation resolution failures
+- slow file operations
+- cloud routing/auth failures
+
+This keeps normal traces clean while improving debuggability.
+
+### Phase 5: Loguru context binding and scoped context inheritance
+
+Add:
+
+- context-local telemetry state in `basic_memory.telemetry`
+- a shared `scope(...)` helper that opens a span and binds stable logger context together
+- context inheritance for routing, sync, and search so downstream `loguru` logs carry the active operation fields
+
+This makes the trace view and the log stream tell the same story without forcing logger rewrites across the codebase.
+
+## Local Dev Playbook
+
+The fastest way to sanity-check the current trace shape is:
+
+```bash
+LOGFIRE_TOKEN=lf_... just telemetry-smoke
+```
+
+What this does:
+
+- creates an isolated temp home, config dir, and project path
+- enables Logfire for the run
+- automatically exports to Logfire when `LOGFIRE_TOKEN` is present
+- defaults `BASIC_MEMORY_SEMANTIC_SEARCH_ENABLED=false` so the smoke run stays fast and trace-friendly
+- disables promo telemetry so the trace is about Basic Memory work, not analytics noise
+- runs a small CLI workflow:
+  - `project add`
+  - `tool write-note`
+  - `tool read-note`
+  - `tool edit-note`
+  - `tool build-context`
+  - `tool search-notes`
+  - `doctor`
+
+If you want to exercise the instrumentation without exporting anything upstream:
+
+```bash
+BASIC_MEMORY_LOGFIRE_SEND_TO_LOGFIRE=false just telemetry-smoke
+```
+
+If you want the smoke run to include vector or hybrid retrieval spans too:
+
+```bash
+LOGFIRE_TOKEN=lf_... BASIC_MEMORY_SEMANTIC_SEARCH_ENABLED=true just telemetry-smoke
+```
+
+The recipe sets `BASIC_MEMORY_LOGFIRE_ENVIRONMENT=telemetry-smoke` by default so these traces are easy to isolate in Logfire. Override it if you want the smoke traces grouped under a different environment name.
+
+### What to look for
+
+You should see a small set of comparable root spans rather than a framework-generated span forest:
+
+- `cli.command.project`
+- `cli.command.tool`
+- `mcp.tool.write_note`
+- `mcp.tool.read_note`
+- `mcp.tool.edit_note`
+- `mcp.tool.build_context`
+- `mcp.tool.search_notes`
+- `sync.project.run`
+
+You should also see correlated logs under those traces with stable fields like:
+
+- `project_name`
+- `route_mode`
+- `tool_name`
+- `entrypoint`
+
+### Expected nuance
+
+`doctor` creates its own temporary project on purpose. That means the sync trace will usually show a different project name than the `telemetry-smoke` write/search traces. That is fine for smoke testing because the goal is to confirm:
+
+- root span names are meaningful
+- scoped logs stay attached to the active trace
+- routing, tool, search, and sync phases are easy to distinguish
+
+## Validation Checklist
+
+We should consider the integration successful when the following are true:
+
+1. With telemetry disabled, Basic Memory behaves exactly as it does today.
+2. With telemetry enabled, one user action produces one obvious root span.
+3. Logs emitted during that action are visible inside the same trace.
+4. A search in Logfire for `mcp.tool.write_note` or `sync.project.run` returns comparable spans across runs.
+5. Trace views show phase timing clearly without drowning in framework noise.
+6. Sensitive payloads are not captured by default.
+
+## Immediate Implementation Direction
+
+When we start coding, the first pass should be:
+
+1. Add `basic_memory.telemetry`
+2. Add config/env switches for `enabled`, `send_to_logfire`, and service name
+3. Wire telemetry bootstrap into CLI, API, and MCP entrypoints
+4. Configure `loguru` to emit to both existing sinks and the Logfire handler when enabled
+5. Add manual root spans around:
+   - CLI commands
+   - API request handlers we care about
+   - MCP tool entrypoints
+   - sync root
+   - search root
+6. Add child spans to the sync and routing phases only after the root span model feels clean
+
+That gives us a strong foundation without repeating the earlier "turn on instrumentation everywhere" approach.

docs/metadata-search.md

@@ -0,0 +1,260 @@
+# Metadata Search Reference
+
+Basic Memory automatically indexes custom frontmatter fields so you can query them with structured filters. Any YAML key in a note's frontmatter beyond the standard set (`title`, `type`, `tags`, `permalink`, `schema`) is stored as `entity_metadata` and becomes searchable.
+
+## Querying with `search_notes`
+
+`search_notes` is the single search tool for all queries — text, metadata filters, or both. The `query` parameter is optional, so you can use metadata filters alone without passing an empty string.
+
+## Filter Syntax
+
+Filters are a JSON dictionary where each key targets a frontmatter field and the value specifies the match condition. Multiple keys combine with **AND** logic — every filter must match.
+
+### Equality
+
+Match a single value exactly.
+
+```json
+{"status": "active"}
+```
+
+Finds notes whose frontmatter contains `status: active`.
+
+### Array Contains (all)
+
+Pass a list to require **all** listed values to be present in the field.
+
+```json
+{"tags": ["security", "oauth"]}
+```
+
+Finds notes tagged with both `security` and `oauth`.
+
+### `$in` (any of)
+
+Match if the field equals **any** value in the list.
+
+```json
+{"priority": {"$in": ["high", "critical"]}}
+```
+
+### `$gt`, `$gte`, `$lt`, `$lte`
+
+Numeric and text comparisons. Numeric values use numeric comparison; strings use lexicographic comparison.
+
+```json
+{"confidence": {"$gt": 0.7}}
+{"score": {"$lte": 100}}
+```
+
+### `$between`
+
+Range filter (inclusive). Takes a `[min, max]` pair.
+
+```json
+{"score": {"$between": [0.3, 0.8]}}
+```
+
+### Nested Access (dot notation)
+
+Access nested frontmatter values using dots.
+
+```json
+{"schema.version": "2"}
+```
+
+This queries the `version` key inside a `schema` object in frontmatter.
+
+### Summary Table
+
+| Operator | Syntax | Example |
+|----------|--------|---------|
+| Equality | `{"field": "value"}` | `{"status": "active"}` |
+| Array contains (all) | `{"field": ["a", "b"]}` | `{"tags": ["security", "oauth"]}` |
+| `$in` (any of) | `{"field": {"$in": [...]}}` | `{"priority": {"$in": ["high", "critical"]}}` |
+| `$gt` / `$gte` | `{"field": {"$gt": N}}` | `{"confidence": {"$gt": 0.7}}` |
+| `$lt` / `$lte` | `{"field": {"$lt": N}}` | `{"score": {"$lt": 0.5}}` |
+| `$between` | `{"field": {"$between": [min, max]}}` | `{"score": {"$between": [0.3, 0.8]}}` |
+| Nested access | `{"a.b": "value"}` | `{"schema.version": "2"}` |
+
+**Key rules:**
+- Filter keys must match `[A-Za-z0-9_-]+` (dots separate nesting levels).
+- Each operator dict must contain exactly one operator.
+- `$in` and array-contains require non-empty lists.
+- `$between` requires exactly two values `[min, max]`.
+
+## MCP Tool — `search_notes`
+
+`search_notes` is the single search tool for text queries, metadata filters, or both. The `query` parameter is optional.
+
+**Relevant parameters:**
+
+| Parameter | Type | Description |
+|-----------|------|-------------|
+| `query` | string (optional) | Text search query. Omit for filter-only searches. |
+| `metadata_filters` | dict | Structured filter dict (see syntax above) |
+| `tags` | list[str] | Convenience shorthand — merged into `metadata_filters["tags"]` |
+| `status` | string | Convenience shorthand — merged into `metadata_filters["status"]` |
+
+**Merging rules:** `tags` and `status` are convenience shortcuts. They are merged into `metadata_filters` using `setdefault` — if the same key already exists in `metadata_filters`, the explicit filter wins.
+
+**Examples:**
+
+```python
+# Text search filtered by metadata
+await search_notes("authentication", metadata_filters={"status": "draft"})
+
+# Filter-only search (no query needed)
+await search_notes(metadata_filters={"type": "spec"})
+
+# Combine text, tags shortcut, and metadata
+await search_notes(
+    "oauth flow",
+    tags=["security"],
+    metadata_filters={"confidence": {"$gt": 0.7}},
+)
+
+# Convenience shortcuts
+await search_notes("planning", status="active")
+await search_notes(tags=["tier1", "alpha"])
+```
+
+## Tag Search Shortcuts
+
+The `tag:` prefix in a search query is a shorthand for tag-based metadata filtering. When `search_notes` receives a query starting with `tag:`, it converts the query into a `tags` filter and clears the text query.
+
+```python
+# These are equivalent:
+await search_notes("tag:tier1")
+await search_notes("", tags=["tier1"])
+
+# Multiple tags (comma or space separated) — all must be present:
+await search_notes("tag:tier1,alpha")
+await search_notes("tag:tier1 alpha")
+```
+
+## CLI Access
+
+The `bm tool search-notes` command exposes metadata filtering via `--meta` and `--filter` flags.
+
+### `--meta` — simple key=value filters
+
+Repeatable flag for equality filters on frontmatter fields.
+
+```bash
+# Single filter
+bm tool search-notes "my query" --meta status=draft
+
+# Multiple filters (AND logic)
+bm tool search-notes "" --meta status=active --meta priority=high
+```
+
+### `--filter` — advanced JSON filters
+
+Pass a full JSON filter dictionary for operator-based queries.
+
+```bash
+# Range filter
+bm tool search-notes "" --filter '{"score": {"$between": [0.3, 0.8]}}'
+
+# $in filter
+bm tool search-notes "" --filter '{"priority": {"$in": ["high", "critical"]}}'
+```
+
+### `--tag` and `--status` — convenience shortcuts
+
+```bash
+bm tool search-notes "query" --tag security --tag oauth
+bm tool search-notes "" --status draft
+```
+
+### Combined example
+
+```bash
+bm tool search-notes "authentication" --tag security --meta status=draft --type spec
+```
+
+## Practical Examples
+
+### Example notes with custom frontmatter
+
+**`specs/auth-design.md`:**
+
+```markdown
+---
+title: Auth Design
+type: spec
+tags: [security, oauth]
+status: in-progress
+priority: high
+confidence: 0.85
+---
+
+# Auth Design
+
+## Observations
+- [decision] Use OAuth 2.1 with PKCE for all client types #security
+- [requirement] Token refresh must be transparent to the user
+
+## Relations
+- implements [[Security Requirements]]
+```
+
+**`specs/search-redesign.md`:**
+
+```markdown
+---
+title: Search Redesign
+type: spec
+tags: [search, performance]
+status: draft
+priority: medium
+confidence: 0.6
+---
+
+# Search Redesign
+
+## Observations
+- [goal] Sub-100ms search response times #performance
+- [approach] Hybrid FTS + vector retrieval
+
+## Relations
+- depends_on [[Database Schema]]
+```
+
+### Queries that find them
+
+```python
+# Find all in-progress specs
+await search_notes(metadata_filters={"status": "in-progress", "type": "spec"})
+# → Auth Design
+
+# Find high-confidence specs
+await search_notes(metadata_filters={"confidence": {"$gt": 0.7}})
+# → Auth Design (confidence: 0.85)
+
+# Find specs with priority high or medium
+await search_notes(metadata_filters={"priority": {"$in": ["high", "medium"]}})
+# → Auth Design, Search Redesign
+
+# Find specs in a confidence range
+await search_notes(metadata_filters={"confidence": {"$between": [0.5, 0.9]}})
+# → Auth Design (0.85), Search Redesign (0.6)
+
+# Find notes tagged with security
+await search_notes("tag:security")
+# → Auth Design
+
+# Combined: text search + metadata filter
+await search_notes("OAuth", metadata_filters={"status": "in-progress"})
+# → Auth Design
+```
+
+### CLI equivalents
+
+```bash
+bm tool search-notes "" --meta status=in-progress --type spec
+bm tool search-notes "" --filter '{"confidence": {"$gt": 0.7}}'
+bm tool search-notes "OAuth" --meta status=in-progress
+bm tool search-notes --tag security
+```

docs/post-v0.18.0-test-plan.md

@@ -79,7 +79,7 @@ These are the most important post-`v0.18.0` feature modules currently under-cove
 ### Acceptance criteria
 
 - `search_type=text|vector|hybrid` returns expected ranked results on canonical semantic corpus.
-- Missing semantic extras fail fast with actionable install guidance.
+- Missing semantic dependencies fail fast with actionable install guidance.
 - Reindex and provider/model changes produce valid vectors without dimension mismatch.
 - SQLite and Postgres produce equivalent behavior for semantic modes on the same dataset.
 - Generated-column migration path is valid on SQLite environments in use.

docs/releases/v0.19.0.md

@@ -0,0 +1,318 @@
+# v0.19.0 Release Notes
+
+## Overview
+
+v0.19.0 is a major release that introduces semantic vector search, a schema validation system,
+project-prefixed permalinks, per-project cloud routing, and a significant upgrade to FastMCP 3.0.
+It includes 90+ commits since v0.18.0 spanning new features, architectural improvements, and
+stability fixes across both SQLite and Postgres backends.
+
+---
+
+## Major Features
+
+### Semantic Vector Search
+
+Full vector and hybrid search for SQLite (via sqlite-vec) and Postgres (via pgvector).
+
+- **Hybrid search mode** combines full-text search (FTS) with vector similarity for best results
+- **Score-based fusion** replaces RRF for hybrid ranking — `max(vec, fts) + 0.3 * min(vec, fts)` preserves dominant signals and rewards dual-source agreement (#577)
+- **Default search mode** is now `hybrid` when semantic search is enabled, `text` when disabled
+- Embedding providers: FastEmbed (local, default) or OpenAI API
+- Configurable similarity threshold via `semantic_min_similarity` (default 0.55)
+- Per-query `min_similarity` override on `search_notes` tool
+- Auto-backfill: existing entities get embeddings generated on first startup
+- Backend-specific distance-to-similarity conversion (cosine for SQLite, inner product for Postgres)
+- FTS fallback: if semantic dependencies are missing, search gracefully degrades to text-only
+- sqlite-vec knn `k` parameter capped at 4096 to prevent backend errors
+
+**Configuration:**
+```json
+{
+  "semantic_search_enabled": true,
+  "semantic_embedding_provider": "fastembed",
+  "semantic_embedding_model": "bge-small-en-v1.5",
+  "semantic_min_similarity": 0.55
+}
+```
+
+**Usage:**
+```
+search_notes("machine learning concepts", search_type="hybrid")
+search_notes("similar to my notes on coffee", search_type="vector")
+search_notes("exact phrase match", search_type="text")
+search_notes("broad search", min_similarity=0.3)  # lower threshold for more results
+```
+
+### Schema System
+
+Validate note structure against user-defined schemas with frontmatter-based rules.
+
+- Define schemas as YAML in note frontmatter with field types, required fields, and constraints
+- Frontmatter validation during sync — malformed notes get clear error messages
+- Schema inference from existing notes to bootstrap schemas from your content
+- Schema diff to compare two schemas and see changes
+- Available via MCP tools and CLI
+
+### Project-Prefixed Permalinks
+
+Permalinks now include the project name for unambiguous cross-project references.
+
+- Memory URLs like `memory://project-name/folder/note` route to the correct project
+- Existing non-prefixed permalinks continue to work (backwards compatible)
+- Controlled by `permalinks_include_project` config (default: true)
+- `build_context` and `search_notes` auto-detect project from URL prefix
+
+### Per-Project Cloud Routing
+
+Individual projects can be routed through the cloud while others stay local.
+
+- Set a project to cloud mode: `bm project set-cloud research`
+- Revert to local: `bm project set-local research`
+- Uses API key authentication: `bm cloud set-key bmc_abc123...`
+- MCP tools automatically route based on each project's mode
+- Local MCP server (`bm mcp`) still uses local routing for all projects by default
+- `--local` and `--cloud` CLI flags override per-command
+
+### Workspace Selection
+
+Cloud projects can target specific workspaces for multi-tenant environments.
+
+- `workspace` parameter on MCP tools for explicit workspace targeting
+- CLI workspace-aware project listing with `bm project list`
+- Spinner feedback while fetching cloud projects
+
+---
+
+## New Tools and Capabilities
+
+### Dashboard (`bm project info`)
+
+`bm project info` now displays an htop-inspired compact dashboard with:
+
+- Horizontal bar charts for note types (top 5)
+- Embedding coverage bar with Unicode block characters
+- Colored status dots for at-a-glance health
+- `EmbeddingStatus` schema and `get_embedding_status()` service method for programmatic access
+
+### Unified Metadata Search
+
+`search_by_metadata` has been merged into `search_notes` — one tool for all searches.
+`query` is now optional, so you can search purely by frontmatter metadata.
+
+```
+search_notes(metadata_filters={"status": "in-progress"})
+search_notes(metadata_filters={"tags": ["security", "oauth"]})
+search_notes(metadata_filters={"priority": {"$in": ["high", "critical"]}})
+search_notes(metadata_filters={"schema.confidence": {"$gt": 0.7}})
+search_notes(tags=["security"])  # convenience shorthand
+search_notes(status="draft")     # convenience shorthand
+```
+
+### JSON Output Mode
+
+All MCP tools now support `output_format="json"` for machine-readable responses.
+
+- Default remains `"text"` for human-readable output (no breaking changes)
+- `build_context` defaults to `"json"` with slimmed payloads (redundant fields stripped)
+- CLI tool commands support `--format json` flag
+
+### `tag:` Search Shorthand
+
+Search by tag using convenient shorthand syntax.
+
+```
+search_notes("tag:security")
+search_notes("tag:coffee AND tag:brewing")
+```
+
+### Entity User Tracking
+
+Entities now track `created_by` and `last_updated_by` fields for attribution.
+
+### Improved Search Result Content (#609)
+
+Search results now surface more relevant context:
+
+- `matched_chunk_text` populated for FTS-only hybrid results (no more fallback to truncated content)
+- `TOP_CHUNKS_PER_RESULT` increased from 3 to 5, catching answers deeper in large notes (~2700 → ~4500 chars)
+- `CONTENT_DISPLAY_LIMIT` doubled from 2000 to 4000 chars for results without matched chunks
+
+### `write_note` Overwrite Guard (#632)
+
+`write_note` is now non-idempotent by default. If a note already exists, the tool returns an
+error instead of silently overwriting. Pass `overwrite=True` to replace, or use `edit_note`
+for incremental updates. Config option `write_note_overwrite_default` restores the old upsert
+behavior.
+
+---
+
+## Architecture Changes
+
+### Score-Based Hybrid Fusion (#577)
+
+RRF (Reciprocal Rank Fusion) compressed all fused scores to ~0.016, destroying ranking
+differentiation. The new formula `max(vec, fts) + FUSION_BONUS * min(vec, fts)` preserves
+dominant signals and rewards dual-source agreement. Zero-score results now produce zero
+fused score instead of receiving a 0.1 weight floor.
+
+### FastMCP 3.0 Upgrade
+
+Upgraded from FastMCP 2.12.3 to 3.0.1.
+
+- Tool annotations (`readOnlyHint`, `openWorldHint`) for better client integration
+- Improved MCP protocol compliance
+- Better error handling and context management
+
+### Prompts Call MCP Tools Directly
+
+MCP prompts (`search`, `continue_conversation`) now call MCP tools directly instead of
+going through API endpoints. This fixes empty results in discovery mode and ensures prompts
+use the same resolution logic as tools (including LinkResolver fallback).
+
+### build_context LinkResolver Fallback
+
+`build_context` now falls back to LinkResolver when an exact permalink lookup returns empty.
+This uses the same 7-strategy resolution pipeline as `read_note`, so callers no longer get
+empty results for valid note identifiers that don't match exact permalinks.
+
+### Sync Handles Semantic Dependency Errors Gracefully
+
+When sqlite-vec or another embedding provider is unavailable, `sync_file` now catches
+`SemanticDependenciesMissingError` separately. The entity is created and FTS-indexed
+successfully — only vector embeddings are skipped, with a clear warning:
+
+```
+WARNING: Semantic search dependencies missing — vector embeddings skipped for path=note.md.
+Run 'bm reindex --embeddings' after resolving the dependency issue.
+```
+
+### Unified Project Path
+
+Cloud projects with bisync now store the local filesystem path in `path` (not the Docker
+container path). Config migration automatically promotes `local_sync_path` → `path` for
+existing configs.
+
+---
+
+## CLI Improvements
+
+### Status and Doctor Default to Local Routing
+
+`bm status` and `bm doctor` now default to local routing since they scan the local filesystem.
+Previously, cloud-mode projects would route these commands to the cloud API, which returned
+Docker-internal paths that don't exist locally.
+
+### `--format json` for CLI Tool Commands
+
+All `bm tool` subcommands support `--format json` for machine-readable output, enabling
+integration with scripts and plugins.
+
+### `--json` for Top-Level CLI Commands
+
+Five additional CLI commands now support `--json` for machine-readable output:
+
+- `bm status --json` — sync report with new/modified/deleted/moved files and skipped files
+- `bm project list --json` — structured project list with name, paths, routing mode, and defaults
+- `bm schema validate --json` — validation report with per-note pass/fail, warnings, and errors
+- `bm schema infer --json` — field frequency analysis and suggested schema definition
+- `bm schema diff --json` — drift report with new fields, dropped fields, and cardinality changes
+
+This complements the existing `bm project info --json` and `bm tool --format json` support,
+making all major CLI commands scriptable for CI pipelines and automation.
+
+### Cloud Promo and Analytics
+
+- Cloud promo panel shown on first run or version bump with OSS discount code
+- Anonymous usage telemetry via Umami Cloud (promo/login funnel events only)
+- Opt out with `BASIC_MEMORY_NO_PROMOS=1`
+- No PII, no file contents, no per-command tracking
+- See [Telemetry](https://github.com/basicmachines-co/basic-memory#telemetry) in README
+
+---
+
+## Bug Fixes
+
+- **#577**: RRF fusion compressed all hybrid scores to ~0.016, destroying ranking differentiation
+- **#582**: build_context returns empty results on valid note identifiers
+- **#575**: Remove hardcoded "main" default from default_project
+- **#595**: recent_activity dedup and pagination across MCP tools
+- **#593**: Backend-specific distance-to-similarity conversion
+- **#592**: Strip NUL bytes from content before PostgreSQL search indexing
+- **#562**: Use VIRTUAL instead of STORED columns in SQLite migration
+- **#558**: Add X-Tigris-Consistent headers to all rclone commands
+- **#541**: Handle EntityCreationError as conflict
+- **#536**: Stabilize metadata filters on Postgres
+- **#533**: Fix recent_activity prompt defaults
+- **#530**: Prevent spurious `metadata: {}` in frontmatter output
+- **#601**: Return matched chunk text in search results
+- **#606**: Accept `null` for `expected_replacements` in `edit_note`
+- **#579, #607**: Guard against closed streams in promo panel and missing vector tables on shutdown
+- **#609**: FTS-only hybrid results missing `matched_chunk_text`; content limits too conservative
+- **#631**: `build_context` related_results schema validation failure — replaced fragile `_slim_context()` stripping with Pydantic `exclude=True` field config
+- **#630**: Skip workspace resolution when client factory is active — prevents 401 errors in cloud MCP server mode
+- **#30**: `tag:` prefix query fails with hybrid search — moved tag prefix parsing to MCP tool level so it works with all search modes
+- **#31**: `search_notes` returns cluttered observation/relation-level results — now defaults to entity-level results
+- **#28**: `schema_infer` and `schema_diff` return raw Pydantic models as "undefined" in LLM output — added markdown formatters
+- Fix `schema_validate` identifier resolution (now uses LinkResolver) and text rendering (markdown formatter)
+- **#634**: `schema_validate` and `schema_diff` use stale database metadata instead of reading schema definitions from file — now reads frontmatter directly from the file with fallback to database metadata
+- Fix `Post(**metadata)` crash when frontmatter contains `content` or `handler` keys
+- Fix list-valued frontmatter fields (`title`, `type`) crashing on `.strip()` — now coerced to strings
+- Cap sqlite-vec knn `k` parameter at 4096 to prevent backend errors
+- Parameterize SQL queries in search repository type filters
+- Double-default display in project list
+- `ensure_frontmatter_on_sync` default changed to `True`
+- Status/doctor commands fail with cloud-mode projects (Docker path error)
+- Prompts return "0 projects" in discovery mode
+
+---
+
+## Security
+
+- Upgrade `cryptography` for CVE advisory
+- Upgrade `python-multipart` for security advisory
+
+---
+
+## Internal / Developer
+
+- **#598**: Upgrade FastMCP 2.12.3 → 3.0.1 with tool annotations
+- **#594**: Add `ty` as supplemental type checker
+- **#538**: Add fast feedback loop tooling (`just fast-check`, `just doctor`, `just testmon`)
+- **#600**: Rename `entity_type` to `note_type` for consistency
+- **#596**: Fix CLI runtime defects and audit regressions
+- CLI refactoring and workspace-aware cloud project listing
+- Split and speed up PR test matrix in CI
+- Fix CI: collect coverage from test jobs instead of re-running all tests
+- Create `search_vector_chunks` in test fixtures for Postgres compatibility
+
+---
+
+## Configuration Changes
+
+| Setting | Old Default | New Default | Notes |
+|---------|-------------|-------------|-------|
+| `semantic_search_enabled` | `false` | `true` | Semantic search on by default |
+| `ensure_frontmatter_on_sync` | `false` | `true` | Frontmatter added during sync |
+| `permalinks_include_project` | `false` | `true` | Project prefix in permalinks |
+
+---
+
+## Upgrade Notes
+
+- **Semantic search dependencies** are now included by default. If sqlite-vec fails to load,
+  search gracefully falls back to FTS. Run `bm reindex --embeddings` to generate embeddings
+  for existing content.
+- **Hybrid search scoring** has changed from RRF to score-based fusion. Search result ordering
+  may differ — results should be more accurate with better score differentiation.
+- **`search_by_metadata`** is removed as a standalone tool. Use `search_notes` with
+  `metadata_filters` instead (same parameters, same behavior).
+- **Project-prefixed permalinks** are enabled by default. Existing notes keep their current
+  permalinks until modified. Set `permalinks_include_project: false` to disable.
+- **Frontmatter on sync** is now enabled by default. Files without frontmatter will have it
+  added on next sync. Set `ensure_frontmatter_on_sync: false` to preserve old behavior.
+- **Config migration** runs automatically for cloud projects with bisync — `local_sync_path`
+  is promoted to `path` so filesystem operations work correctly.
+- **`write_note` is no longer idempotent** — calls to `write_note` for existing notes now
+  return an error unless `overwrite=True` is passed. Use `edit_note` for incremental changes,
+  or set `write_note_overwrite_default: true` in config to restore the old behavior.

docs/semantic-search.md

@@ -1,26 +1,26 @@
 # Semantic Search
 
-This guide covers Basic Memory's optional semantic (vector) search feature, which adds meaning-based retrieval alongside the existing full-text search.
+This guide covers Basic Memory's semantic (vector) search feature, which adds meaning-based retrieval alongside the existing full-text search.
 
 ## Overview
 
-Basic Memory's default search uses full-text search (FTS) — keyword matching with boolean operators. Semantic search adds vector embeddings that capture the *meaning* of your content, enabling:
+Basic Memory's search supports both full-text search (FTS) and semantic retrieval. Semantic search adds vector embeddings that capture the *meaning* of your content, enabling:
 
 - **Paraphrase matching**: Find "authentication flow" when searching for "login process"
 - **Conceptual queries**: Search for "ways to improve performance" and find notes about caching, indexing, and optimization
 - **Hybrid retrieval**: Combine the precision of keyword search with the recall of semantic similarity
 
-Semantic search is **opt-in** — existing behavior is completely unchanged unless you enable it. It works on both SQLite (local) and Postgres (cloud) backends.
+Semantic search is enabled by default when semantic dependencies are available at runtime. It works on both SQLite (local) and Postgres (cloud) backends.
 
 ## Installation
 
-Semantic search dependencies (fastembed, sqlite-vec, openai) are **optional extras** — they are not installed with the base `basic-memory` package. Install them with:
+Semantic search dependencies (fastembed, sqlite-vec, openai) are included in the default `basic-memory` install.
 
 ```bash
-pip install 'basic-memory[semantic]'
+pip install basic-memory
 ```
 
-This keeps the base install lightweight and avoids platform-specific issues with ONNX Runtime wheels.
+You can always override with `BASIC_MEMORY_SEMANTIC_SEARCH_ENABLED=true|false`.
 
 ### Platform Compatibility
 
@@ -34,36 +34,40 @@ This keeps the base install lightweight and avoids platform-specific issues with
 
 #### Intel Mac Workaround
 
-The default FastEmbed provider uses ONNX Runtime, which dropped Intel Mac (x86_64) wheels starting in v1.24. Intel Mac users have two options:
+The default install includes FastEmbed, which depends on ONNX Runtime. ONNX Runtime dropped Intel Mac (x86_64) wheels starting in v1.24, so install with a compatible ONNX Runtime pin first:
+
+```bash
+pip install basic-memory 'onnxruntime<1.24'
+```
+
+After installation, Intel Mac users have two runtime options:
 
 **Option 1: Use OpenAI embeddings (recommended)**
 
-Install only the OpenAI dependency manually — no ONNX Runtime or FastEmbed needed:
-
 ```bash
-pip install openai sqlite-vec
 export BASIC_MEMORY_SEMANTIC_SEARCH_ENABLED=true
 export BASIC_MEMORY_SEMANTIC_EMBEDDING_PROVIDER=openai
 export OPENAI_API_KEY=sk-...
 ```
 
-**Option 2: Pin an older ONNX Runtime**
+**Option 2: Use FastEmbed locally**
 
-FastEmbed's ONNX Runtime dependency is unpinned, so you can constrain it to an older version that still ships Intel Mac wheels by passing both requirements in the same install command:
+Keep the same pinned installation and use FastEmbed (default provider):
 
 ```bash
-pip install 'basic-memory[semantic]' 'onnxruntime<1.24'
+export BASIC_MEMORY_SEMANTIC_SEARCH_ENABLED=true
+export BASIC_MEMORY_SEMANTIC_EMBEDDING_PROVIDER=fastembed
 ```
 
 ## Quick Start
 
-1. Install semantic extras:
+1. Install Basic Memory:
 
 ```bash
-pip install 'basic-memory[semantic]'
+pip install basic-memory
 ```
 
-2. Enable semantic search:
+2. (Optional) Explicitly enable semantic search:
 
 ```bash
 export BASIC_MEMORY_SEMANTIC_SEARCH_ENABLED=true
@@ -84,7 +88,7 @@ search_notes("login process", search_type="vector")
 # Hybrid: combines FTS precision with vector recall (recommended)
 search_notes("login process", search_type="hybrid")
 
-# Traditional full-text search (still the default)
+# Explicit full-text search
 search_notes("login process", search_type="text")
 ```
 
@@ -94,7 +98,7 @@ All settings are fields on `BasicMemoryConfig` and can be set via environment va
 
 | Config Field | Env Var | Default | Description |
 |---|---|---|---|
-| `semantic_search_enabled` | `BASIC_MEMORY_SEMANTIC_SEARCH_ENABLED` | `false` | Enable semantic search. Required before vector/hybrid modes work. |
+| `semantic_search_enabled` | `BASIC_MEMORY_SEMANTIC_SEARCH_ENABLED` | Auto (`true` when semantic deps are available) | Enable semantic search. Required before vector/hybrid modes work. |
 | `semantic_embedding_provider` | `BASIC_MEMORY_SEMANTIC_EMBEDDING_PROVIDER` | `"fastembed"` | Embedding provider: `"fastembed"` (local) or `"openai"` (API). |
 | `semantic_embedding_model` | `BASIC_MEMORY_SEMANTIC_EMBEDDING_MODEL` | `"bge-small-en-v1.5"` | Model identifier. Auto-adjusted per provider if left at default. |
 | `semantic_embedding_dimensions` | `BASIC_MEMORY_SEMANTIC_EMBEDDING_DIMENSIONS` | Auto-detected | Vector dimensions. 384 for FastEmbed, 1536 for OpenAI. Override only if using a non-default model. |
@@ -112,8 +116,8 @@ FastEmbed runs entirely locally using ONNX models — no API key, no network cal
 - **Tradeoff**: Smaller model, fast inference, good quality for most use cases
 
 ```bash
-# Install semantic extras and enable
-pip install 'basic-memory[semantic]'
+# Install basic-memory and enable semantic search
+pip install basic-memory
 export BASIC_MEMORY_SEMANTIC_SEARCH_ENABLED=true
 ```
 
@@ -161,13 +165,13 @@ Returns results ranked by cosine similarity. Individual observations and relatio
 
 ### `hybrid`
 
-Combines FTS and vector results using reciprocal rank fusion (RRF). This is generally the best mode when you want both keyword precision and semantic recall.
+Combines FTS and vector results using score-based fusion. This is generally the best mode when you want both keyword precision and semantic recall.
 
 ```python
 search_notes("authentication security", search_type="hybrid")
 ```
 
-RRF merges the two ranked lists so that items appearing in both get a score boost, while items found by only one method still appear.
+Score-based fusion uses the formula `max(vec, fts) + bonus * min(vec, fts)` to preserve the dominant signal while rewarding results found by both methods.
 
 ### When to Use Which
 
@@ -197,7 +201,8 @@ bm reindex -p my-project
 
 ### When You Need to Reindex
 
-- **First enable**: After turning on `semantic_search_enabled` for the first time
+- **Upgrade note**: Migration now performs a one-time automatic embedding backfill on upgrade.
+- **Manual enable case**: If you explicitly had `semantic_search_enabled=false` and then turn it on
 - **Provider change**: After switching between `fastembed` and `openai`
 - **Model change**: After changing `semantic_embedding_model`
 - **Dimension change**: After changing `semantic_embedding_dimensions`
@@ -231,14 +236,14 @@ Each chunk has a `source_hash` (SHA-256 of the chunk text). On re-sync, unchange
 
 ### Hybrid Fusion
 
-Hybrid search uses reciprocal rank fusion (RRF) to merge FTS and vector results:
+Hybrid search uses score-based fusion to merge FTS and vector results:
 
-1. Run FTS search to get keyword-ranked results
-2. Run vector search to get similarity-ranked results
-3. For each result, compute: `score = 1/(k + fts_rank) + 1/(k + vector_rank)` where `k = 60`
+1. Run FTS search to get keyword-ranked results; normalize scores to [0, 1]
+2. Run vector search to get similarity-ranked results (already [0, 1])
+3. For each result, compute: `fused = max(vec_score, fts_score) + 0.3 * min(vec_score, fts_score)`
 4. Sort by fused score
 
-Items found by both methods get a natural score boost. Items found by only one method still appear but rank lower.
+The dominant signal (whichever source scored higher) is preserved, and dual-source agreement adds a bonus. Unlike rank-based fusion, this approach retains score magnitude — a strong vector match stays strong even without an FTS hit.
 
 ### Observation-Level Results
 

docs/specs/SPEC-SCHEMA-IMPL.md

@@ -64,6 +64,7 @@ class SchemaDefinition:
     version: int                 # Schema version
     fields: list[SchemaField]    # Parsed fields
     validation_mode: str         # "warn" | "strict" | "off"
+    frontmatter_fields: list[SchemaField]  # From settings.frontmatter (default: [])
 
 
 def parse_picoschema(yaml_dict: dict) -> list[SchemaField]:
@@ -145,14 +146,16 @@ class ValidationResult:
 async def validate_note(
     note: Note,
     schema: SchemaDefinition,
+    frontmatter: dict | None = None,
 ) -> ValidationResult:
     """Validate a note against a schema definition.
 
     Mapping rules:
-    - field: string       → observation [field] exists
-    - field?(array): type → multiple [field] observations
-    - field?: EntityType  → relation 'field [[...]]' exists
-    - field?(enum): [v]   → observation [field] value ∈ enum values
+    - field: string              → observation [field] exists
+    - field?(array): type        → multiple [field] observations
+    - field?: EntityType         → relation 'field [[...]]' exists
+    - field?(enum): [v]          → observation [field] value ∈ enum values
+    - settings.frontmatter field → frontmatter key presence/value
     """
 ```
 

docs/specs/SPEC-SCHEMA.md

@@ -73,6 +73,7 @@ authors to learn.
 | `field?(array): EntityType` | Multiple `field` relations | `- authored [[Book]]` (×N) |
 | `tags` | Frontmatter `tags` array | `tags: [startups, essays]` |
 | `field?(enum): [values]` | Observation `[field] value` where value ∈ set | `- [status] active` |
+| `settings.frontmatter` field | Frontmatter key presence/value | `tags: [python, ai]` |
 
 ### Key Insight
 
@@ -99,6 +100,9 @@ schema:
   expertise?(array): string, areas of knowledge
 settings:
   validation: warn    # warn | strict | off
+  frontmatter:
+    tags?(array): string, note categories
+    status?(enum): [draft, review, published]
 ---
 
 # Person
@@ -230,6 +234,32 @@ $ bm schema validate people/ada-lovelace.md
 "Unmatched" items are informational — observations and relations the schema doesn't cover.
 They're valid. Schemas are a subset, not a straitjacket.
 
+### Frontmatter Validation
+
+Schema notes can declare validation rules for frontmatter keys under `settings.frontmatter`
+using the same Picoschema syntax as the `schema` block:
+
+```yaml
+settings:
+  validation: warn
+  frontmatter:
+    tags?(array): string
+    status?(enum): [draft, review, published]
+```
+
+- Frontmatter rules use the same Picoschema key syntax (`?` for optional, `(enum)`, `(array)`)
+- Only available on schema notes (inline schemas skip frontmatter validation)
+- Checks key presence (required vs optional) and enum value membership
+- Unmatched frontmatter keys not in the schema are silently ignored
+- Missing required frontmatter keys produce a warning (or error in strict mode)
+
+Example output for a missing required frontmatter key:
+
+```
+⚠ Person schema validation:
+  - Missing required frontmatter key: status
+```
+
 ### Batch Validation
 
 ```

justfile

@@ -2,7 +2,7 @@
 
 # Install dependencies
 install:
-    uv sync --extra semantic
+    uv sync
     @echo ""
     @echo "💡 Remember to activate the virtual environment by running: source .venv/bin/activate"
 
@@ -62,20 +62,20 @@ test-int-postgres:
     fi
 
 # Run tests impacted by recent changes (requires pytest-testmon)
+# Pass paths or node ids after `just testmon` to limit the candidate set further.
 testmon *args:
-    BASIC_MEMORY_ENV=test uv run pytest -p pytest_mock -v --no-cov --testmon --testmon-forceselect {{args}}
+    BASIC_MEMORY_ENV=test uv run pytest -p pytest_mock -v --no-cov --testmon {{args}}
 
 # Run MCP smoke test (fast end-to-end loop)
 test-smoke:
     BASIC_MEMORY_ENV=test uv run pytest -p pytest_mock -v --no-cov -m smoke test-int/mcp/test_smoke_integration.py
 
-# Fast local loop: lint, format, typecheck, impacted tests
+# Fast local loop: lint, format, typecheck, impacted tests via pytest-testmon
 fast-check:
     just fix
     just format
     just typecheck
     just testmon
-    just test-smoke
 
 # Reset Postgres test database (drops and recreates schema)
 # Useful when Alembic migration state gets out of sync during development
@@ -170,10 +170,18 @@ lint: fix
 fix:
     uv run ruff check --fix --unsafe-fixes src tests test-int
 
-# Type check code
+# Type check code (ty)
 typecheck:
+    uv run ty check src tests test-int
+
+# Type check code (pyright)
+typecheck-pyright:
     uv run pyright
 
+# Type check code (ty)
+typecheck-ty:
+    just typecheck
+
 # Clean build artifacts and cache files
 clean:
     find . -type f -name '*.pyc' -delete
@@ -201,6 +209,51 @@ doctor:
     BASIC_MEMORY_CONFIG_DIR="$TMP_CONFIG" \
     ./.venv/bin/python -m basic_memory.cli.main doctor --local
 
+# Run an isolated Logfire smoke workflow for local trace inspection
+telemetry-smoke:
+    #!/usr/bin/env bash
+    set -euo pipefail
+    TMP_HOME=$(mktemp -d)
+    TMP_CONFIG=$(mktemp -d)
+    TMP_PROJECT=$(mktemp -d)
+    export HOME="$TMP_HOME"
+    export BASIC_MEMORY_ENV="${BASIC_MEMORY_ENV:-dev}"
+    export BASIC_MEMORY_HOME="$TMP_PROJECT/home-root"
+    export BASIC_MEMORY_CONFIG_DIR="$TMP_CONFIG"
+    export BASIC_MEMORY_NO_PROMOS=1
+    export BASIC_MEMORY_LOG_LEVEL="${BASIC_MEMORY_LOG_LEVEL:-INFO}"
+    export BASIC_MEMORY_SEMANTIC_SEARCH_ENABLED="${BASIC_MEMORY_SEMANTIC_SEARCH_ENABLED:-false}"
+    export BASIC_MEMORY_LOGFIRE_ENABLED="${BASIC_MEMORY_LOGFIRE_ENABLED:-true}"
+    export BASIC_MEMORY_LOGFIRE_ENVIRONMENT="${BASIC_MEMORY_LOGFIRE_ENVIRONMENT:-telemetry-smoke}"
+    if [[ -z "${BASIC_MEMORY_LOGFIRE_SEND_TO_LOGFIRE:-}" ]]; then
+        if [[ -n "${LOGFIRE_TOKEN:-}" ]]; then
+            export BASIC_MEMORY_LOGFIRE_SEND_TO_LOGFIRE=true
+        else
+            export BASIC_MEMORY_LOGFIRE_SEND_TO_LOGFIRE=false
+        fi
+    fi
+    mkdir -p "$BASIC_MEMORY_HOME"
+    echo "Telemetry smoke setup:"
+    echo "  logfire_enabled=$BASIC_MEMORY_LOGFIRE_ENABLED"
+    echo "  send_to_logfire=$BASIC_MEMORY_LOGFIRE_SEND_TO_LOGFIRE"
+    echo "  log_level=$BASIC_MEMORY_LOG_LEVEL"
+    echo "  semantic_search_enabled=$BASIC_MEMORY_SEMANTIC_SEARCH_ENABLED"
+    echo "  logfire_environment=$BASIC_MEMORY_LOGFIRE_ENVIRONMENT"
+    echo "  project_path=$TMP_PROJECT"
+    ./.venv/bin/python -m basic_memory.cli.main project add telemetry-smoke "$TMP_PROJECT" --default --local
+    ./.venv/bin/python -m basic_memory.cli.main tool write-note --title "Telemetry Smoke" --folder notes --content "hello from smoke" --project telemetry-smoke --local
+    ./.venv/bin/python -m basic_memory.cli.main tool read-note notes/telemetry-smoke --project telemetry-smoke --local
+    ./.venv/bin/python -m basic_memory.cli.main tool edit-note notes/telemetry-smoke --operation append --content $'\n\nsmoke edit line' --project telemetry-smoke --local
+    ./.venv/bin/python -m basic_memory.cli.main tool build-context notes/telemetry-smoke --project telemetry-smoke --local --page-size 5 --max-related 5
+    ./.venv/bin/python -m basic_memory.cli.main tool search-notes telemetry --project telemetry-smoke --local
+    ./.venv/bin/python -m basic_memory.cli.main doctor --local
+    echo ""
+    echo "Telemetry smoke complete."
+    echo "Search Logfire for:"
+    echo "  service_name: basic-memory-cli"
+    echo "  environment: $BASIC_MEMORY_LOGFIRE_ENVIRONMENT"
+    echo "  span names: mcp.tool.write_note, mcp.tool.read_note, mcp.tool.edit_note, mcp.tool.build_context, mcp.tool.search_notes, sync.project.run"
+
 
 # Update all dependencies to latest versions
 update-deps:

llms-install.md

@@ -54,6 +54,22 @@ Or for a one-time sync:
 basic-memory sync
 ```
 
+### 4. Updating Basic Memory
+
+Basic Memory supports automatic updates by default for `uv tool` and Homebrew installs.
+
+For manual checks and upgrades:
+
+```bash
+# Check now and install if supported
+bm update
+
+# Check only, do not install
+bm update --check
+```
+
+To disable automatic updates, set `"auto_update": false` in `~/.basic-memory/config.json`.
+
 ## Configuration Options
 
 ### Custom Directory
@@ -125,4 +141,4 @@ If you encounter issues:
    cat ~/.basic-memory/basic-memory.log
    ```
 
-For more detailed information, refer to the [full documentation](https://memory.basicmachines.co/).
+For more detailed information, refer to the [full documentation](https://docs.basicmemory.com/).

pyproject.toml

@@ -29,11 +29,11 @@ dependencies = [
     "alembic>=1.14.1",
     "pillow>=11.1.0",
     "pybars3>=0.9.7",
-    "fastmcp==2.12.3", # Pinned - 2.14.x breaks MCP tools visibility (issue #463)
+    "fastmcp>=3.0.1,<4",
     "pyjwt>=2.10.1",
     "python-dotenv>=1.1.0",
     "pytest-aio>=1.9.0",
-    "aiofiles>=24.1.0", # Optional observability (disabled by default via config)
+    "aiofiles>=24.1.0",
     "asyncpg>=0.30.0",
     "nest-asyncio>=1.6.0", # For Alembic migrations with Postgres
     "pytest-asyncio>=1.2.0",
@@ -44,13 +44,11 @@ dependencies = [
     "sniffio>=1.3.1",
     "anyio>=4.10.0",
     "httpx>=0.28.0",
-]
-
-[project.optional-dependencies]
-semantic = [
     "fastembed>=0.7.4",
     "sqlite-vec>=0.1.6",
     "openai>=1.100.2",
+    "logfire>=4.19.0",
+    "psutil>=5.9.0",
 ]
 
 [project.urls]
@@ -72,13 +70,19 @@ addopts = "--cov=basic_memory --cov-report term-missing"
 testpaths = ["tests", "test-int"]
 asyncio_mode = "strict"
 asyncio_default_fixture_loop_scope = "function"
+filterwarnings = [
+    "ignore:The @wait_container_is_ready decorator is deprecated.*:DeprecationWarning:testcontainers\\.core\\.waiting_utils",
+    "ignore:The default datetime adapter is deprecated as of Python 3\\.12.*:DeprecationWarning:aiosqlite\\.core",
+    "ignore:codecs\\.open\\(\\) is deprecated\\. Use open\\(\\) instead\\.:DeprecationWarning:frontmatter",
+    "ignore:Parsing dates involving a day of month without a year specified is ambiguous.*:DeprecationWarning:dateparser\\.utils\\.strptime",
+]
 markers = [
     "benchmark: Performance benchmark tests (deselect with '-m \"not benchmark\"')",
     "slow: Slow-running tests (deselect with '-m \"not slow\"')",
     "postgres: Tests that run against Postgres backend (deselect with '-m \"not postgres\"')",
     "windows: Windows-specific tests (deselect with '-m \"not windows\"')",
     "smoke: Fast end-to-end smoke tests for MCP flows",
-    "semantic: Tests requiring [semantic] extras (fastembed, sqlite-vec, openai)",
+    "semantic: Tests requiring semantic dependencies (fastembed, sqlite-vec, openai)",
 ]
 
 [tool.ruff]
@@ -87,6 +91,7 @@ target-version = "py312"
 
 [dependency-groups]
 dev = [
+    "logfire>=4.19.0",
     "gevent>=24.11.1",
     "icecream>=2.1.3",
     "pytest>=8.3.4",
@@ -100,6 +105,9 @@ dev = [
     "psycopg>=3.2.0",
     "pyright>=1.1.408",
     "pytest-testmon>=2.2.0",
+    "ty>=0.0.18",
+    "cst-lsp>=0.1.3",
+    "libcst>=1.8.6",
 ]
 
 [tool.hatch.version]
@@ -118,6 +126,7 @@ ignore = ["test/"]
 defineConstant = { DEBUG = true }
 reportMissingImports = "error"
 reportMissingTypeStubs = false
+reportUnusedImport = "none"
 pythonVersion = "3.12"
 
 

server.json

@@ -6,12 +6,12 @@
     "url": "https://github.com/basicmachines-co/basic-memory.git",
     "source": "github"
   },
-  "version": "0.18.3",
+  "version": "0.20.3",
   "packages": [
     {
       "registryType": "pypi",
       "identifier": "basic-memory",
-      "version": "0.18.3",
+      "version": "0.20.3",
       "runtimeHint": "uvx",
       "runtimeArguments": [
         {"type": "positional", "value": "basic-memory"},

skills-lock.json

@@ -0,0 +1,10 @@
+{
+  "version": 1,
+  "skills": {
+    "instrumentation": {
+      "source": "pydantic/skills",
+      "sourceType": "github",
+      "computedHash": "0727bffc6a92fdeaf675ae5796ae25341e193327e8c95cd06b188dc4a0a4e62e"
+    }
+  }
+}

src/basic_memory/__init__.py

@@ -1,7 +1,7 @@
 """basic-memory - Local-first knowledge management combining Zettelkasten with knowledge graphs"""
 
 # Package version - updated by release automation
-__version__ = "0.18.3"
+__version__ = "0.20.3"
 
 # API version for FastAPI - independent of package version
 __api_version__ = "v0"

src/basic_memory/alembic/env.py

@@ -66,7 +66,7 @@ target_metadata = Base.metadata
 
 
 # Add this function to tell Alembic what to include/exclude
-def include_object(object, name, type_, reflected, compare_to):
+def include_object(obj, name, type_, reflected, compare_to):
     # Ignore SQLite FTS tables
     if type_ == "table" and name.startswith("search_index"):
         return False
@@ -118,6 +118,54 @@ async def run_async_migrations(connectable):
     await connectable.dispose()
 
 
+def _run_async_migrations_with_asyncio_run(connectable) -> None:
+    """Run async migrations with asyncio.run while closing failed coroutines.
+
+    Trigger: asyncio.run() may reject execution when another event loop is already active.
+    Why: Python raises before awaiting the coroutine, which otherwise leaks a
+    RuntimeWarning about an un-awaited coroutine.
+    Outcome: close the pending coroutine before bubbling the RuntimeError to the
+    fallback path.
+    """
+    migration_coro = run_async_migrations(connectable)
+    try:
+        asyncio.run(migration_coro)
+    except RuntimeError:
+        migration_coro.close()
+        raise
+
+
+def _run_async_migrations_in_thread(connectable) -> None:
+    """Run async migrations in a dedicated thread with its own event loop."""
+    import concurrent.futures
+
+    def run_in_thread():
+        """Run async migrations in a new event loop in a separate thread."""
+        new_loop = asyncio.new_event_loop()
+        asyncio.set_event_loop(new_loop)
+        try:
+            new_loop.run_until_complete(run_async_migrations(connectable))
+        finally:
+            new_loop.close()
+
+    with concurrent.futures.ThreadPoolExecutor() as executor:
+        future = executor.submit(run_in_thread)
+        future.result()  # Wait for completion and re-raise any exceptions
+
+
+def _run_async_engine_migrations(connectable) -> None:
+    """Run async-engine migrations with a running-loop fallback."""
+    try:
+        _run_async_migrations_with_asyncio_run(connectable)
+    except RuntimeError as e:
+        if "cannot be called from a running event loop" in str(e):
+            # We're in a running event loop (likely uvloop or Python 3.14+ tests).
+            # Switch to a dedicated thread so Alembic can finish without nesting loops.
+            _run_async_migrations_in_thread(connectable)
+        else:
+            raise
+
+
 def run_migrations_online() -> None:
     """Run migrations in 'online' mode.
 
@@ -148,30 +196,10 @@ def run_migrations_online() -> None:
 
     # Handle async engines (PostgreSQL with asyncpg)
     if isinstance(connectable, AsyncEngine):
-        # Try to run async migrations
-        # nest_asyncio allows asyncio.run() from within event loops, but doesn't work with uvloop
-        try:
-            asyncio.run(run_async_migrations(connectable))
-        except RuntimeError as e:
-            if "cannot be called from a running event loop" in str(e):
-                # We're in a running event loop (likely uvloop) - need to use a different approach
-                # Create a new thread to run the async migrations
-                import concurrent.futures
-
-                def run_in_thread():
-                    """Run async migrations in a new event loop in a separate thread."""
-                    new_loop = asyncio.new_event_loop()
-                    asyncio.set_event_loop(new_loop)
-                    try:
-                        new_loop.run_until_complete(run_async_migrations(connectable))
-                    finally:
-                        new_loop.close()
-
-                with concurrent.futures.ThreadPoolExecutor() as executor:
-                    future = executor.submit(run_in_thread)
-                    future.result()  # Wait for completion and re-raise any exceptions
-            else:
-                raise
+        # Trigger: async engines need Alembic work to cross the sync/async boundary.
+        # Why: most callers can use asyncio.run(), but running-loop contexts need a thread fallback.
+        # Outcome: migrations complete without leaking un-awaited coroutines.
+        _run_async_engine_migrations(connectable)
     else:
         # Handle sync engines (SQLite) or sync connections
         if hasattr(connectable, "connect"):

src/basic_memory/alembic/versions/i2c3d4e5f6g7_auto_backfill_semantic_embeddings.py

@@ -0,0 +1,29 @@
+"""Trigger automatic semantic embedding backfill during migration.
+
+Revision ID: i2c3d4e5f6g7
+Revises: h1b2c3d4e5f6
+Create Date: 2026-02-19 00:00:00.000000
+
+"""
+
+from typing import Sequence, Union
+
+# revision identifiers, used by Alembic.
+revision: str = "i2c3d4e5f6g7"
+down_revision: Union[str, None] = "h1b2c3d4e5f6"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    """No schema change.
+
+    Trigger: this revision is newly applied.
+    Why: db.run_migrations() detects this revision transition and runs the existing
+    sync_entity_vectors() pipeline to backfill semantic embeddings automatically.
+    Outcome: users no longer need to run `bm reindex --embeddings` after upgrading.
+    """
+
+
+def downgrade() -> None:
+    """No-op downgrade."""

src/basic_memory/alembic/versions/j3d4e5f6g7h8_rename_entity_type_to_note_type.py

@@ -0,0 +1,164 @@
+"""Rename entity_type column to note_type
+
+Revision ID: j3d4e5f6g7h8
+Revises: i2c3d4e5f6g7
+Create Date: 2026-02-22 12:00:00.000000
+
+"""
+
+from typing import Sequence, Union
+
+from alembic import op
+from sqlalchemy import text
+
+# revision identifiers, used by Alembic.
+revision: str = "j3d4e5f6g7h8"
+down_revision: Union[str, None] = "i2c3d4e5f6g7"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def table_exists(connection, table_name: str) -> bool:
+    """Check if a table exists (idempotent migration support)."""
+    if connection.dialect.name == "postgresql":
+        result = connection.execute(
+            text("SELECT 1 FROM information_schema.tables WHERE table_name = :table_name"),
+            {"table_name": table_name},
+        )
+        return result.fetchone() is not None
+    # SQLite
+    result = connection.execute(
+        text("SELECT 1 FROM sqlite_master WHERE type='table' AND name = :table_name"),
+        {"table_name": table_name},
+    )
+    return result.fetchone() is not None
+
+
+def index_exists(connection, index_name: str) -> bool:
+    """Check if an index exists (idempotent migration support)."""
+    if connection.dialect.name == "postgresql":
+        result = connection.execute(
+            text("SELECT 1 FROM pg_indexes WHERE indexname = :index_name"),
+            {"index_name": index_name},
+        )
+        return result.fetchone() is not None
+    # SQLite
+    result = connection.execute(
+        text("SELECT 1 FROM sqlite_master WHERE type='index' AND name = :index_name"),
+        {"index_name": index_name},
+    )
+    return result.fetchone() is not None
+
+
+def column_exists(connection, table: str, column: str) -> bool:
+    """Check if a column exists in a table (idempotent migration support)."""
+    if connection.dialect.name == "postgresql":
+        result = connection.execute(
+            text(
+                "SELECT 1 FROM information_schema.columns "
+                "WHERE table_name = :table AND column_name = :column"
+            ),
+            {"table": table, "column": column},
+        )
+        return result.fetchone() is not None
+    # SQLite
+    result = connection.execute(text(f"PRAGMA table_info({table})"))
+    columns = [row[1] for row in result]
+    return column in columns
+
+
+def upgrade() -> None:
+    """Rename entity_type → note_type on the entity table."""
+    connection = op.get_bind()
+    dialect = connection.dialect.name
+
+    # Skip if already migrated (idempotent)
+    if column_exists(connection, "entity", "note_type"):
+        return
+
+    if dialect == "postgresql":
+        # Postgres supports direct column rename
+        op.execute("ALTER TABLE entity RENAME COLUMN entity_type TO note_type")
+
+        # Recreate the index with new name
+        op.execute("DROP INDEX IF EXISTS ix_entity_type")
+        op.execute("CREATE INDEX ix_note_type ON entity (note_type)")
+    else:
+        # SQLite 3.25.0+ supports ALTER TABLE RENAME COLUMN directly.
+        # Avoids batch_alter_table which fails on tables with generated columns
+        # (duplicate column name error when recreating the table).
+        op.execute("ALTER TABLE entity RENAME COLUMN entity_type TO note_type")
+
+        # Recreate the index with new name
+        if index_exists(connection, "ix_entity_type"):
+            op.drop_index("ix_entity_type", table_name="entity")
+        op.create_index("ix_note_type", "entity", ["note_type"])
+
+    # Update search index metadata: rename entity_type → note_type in JSON
+    # This updates the stored metadata so search results use the new field name
+    # Guard: search_index may not exist on a fresh DB (created by an earlier migration)
+    if not table_exists(connection, "search_index"):
+        return
+
+    if dialect == "postgresql":
+        op.execute(
+            text("""
+                UPDATE search_index
+                SET metadata = metadata - 'entity_type' || jsonb_build_object('note_type', metadata->'entity_type')
+                WHERE metadata ? 'entity_type'
+            """)
+        )
+    else:
+        op.execute(
+            text("""
+                UPDATE search_index
+                SET metadata = json_set(
+                    json_remove(metadata, '$.entity_type'),
+                    '$.note_type',
+                    json_extract(metadata, '$.entity_type')
+                )
+                WHERE json_extract(metadata, '$.entity_type') IS NOT NULL
+            """)
+        )
+
+
+def downgrade() -> None:
+    """Rename note_type → entity_type on the entity table."""
+    connection = op.get_bind()
+    dialect = connection.dialect.name
+
+    if dialect == "postgresql":
+        op.execute("ALTER TABLE entity RENAME COLUMN note_type TO entity_type")
+        op.execute("DROP INDEX IF EXISTS ix_note_type")
+        op.execute("CREATE INDEX ix_entity_type ON entity (entity_type)")
+    else:
+        op.execute("ALTER TABLE entity RENAME COLUMN note_type TO entity_type")
+
+        if index_exists(connection, "ix_note_type"):
+            op.drop_index("ix_note_type", table_name="entity")
+        op.create_index("ix_entity_type", "entity", ["entity_type"])
+
+    # Revert search index metadata
+    if not table_exists(connection, "search_index"):
+        return
+
+    if dialect == "postgresql":
+        op.execute(
+            text("""
+                UPDATE search_index
+                SET metadata = metadata - 'note_type' || jsonb_build_object('entity_type', metadata->'note_type')
+                WHERE metadata ? 'note_type'
+            """)
+        )
+    else:
+        op.execute(
+            text("""
+                UPDATE search_index
+                SET metadata = json_set(
+                    json_remove(metadata, '$.note_type'),
+                    '$.entity_type',
+                    json_extract(metadata, '$.note_type')
+                )
+                WHERE json_extract(metadata, '$.note_type') IS NOT NULL
+            """)
+        )

src/basic_memory/alembic/versions/k4e5f6g7h8i9_add_created_by_and_last_updated_by_to_entity.py

@@ -0,0 +1,74 @@
+"""Add created_by and last_updated_by columns to entity table.
+
+Revision ID: k4e5f6g7h8i9
+Revises: j3d4e5f6g7h8
+Create Date: 2026-02-23 00:00:00.000000
+
+These columns track which cloud user created and last modified each entity.
+Both are nullable — NULL for local/CLI usage and existing entities.
+"""
+
+from typing import Sequence, Union
+
+import sqlalchemy as sa
+from alembic import op
+from sqlalchemy import text
+
+# revision identifiers, used by Alembic.
+revision: str = "k4e5f6g7h8i9"
+down_revision: Union[str, None] = "j3d4e5f6g7h8"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def column_exists(connection, table: str, column: str) -> bool:
+    """Check if a column exists in a table (idempotent migration support)."""
+    if connection.dialect.name == "postgresql":
+        result = connection.execute(
+            text(
+                "SELECT 1 FROM information_schema.columns "
+                "WHERE table_name = :table AND column_name = :column"
+            ),
+            {"table": table, "column": column},
+        )
+        return result.fetchone() is not None
+    else:
+        # SQLite
+        result = connection.execute(text(f"PRAGMA table_info({table})"))
+        columns = [row[1] for row in result]
+        return column in columns
+
+
+def upgrade() -> None:
+    """Add created_by and last_updated_by columns to entity table.
+
+    Both columns are nullable strings that store cloud user_profile_id UUIDs.
+    No data backfill — existing rows get NULL.
+    """
+    connection = op.get_bind()
+
+    if not column_exists(connection, "entity", "created_by"):
+        op.add_column("entity", sa.Column("created_by", sa.String(), nullable=True))
+
+    if not column_exists(connection, "entity", "last_updated_by"):
+        op.add_column("entity", sa.Column("last_updated_by", sa.String(), nullable=True))
+
+
+def downgrade() -> None:
+    """Remove created_by and last_updated_by columns from entity table."""
+    connection = op.get_bind()
+    dialect = connection.dialect.name
+
+    if column_exists(connection, "entity", "last_updated_by"):
+        if dialect == "postgresql":
+            op.drop_column("entity", "last_updated_by")
+        else:
+            with op.batch_alter_table("entity") as batch_op:
+                batch_op.drop_column("last_updated_by")
+
+    if column_exists(connection, "entity", "created_by"):
+        if dialect == "postgresql":
+            op.drop_column("entity", "created_by")
+        else:
+            with op.batch_alter_table("entity") as batch_op:
+                batch_op.drop_column("created_by")

src/basic_memory/alembic/versions/l5g6h7i8j9k0_add_note_content_table.py

@@ -0,0 +1,65 @@
+"""Add note_content table
+
+Revision ID: l5g6h7i8j9k0
+Revises: k4e5f6g7h8i9
+Create Date: 2026-04-04 12:00:00.000000
+
+"""
+
+from typing import Sequence, Union
+
+import sqlalchemy as sa
+from alembic import op
+
+
+# revision identifiers, used by Alembic.
+revision: str = "l5g6h7i8j9k0"
+down_revision: Union[str, None] = "k4e5f6g7h8i9"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    """Create note_content for materialized note content and sync state."""
+    op.create_table(
+        "note_content",
+        sa.Column("entity_id", sa.Integer(), nullable=False),
+        sa.Column("project_id", sa.Integer(), nullable=False),
+        sa.Column("external_id", sa.String(), nullable=False),
+        sa.Column("file_path", sa.String(), nullable=False),
+        sa.Column("markdown_content", sa.Text(), nullable=False),
+        sa.Column("db_version", sa.BigInteger(), nullable=False),
+        sa.Column("db_checksum", sa.String(), nullable=False),
+        sa.Column("file_version", sa.BigInteger(), nullable=True),
+        sa.Column("file_checksum", sa.String(), nullable=True),
+        sa.Column("file_write_status", sa.String(), nullable=False),
+        sa.Column("last_source", sa.String(), nullable=True),
+        sa.Column("updated_at", sa.DateTime(timezone=True), nullable=False),
+        sa.Column("file_updated_at", sa.DateTime(timezone=True), nullable=True),
+        sa.Column("last_materialization_error", sa.Text(), nullable=True),
+        sa.Column("last_materialization_attempt_at", sa.DateTime(timezone=True), nullable=True),
+        sa.CheckConstraint(
+            "file_write_status IN ("
+            "'pending', "
+            "'writing', "
+            "'synced', "
+            "'failed', "
+            "'external_change_detected'"
+            ")",
+            name="ck_note_content_file_write_status",
+        ),
+        sa.ForeignKeyConstraint(["entity_id"], ["entity.id"], ondelete="CASCADE"),
+        sa.ForeignKeyConstraint(["project_id"], ["project.id"], ondelete="CASCADE"),
+        sa.PrimaryKeyConstraint("entity_id"),
+    )
+    op.create_index("ix_note_content_project_id", "note_content", ["project_id"], unique=False)
+    op.create_index("ix_note_content_file_path", "note_content", ["file_path"], unique=False)
+    op.create_index("ix_note_content_external_id", "note_content", ["external_id"], unique=True)
+
+
+def downgrade() -> None:
+    """Drop note_content and its supporting indexes."""
+    op.drop_index("ix_note_content_external_id", table_name="note_content")
+    op.drop_index("ix_note_content_file_path", table_name="note_content")
+    op.drop_index("ix_note_content_project_id", table_name="note_content")
+    op.drop_table("note_content")

src/basic_memory/alembic/versions/m6h7i8j9k0l1_add_vector_sync_fingerprints.py

@@ -0,0 +1,84 @@
+"""Persist vector sync fingerprints on chunk metadata.
+
+Revision ID: m6h7i8j9k0l1
+Revises: l5g6h7i8j9k0
+Create Date: 2026-04-07 00:00:00.000000
+
+"""
+
+from typing import Sequence, Union
+
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision: str = "m6h7i8j9k0l1"
+down_revision: Union[str, None] = "l5g6h7i8j9k0"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    """Add entity fingerprint + embedding model metadata to Postgres chunk rows.
+
+    Trigger: vector sync now fast-skips unchanged entities using persisted
+    semantic fingerprints.
+    Why: chunk rows already own the per-entity derived metadata we diff against,
+    so persisting the fingerprint on that table avoids a second sync-state table.
+    Outcome: existing rows get empty-string placeholders and will be refreshed on
+    the next vector sync before they become eligible for skip checks.
+    """
+    connection = op.get_bind()
+    if connection.dialect.name != "postgresql":
+        return
+
+    op.execute(
+        """
+        ALTER TABLE search_vector_chunks
+        ADD COLUMN IF NOT EXISTS entity_fingerprint TEXT
+        """
+    )
+    op.execute(
+        """
+        ALTER TABLE search_vector_chunks
+        ADD COLUMN IF NOT EXISTS embedding_model TEXT
+        """
+    )
+    op.execute(
+        """
+        UPDATE search_vector_chunks
+        SET entity_fingerprint = COALESCE(entity_fingerprint, ''),
+            embedding_model = COALESCE(embedding_model, '')
+        """
+    )
+    op.execute(
+        """
+        ALTER TABLE search_vector_chunks
+        ALTER COLUMN entity_fingerprint SET NOT NULL
+        """
+    )
+    op.execute(
+        """
+        ALTER TABLE search_vector_chunks
+        ALTER COLUMN embedding_model SET NOT NULL
+        """
+    )
+
+
+def downgrade() -> None:
+    """Remove vector sync fingerprint columns from Postgres chunk rows."""
+    connection = op.get_bind()
+    if connection.dialect.name != "postgresql":
+        return
+
+    op.execute(
+        """
+        ALTER TABLE search_vector_chunks
+        DROP COLUMN IF EXISTS embedding_model
+        """
+    )
+    op.execute(
+        """
+        ALTER TABLE search_vector_chunks
+        DROP COLUMN IF EXISTS entity_fingerprint
+        """
+    )

src/basic_memory/api/app.py

@@ -4,6 +4,7 @@ from contextlib import asynccontextmanager
 
 from fastapi import FastAPI, HTTPException, Request
 from fastapi.exception_handlers import http_exception_handler
+from fastapi.responses import JSONResponse
 from fastapi.routing import APIRouter
 from loguru import logger
 
@@ -25,9 +26,16 @@ from basic_memory.api.v2.routers.project_router import (
     list_projects,
     synchronize_projects,
 )
+import logfire
 from basic_memory.config import init_api_logging
 from basic_memory.services.exceptions import EntityAlreadyExistsError
 from basic_memory.services.initialization import initialize_app
+from basic_memory.workspace_context import (
+    WORKSPACE_SLUG_HEADER,
+    WORKSPACE_TYPE_HEADER,
+    workspace_permalink_context_validation_error,
+    workspace_permalink_context,
+)
 
 
 @asynccontextmanager
@@ -43,30 +51,39 @@ async def lifespan(app: FastAPI):  # pragma: no cover
     set_container(container)
     app.state.container = container
 
-    logger.info(f"Starting Basic Memory API (mode={container.mode.name})")
+    with logfire.span(
+        "api.lifecycle.startup",
+        entrypoint="api",
+        mode=container.mode.name.lower(),
+    ):
+        logger.info(f"Starting Basic Memory API (mode={container.mode.name})")
 
-    await initialize_app(container.config)
+        await initialize_app(container.config)
 
-    # Cache database connections in app state for performance
-    logger.info("Initializing database and caching connections...")
-    engine, session_maker = await container.init_database()
-    app.state.engine = engine
-    app.state.session_maker = session_maker
-    logger.info("Database connections cached in app state")
+        # Cache database connections in app state for performance
+        logger.info("Initializing database and caching connections...")
+        engine, session_maker = await container.init_database()
+        app.state.engine = engine
+        app.state.session_maker = session_maker
+        logger.info("Database connections cached in app state")
 
-    # Create and start sync coordinator (lifecycle centralized in coordinator)
-    sync_coordinator = container.create_sync_coordinator()
-    await sync_coordinator.start()
-    app.state.sync_coordinator = sync_coordinator
+        # Create and start sync coordinator (lifecycle centralized in coordinator)
+        sync_coordinator = container.create_sync_coordinator()
+        await sync_coordinator.start()
+        app.state.sync_coordinator = sync_coordinator
 
     # Proceed with startup
     yield
 
     # Shutdown - coordinator handles clean task cancellation
-    logger.info("Shutting down Basic Memory API")
-    await sync_coordinator.stop()
-
-    await container.shutdown_database()
+    with logfire.span(
+        "api.lifecycle.shutdown",
+        entrypoint="api",
+        mode=container.mode.name.lower(),
+    ):
+        logger.info("Shutting down Basic Memory API")
+        await sync_coordinator.stop()
+        await container.shutdown_database()
 
 
 # Initialize FastAPI app
@@ -77,6 +94,32 @@ app = FastAPI(
     lifespan=lifespan,
 )
 
+
+@app.middleware("http")
+async def workspace_permalink_context_middleware(request: Request, call_next):
+    """Populate workspace permalink context from request headers."""
+    workspace_slug = request.headers.get(WORKSPACE_SLUG_HEADER)
+    workspace_type = request.headers.get(WORKSPACE_TYPE_HEADER)
+
+    validation_error = workspace_permalink_context_validation_error(workspace_slug, workspace_type)
+    if validation_error is not None:
+        return JSONResponse(
+            status_code=400,
+            content={"detail": validation_error},
+        )
+
+    if not workspace_slug:
+        return await call_next(request)
+
+    # ContextVar state remains active across the awaited downstream handler while
+    # this context manager is open, so entity creation can see request metadata.
+    with workspace_permalink_context(
+        workspace_slug=workspace_slug,
+        workspace_type=workspace_type,
+    ):
+        return await call_next(request)
+
+
 # Include v2 routers FIRST (more specific paths must match before /{project} catch-all)
 app.include_router(v2_knowledge, prefix="/v2/projects/{project_id}")
 app.include_router(v2_memory, prefix="/v2/projects/{project_id}")
@@ -136,4 +179,7 @@ async def exception_handler(request, exc):  # pragma: no cover
         error_type=type(exc).__name__,
         error=str(exc),
     )
-    return await http_exception_handler(request, HTTPException(status_code=500, detail=str(exc)))
+    return await http_exception_handler(
+        request,
+        HTTPException(status_code=500, detail="Internal server error"),
+    )

src/basic_memory/api/v2/routers/knowledge_router.py

@@ -10,9 +10,10 @@ Key improvements:
 - Simplified caching strategies
 """
 
-from fastapi import APIRouter, HTTPException, BackgroundTasks, Depends, Response, Path, Query
+from fastapi import APIRouter, HTTPException, Response, Path
 from loguru import logger
 
+import logfire
 from basic_memory.deps import (
     EntityServiceV2ExternalDep,
     SearchServiceV2ExternalDep,
@@ -20,9 +21,9 @@ from basic_memory.deps import (
     ProjectConfigV2ExternalDep,
     AppConfigDep,
     EntityRepositoryV2ExternalDep,
+    RelationRepositoryV2ExternalDep,
     ProjectExternalIdPathDep,
     TaskSchedulerDep,
-    FileServiceV2ExternalDep,
 )
 from basic_memory.schemas import DeleteEntitiesResponse
 from basic_memory.schemas.base import Entity
@@ -31,6 +32,9 @@ from basic_memory.schemas.v2 import (
     EntityResolveRequest,
     EntityResolveResponse,
     EntityResponseV2,
+    GraphEdge,
+    GraphNode,
+    GraphResponse,
     MoveEntityRequestV2,
     MoveDirectoryRequestV2,
     DeleteDirectoryRequestV2,
@@ -56,6 +60,56 @@ def _schedule_vector_sync_if_enabled(
         )
 
 
+## Graph endpoint
+
+
+@router.get("/graph", response_model=GraphResponse)
+async def get_graph(
+    project_id: ProjectExternalIdPathDep,
+    entity_repository: EntityRepositoryV2ExternalDep,
+    relation_repository: RelationRepositoryV2ExternalDep,
+) -> GraphResponse:
+    """Return all entities and resolved relations for knowledge graph visualization.
+
+    Returns a flat node/edge structure optimized for rendering with graph libraries.
+    Only includes resolved relations (where to_id is not null).
+    """
+    with logfire.span(
+        "api.request.knowledge.get_graph",
+        entrypoint="api",
+        domain="knowledge",
+        action="get_graph",
+    ):
+        logger.info("API v2 request: get_graph")
+
+        # Fetch all entities for this project
+        entities = await entity_repository.find_all(use_load_options=False)
+        nodes = [
+            GraphNode(
+                external_id=entity.external_id,
+                title=entity.title,
+                note_type=entity.note_type,
+                file_path=entity.file_path,
+            )
+            for entity in entities
+        ]
+
+        # Fetch all resolved relations (to_id is not null) with eager-loaded entities
+        relations = await relation_repository.find_all()
+        edges = [
+            GraphEdge(
+                from_id=relation.from_entity.external_id,
+                to_id=relation.to_entity.external_id,
+                relation_type=relation.relation_type,
+            )
+            for relation in relations
+            if relation.to_entity is not None
+        ]
+
+        logger.info(f"API v2 response: graph with {len(nodes)} nodes and {len(edges)} edges")
+        return GraphResponse(nodes=nodes, edges=edges)
+
+
 ## Resolution endpoint
 
 
@@ -94,47 +148,48 @@ async def resolve_identifier(
             "resolution_method": "permalink"
         }
     """
-    logger.info(f"API v2 request: resolve_identifier for '{data.identifier}'")
+    with logfire.span(
+        "api.request.knowledge.resolve_entity",
+        entrypoint="api",
+        domain="knowledge",
+        action="resolve_entity",
+    ):
+        logger.info(f"API v2 request: resolve_identifier for '{data.identifier}'")
 
-    # Try to resolve by external_id first
-    entity = await entity_repository.get_by_external_id(data.identifier)
-    resolution_method = "external_id" if entity else "search"
+        entity = await entity_repository.get_by_external_id(data.identifier)
+        resolution_method = "external_id" if entity else "search"
 
-    # If not found by external_id, try other resolution methods
-    # Pass source_path for context-aware resolution (prefers notes closer to source)
-    # Pass strict to control fuzzy search fallback (default False allows fuzzy matching)
-    if not entity:
-        entity = await link_resolver.resolve_link(
-            data.identifier, source_path=data.source_path, strict=data.strict
+        if not entity:
+            entity = await link_resolver.resolve_link(
+                data.identifier, source_path=data.source_path, strict=data.strict
+            )
+            if entity:
+                if entity.permalink == data.identifier:
+                    resolution_method = "permalink"
+                elif entity.title == data.identifier:
+                    resolution_method = "title"
+                elif entity.file_path == data.identifier:
+                    resolution_method = "path"
+                else:
+                    resolution_method = "search"
+
+        if not entity:
+            raise HTTPException(status_code=404, detail=f"Entity not found: '{data.identifier}'")
+
+        result = EntityResolveResponse(
+            external_id=entity.external_id,
+            entity_id=entity.id,
+            permalink=entity.permalink,
+            file_path=entity.file_path,
+            title=entity.title,
+            resolution_method=resolution_method,
         )
-        if entity:
-            # Determine resolution method
-            if entity.permalink == data.identifier:
-                resolution_method = "permalink"
-            elif entity.title == data.identifier:
-                resolution_method = "title"
-            elif entity.file_path == data.identifier:
-                resolution_method = "path"
-            else:
-                resolution_method = "search"
 
-    if not entity:
-        raise HTTPException(status_code=404, detail=f"Entity not found: '{data.identifier}'")
+        logger.debug(
+            f"API v2 response: resolved '{data.identifier}' to external_id={result.external_id} via {resolution_method}"
+        )
 
-    result = EntityResolveResponse(
-        external_id=entity.external_id,
-        entity_id=entity.id,
-        permalink=entity.permalink,
-        file_path=entity.file_path,
-        title=entity.title,
-        resolution_method=resolution_method,
-    )
-
-    logger.info(
-        f"API v2 response: resolved '{data.identifier}' to external_id={result.external_id} via {resolution_method}"
-    )
-
-    return result
+        return result
 
 
 ## Read endpoints
@@ -160,18 +215,24 @@ async def get_entity_by_id(
     Raises:
         HTTPException: 404 if entity not found
     """
-    logger.info(f"API v2 request: get_entity_by_id entity_id={entity_id}")
+    with logfire.span(
+        "api.request.knowledge.get_entity",
+        entrypoint="api",
+        domain="knowledge",
+        action="get_entity",
+    ):
+        logger.info(f"API v2 request: get_entity_by_id entity_id={entity_id}")
 
-    entity = await entity_repository.get_by_external_id(entity_id)
-    if not entity:
-        raise HTTPException(
-            status_code=404, detail=f"Entity with external_id '{entity_id}' not found"
-        )
+        entity = await entity_repository.get_by_external_id(entity_id)
+        if not entity:
+            raise HTTPException(
+                status_code=404, detail=f"Entity with external_id '{entity_id}' not found"
+            )
 
-    result = EntityResponseV2.model_validate(entity)
-    logger.info(f"API v2 response: external_id={entity_id}, title='{result.title}'")
+        result = EntityResponseV2.model_validate(entity)
+        logger.info(f"API v2 response: external_id={entity_id}, title='{result.title}'")
 
-    return result
+        return result
 
 
 ## Create endpoints
@@ -181,39 +242,34 @@ async def get_entity_by_id(
 async def create_entity(
     project_id: ProjectExternalIdPathDep,
     data: Entity,
-    background_tasks: BackgroundTasks,
     entity_service: EntityServiceV2ExternalDep,
     search_service: SearchServiceV2ExternalDep,
     task_scheduler: TaskSchedulerDep,
-    file_service: FileServiceV2ExternalDep,
     app_config: AppConfigDep,
-    fast: bool = Query(
-        True, description="If true, write quickly and defer indexing to background tasks."
-    ),
 ) -> EntityResponseV2:
     """Create a new entity.
 
     Args:
         data: Entity data to create
-        fast: If True, defer indexing to background tasks
 
     Returns:
         Created entity with generated external_id (UUID) and file content
     """
-    logger.info(
-        "API v2 request", endpoint="create_entity", entity_type=data.entity_type, title=data.title
-    )
-
-    if fast:
-        entity = await entity_service.fast_write_entity(data)
-        task_scheduler.schedule(
-            "reindex_entity",
-            entity_id=entity.id,
-            project_id=project_id,
+    with logfire.span(
+        "api.request.knowledge.create_entity",
+        entrypoint="api",
+        domain="knowledge",
+        action="create_entity",
+    ):
+        logger.info(
+            "API v2 request", endpoint="create_entity", note_type=data.note_type, title=data.title
         )
-    else:
-        entity = await entity_service.create_entity(data)
-        await search_service.index_entity(entity)
+
+        # Note writes are now internally consistent before the response returns. We only leave
+        # truly derived work, like semantic vectors, on the async scheduler.
+        write_result = await entity_service.create_entity_with_content(data)
+        entity = write_result.entity
+        await search_service.index_entity(entity, content=write_result.search_content)
         _schedule_vector_sync_if_enabled(
             task_scheduler=task_scheduler,
             app_config=app_config,
@@ -221,18 +277,14 @@ async def create_entity(
             project_id=project_id,
         )
 
-    result = EntityResponseV2.model_validate(entity)
-    if fast:
-        result = result.model_copy(update={"observations": [], "relations": []})
+        result = EntityResponseV2.model_validate(entity)
+        # The write service already returns the canonical markdown accepted for this request.
+        result = result.model_copy(update={"content": write_result.content})
 
-    # Always read and return file content
-    content = await file_service.read_file_content(entity.file_path)
-    result = result.model_copy(update={"content": content})
-
-    logger.info(
-        f"API v2 response: endpoint='create_entity' external_id={entity.external_id}, title={result.title}, permalink={result.permalink}, status_code=201"
-    )
-    return result
+        logger.info(
+            f"API v2 response: endpoint='create_entity' external_id={entity.external_id}, title={result.title}, permalink={result.permalink}, status_code=201"
+        )
+        return result
 
 
 ## Update endpoints
@@ -242,18 +294,13 @@ async def create_entity(
 async def update_entity_by_id(
     data: Entity,
     response: Response,
-    background_tasks: BackgroundTasks,
     project_id: ProjectExternalIdPathDep,
     entity_service: EntityServiceV2ExternalDep,
     search_service: SearchServiceV2ExternalDep,
     entity_repository: EntityRepositoryV2ExternalDep,
     task_scheduler: TaskSchedulerDep,
-    file_service: FileServiceV2ExternalDep,
     app_config: AppConfigDep,
     entity_id: str = Path(..., description="Entity external ID (UUID)"),
-    fast: bool = Query(
-        True, description="If true, write quickly and defer indexing to background tasks."
-    ),
 ) -> EntityResponseV2:
     """Update an entity by external ID.
 
@@ -262,39 +309,35 @@ async def update_entity_by_id(
     Args:
         entity_id: External ID (UUID string)
         data: Updated entity data
-        fast: If True, defer indexing to background tasks
 
     Returns:
         Updated entity with file content
     """
-    logger.info(f"API v2 request: update_entity_by_id entity_id={entity_id}")
+    with logfire.span(
+        "api.request.knowledge.update_entity",
+        entrypoint="api",
+        domain="knowledge",
+        action="update_entity",
+    ):
+        logger.info(f"API v2 request: update_entity_by_id entity_id={entity_id}")
 
-    # Check if entity exists (external_id is the source of truth for v2)
-    existing = await entity_repository.get_by_external_id(entity_id)
-    created = existing is None
+        existing = await entity_repository.get_by_external_id(entity_id)
+        created = existing is None
 
-    if fast:
-        entity = await entity_service.fast_write_entity(data, external_id=entity_id)
-        response.status_code = 200 if existing else 201
-        task_scheduler.schedule(
-            "reindex_entity",
-            entity_id=entity.id,
-            project_id=project_id,
-            resolve_relations=created,
-        )
-    else:
         if existing:
-            # Update the existing entity in-place to avoid path-based duplication
-            entity = await entity_service.update_entity(existing, data)
+            write_result = await entity_service.update_entity_with_content(existing, data)
+            entity = write_result.entity
             response.status_code = 200
         else:
-            # Create new entity, then bind external_id to the requested UUID
-            entity = await entity_service.create_entity(data)
+            write_result = await entity_service.create_entity_with_content(data)
+            entity = write_result.entity
             if entity.external_id != entity_id:
                 entity = await entity_repository.update(
                     entity.id,
                     {"external_id": entity_id},
                 )
+                # external_id fixup only changes the DB row. The file content is unchanged,
+                # so the markdown captured during the write remains valid downstream.
                 if not entity:
                     raise HTTPException(
                         status_code=404,
@@ -302,7 +345,7 @@ async def update_entity_by_id(
                     )
             response.status_code = 201
 
-        await search_service.index_entity(entity)
+        await search_service.index_entity(entity, content=write_result.search_content)
         _schedule_vector_sync_if_enabled(
             task_scheduler=task_scheduler,
             app_config=app_config,
@@ -310,42 +353,31 @@ async def update_entity_by_id(
             project_id=project_id,
         )
 
-    result = EntityResponseV2.model_validate(entity)
-    if fast:
-        result = result.model_copy(update={"observations": [], "relations": []})
+        result = EntityResponseV2.model_validate(entity)
+        result = result.model_copy(update={"content": write_result.content})
 
-    # Always read and return file content
-    content = await file_service.read_file_content(entity.file_path)
-    result = result.model_copy(update={"content": content})
-
-    logger.info(
-        f"API v2 response: external_id={entity_id}, created={created}, status_code={response.status_code}"
-    )
-    return result
+        logger.info(
+            f"API v2 response: external_id={entity_id}, created={created}, status_code={response.status_code}"
+        )
+        return result
 
 
 @router.patch("/entities/{entity_id}", response_model=EntityResponseV2)
 async def edit_entity_by_id(
     data: EditEntityRequest,
-    background_tasks: BackgroundTasks,
     project_id: ProjectExternalIdPathDep,
     entity_service: EntityServiceV2ExternalDep,
     search_service: SearchServiceV2ExternalDep,
     entity_repository: EntityRepositoryV2ExternalDep,
     task_scheduler: TaskSchedulerDep,
-    file_service: FileServiceV2ExternalDep,
     app_config: AppConfigDep,
     entity_id: str = Path(..., description="Entity external ID (UUID)"),
-    fast: bool = Query(
-        True, description="If true, write quickly and defer indexing to background tasks."
-    ),
 ) -> EntityResponseV2:
     """Edit an existing entity by external ID using operations like append, prepend, etc.
 
     Args:
         entity_id: External ID (UUID string)
         data: Edit operation details
-        fast: If True, defer indexing to background tasks
 
     Returns:
         Updated entity with file content
@@ -353,36 +385,25 @@ async def edit_entity_by_id(
     Raises:
         HTTPException: 404 if entity not found, 400 if edit fails
     """
-    logger.info(
-        f"API v2 request: edit_entity_by_id entity_id={entity_id}, operation='{data.operation}'"
-    )
-
-    # Verify entity exists
-    entity = await entity_repository.get_by_external_id(entity_id)
-    if not entity:  # pragma: no cover
-        raise HTTPException(
-            status_code=404, detail=f"Entity with external_id '{entity_id}' not found"
+    with logfire.span(
+        "api.request.knowledge.edit_entity",
+        entrypoint="api",
+        domain="knowledge",
+        action="edit_entity",
+    ):
+        logger.info(
+            f"API v2 request: edit_entity_by_id entity_id={entity_id}, operation='{data.operation}'"
         )
 
-    try:
-        if fast:
-            updated_entity = await entity_service.fast_edit_entity(
-                entity=entity,
-                operation=data.operation,
-                content=data.content,
-                section=data.section,
-                find_text=data.find_text,
-                expected_replacements=data.expected_replacements,
+        entity = await entity_repository.get_by_external_id(entity_id)
+        if not entity:  # pragma: no cover
+            raise HTTPException(
+                status_code=404, detail=f"Entity with external_id '{entity_id}' not found"
             )
-            task_scheduler.schedule(
-                "reindex_entity",
-                entity_id=updated_entity.id,
-                project_id=project_id,
-            )
-        else:
-            # Edit using the entity's permalink or path
+
+        try:
             identifier = entity.permalink or entity.file_path
-            updated_entity = await entity_service.edit_entity(
+            write_result = await entity_service.edit_entity_with_content(
                 identifier=identifier,
                 operation=data.operation,
                 content=data.content,
@@ -390,8 +411,8 @@ async def edit_entity_by_id(
                 find_text=data.find_text,
                 expected_replacements=data.expected_replacements,
             )
-
-            await search_service.index_entity(updated_entity)
+            updated_entity = write_result.entity
+            await search_service.index_entity(updated_entity, content=write_result.search_content)
             _schedule_vector_sync_if_enabled(
                 task_scheduler=task_scheduler,
                 app_config=app_config,
@@ -399,23 +420,18 @@ async def edit_entity_by_id(
                 project_id=project_id,
             )
 
-        result = EntityResponseV2.model_validate(updated_entity)
-        if fast:
-            result = result.model_copy(update={"observations": [], "relations": []})
+            result = EntityResponseV2.model_validate(updated_entity)
+            result = result.model_copy(update={"content": write_result.content})
 
-        # Always read and return file content
-        content = await file_service.read_file_content(updated_entity.file_path)
-        result = result.model_copy(update={"content": content})
+            logger.info(
+                f"API v2 response: external_id={entity_id}, operation='{data.operation}', status_code=200"
+            )
 
-        logger.info(
-            f"API v2 response: external_id={entity_id}, operation='{data.operation}', status_code=200"
-        )
+            return result
 
-        return result
-
-    except Exception as e:
-        logger.error(f"Error editing entity {entity_id}: {e}")
-        raise HTTPException(status_code=400, detail=str(e))
+        except Exception as e:
+            logger.error(f"Error editing entity {entity_id}: {e}")
+            raise HTTPException(status_code=400, detail=str(e))
 
 
 ## Delete endpoints
@@ -423,12 +439,10 @@ async def edit_entity_by_id(
 
 @router.delete("/entities/{entity_id}", response_model=DeleteEntitiesResponse)
 async def delete_entity_by_id(
-    background_tasks: BackgroundTasks,
     project_id: ProjectExternalIdPathDep,
     entity_service: EntityServiceV2ExternalDep,
     entity_repository: EntityRepositoryV2ExternalDep,
     entity_id: str = Path(..., description="Entity external ID (UUID)"),
-    search_service=Depends(lambda: None),  # Optional for now
 ) -> DeleteEntitiesResponse:
     """Delete an entity by external ID.
 
@@ -440,23 +454,25 @@ async def delete_entity_by_id(
 
     Note: Returns deleted=False if entity doesn't exist (idempotent)
     """
-    logger.info(f"API v2 request: delete_entity_by_id entity_id={entity_id}")
+    with logfire.span(
+        "api.request.knowledge.delete_entity",
+        entrypoint="api",
+        domain="knowledge",
+        action="delete_entity",
+    ):
+        logger.info(f"API v2 request: delete_entity_by_id entity_id={entity_id}")
 
-    entity = await entity_repository.get_by_external_id(entity_id)
-    if entity is None:
-        logger.info(f"API v2 response: external_id={entity_id} not found, deleted=False")
-        return DeleteEntitiesResponse(deleted=False)
+        entity = await entity_repository.get_by_external_id(entity_id)
+        if entity is None:
+            logger.info(f"API v2 response: external_id={entity_id} not found, deleted=False")
+            return DeleteEntitiesResponse(deleted=False)
 
-    # Delete the entity using internal ID
-    deleted = await entity_service.delete_entity(entity.id)
+        # Delete the entity using internal ID
+        deleted = await entity_service.delete_entity(entity.id)
 
-    # Remove from search index if search service available
-    if search_service:
-        background_tasks.add_task(search_service.handle_delete, entity)  # pragma: no cover
+        logger.info(f"API v2 response: external_id={entity_id}, deleted={deleted}")
 
-    logger.info(f"API v2 response: external_id={entity_id}, deleted={deleted}")
-
-    return DeleteEntitiesResponse(deleted=deleted)
+        return DeleteEntitiesResponse(deleted=deleted)
 
 
 ## Move endpoint
@@ -465,7 +481,6 @@ async def delete_entity_by_id(
 @router.put("/entities/{entity_id}/move", response_model=EntityResponseV2)
 async def move_entity(
     data: MoveEntityRequestV2,
-    background_tasks: BackgroundTasks,
     project_id: ProjectExternalIdPathDep,
     entity_service: EntityServiceV2ExternalDep,
     entity_repository: EntityRepositoryV2ExternalDep,
@@ -488,48 +503,58 @@ async def move_entity(
     Returns:
         Updated entity with new file path
     """
-    logger.info(
-        f"API v2 request: move_entity entity_id={entity_id}, destination='{data.destination_path}'"
-    )
-
-    try:
-        # First, get the entity by external_id to verify it exists
-        entity = await entity_repository.get_by_external_id(entity_id)
-        if not entity:  # pragma: no cover
-            raise HTTPException(
-                status_code=404, detail=f"Entity with external_id '{entity_id}' not found"
-            )
-
-        # Move the entity using its current file path as identifier
-        moved_entity = await entity_service.move_entity(
-            identifier=entity.file_path,  # Use file path for resolution
-            destination_path=data.destination_path,
-            project_config=project_config,
-            app_config=app_config,
+    with logfire.span(
+        "api.request.knowledge.move_entity",
+        entrypoint="api",
+        domain="knowledge",
+        action="move_entity",
+    ):
+        logger.info(
+            f"API v2 request: move_entity entity_id={entity_id}, destination='{data.destination_path}'"
         )
 
-        # Reindex at new location
-        reindexed_entity = await entity_service.link_resolver.resolve_link(data.destination_path)
-        if reindexed_entity:
-            await search_service.index_entity(reindexed_entity)
-            _schedule_vector_sync_if_enabled(
-                task_scheduler=task_scheduler,
+        try:
+            # First, get the entity by external_id to verify it exists
+            entity = await entity_repository.get_by_external_id(entity_id)
+            if not entity:  # pragma: no cover
+                raise HTTPException(
+                    status_code=404, detail=f"Entity with external_id '{entity_id}' not found"
+                )
+
+            # Move the entity using its current file path as identifier
+            moved_entity = await entity_service.move_entity(
+                identifier=entity.file_path,  # Use file path for resolution
+                destination_path=data.destination_path,
+                project_config=project_config,
                 app_config=app_config,
-                entity_id=reindexed_entity.id,
-                project_id=project_id,
             )
 
-        result = EntityResponseV2.model_validate(moved_entity)
+            # Reindex at new location
+            reindexed_entity = await entity_service.link_resolver.resolve_link(
+                data.destination_path
+            )
+            if reindexed_entity:
+                await search_service.index_entity(reindexed_entity)
+                _schedule_vector_sync_if_enabled(
+                    task_scheduler=task_scheduler,
+                    app_config=app_config,
+                    entity_id=reindexed_entity.id,
+                    project_id=project_id,
+                )
 
-        logger.info(f"API v2 response: moved external_id={entity_id} to '{data.destination_path}'")
+            result = EntityResponseV2.model_validate(moved_entity)
 
-        return result
+            logger.info(
+                f"API v2 response: moved external_id={entity_id} to '{data.destination_path}'"
+            )
 
-    except HTTPException:  # pragma: no cover
-        raise  # pragma: no cover
-    except Exception as e:
-        logger.error(f"Error moving entity: {e}")
-        raise HTTPException(status_code=400, detail=str(e))
+            return result
+
+        except HTTPException:  # pragma: no cover
+            raise  # pragma: no cover
+        except Exception as e:
+            logger.error(f"Error moving entity: {e}")
+            raise HTTPException(status_code=400, detail=str(e))
 
 
 ## Move directory endpoint
@@ -538,7 +563,6 @@ async def move_entity(
 @router.post("/move-directory", response_model=DirectoryMoveResult)
 async def move_directory(
     data: MoveDirectoryRequestV2,
-    background_tasks: BackgroundTasks,
     project_id: ProjectExternalIdPathDep,
     entity_service: EntityServiceV2ExternalDep,
     project_config: ProjectConfigV2ExternalDep,
@@ -559,40 +583,46 @@ async def move_directory(
     Returns:
         DirectoryMoveResult with counts and details of moved files
     """
-    logger.info(
-        f"API v2 request: move_directory source='{data.source_directory}', destination='{data.destination_directory}'"
-    )
-
-    try:
-        # Move the directory using the service
-        result = await entity_service.move_directory(
-            source_directory=data.source_directory,
-            destination_directory=data.destination_directory,
-            project_config=project_config,
-            app_config=app_config,
-        )
-
-        # Reindex moved entities
-        for file_path in result.moved_files:
-            entity = await entity_service.link_resolver.resolve_link(file_path)
-            if entity:
-                await search_service.index_entity(entity)
-                _schedule_vector_sync_if_enabled(
-                    task_scheduler=task_scheduler,
-                    app_config=app_config,
-                    entity_id=entity.id,
-                    project_id=project_id,
-                )
-
+    with logfire.span(
+        "api.request.knowledge.move_directory",
+        entrypoint="api",
+        domain="knowledge",
+        action="move_directory",
+    ):
         logger.info(
-            f"API v2 response: move_directory "
-            f"total={result.total_files}, success={result.successful_moves}, failed={result.failed_moves}"
+            f"API v2 request: move_directory source='{data.source_directory}', destination='{data.destination_directory}'"
         )
-        return result
 
-    except Exception as e:
-        logger.error(f"Error moving directory: {e}")
-        raise HTTPException(status_code=400, detail=str(e))
+        try:
+            # Move the directory using the service
+            result = await entity_service.move_directory(
+                source_directory=data.source_directory,
+                destination_directory=data.destination_directory,
+                project_config=project_config,
+                app_config=app_config,
+            )
+
+            # Reindex moved entities
+            for file_path in result.moved_files:
+                entity = await entity_service.link_resolver.resolve_link(file_path)
+                if entity:
+                    await search_service.index_entity(entity)
+                    _schedule_vector_sync_if_enabled(
+                        task_scheduler=task_scheduler,
+                        app_config=app_config,
+                        entity_id=entity.id,
+                        project_id=project_id,
+                    )
+
+            logger.info(
+                f"API v2 response: move_directory "
+                f"total={result.total_files}, success={result.successful_moves}, failed={result.failed_moves}"
+            )
+            return result
+
+        except Exception as e:
+            logger.error(f"Error moving directory: {e}")
+            raise HTTPException(status_code=400, detail=str(e))
 
 
 ## Delete directory endpoint
@@ -617,20 +647,26 @@ async def delete_directory(
     Returns:
         DirectoryDeleteResult with counts and details of deleted files
     """
-    logger.info(f"API v2 request: delete_directory directory='{data.directory}'")
+    with logfire.span(
+        "api.request.knowledge.delete_directory",
+        entrypoint="api",
+        domain="knowledge",
+        action="delete_directory",
+    ):
+        logger.info(f"API v2 request: delete_directory directory='{data.directory}'")
 
-    try:
-        # Delete the directory using the service
-        result = await entity_service.delete_directory(
-            directory=data.directory,
-        )
+        try:
+            # Delete the directory using the service
+            result = await entity_service.delete_directory(
+                directory=data.directory,
+            )
 
-        logger.info(
-            f"API v2 response: delete_directory "
-            f"total={result.total_files}, success={result.successful_deletes}, failed={result.failed_deletes}"
-        )
-        return result
+            logger.info(
+                f"API v2 response: delete_directory "
+                f"total={result.total_files}, success={result.successful_deletes}, failed={result.failed_deletes}"
+            )
+            return result
 
-    except Exception as e:
-        logger.error(f"Error deleting directory: {e}")
-        raise HTTPException(status_code=400, detail=str(e))
+        except Exception as e:
+            logger.error(f"Error deleting directory: {e}")
+            raise HTTPException(status_code=400, detail=str(e))

src/basic_memory/api/v2/routers/memory_router.py

@@ -9,6 +9,7 @@ from typing import Annotated, Optional
 from fastapi import APIRouter, Query, Path
 from loguru import logger
 
+import logfire
 from basic_memory.deps import ContextServiceV2ExternalDep, EntityRepositoryV2ExternalDep
 from basic_memory.schemas.base import TimeFrame, parse_timeframe
 from basic_memory.schemas.memory import (
@@ -50,30 +51,55 @@ async def recent(
     Returns:
         GraphContext with recent activity and related entities
     """
-    # return all types by default
-    types = (
-        [SearchItemType.ENTITY, SearchItemType.RELATION, SearchItemType.OBSERVATION]
-        if not type
-        else type
-    )
+    with logfire.span(
+        "api.request.memory.recent_activity",
+        entrypoint="api",
+        domain="memory",
+        action="recent_activity",
+        page=page,
+        page_size=page_size,
+    ):
+        types = (
+            [SearchItemType.ENTITY, SearchItemType.RELATION, SearchItemType.OBSERVATION]
+            if not type
+            else type
+        )
 
-    logger.debug(
-        f"V2 Getting recent context for project {project_id}: `{types}` depth: `{depth}` timeframe: `{timeframe}` page: `{page}` page_size: `{page_size}` max_related: `{max_related}`"
-    )
-    # Parse timeframe
-    since = parse_timeframe(timeframe)
-    limit = page_size
-    offset = (page - 1) * page_size
+        logger.debug(
+            f"V2 Getting recent context for project {project_id}: `{types}` depth: `{depth}` timeframe: `{timeframe}` page: `{page}` page_size: `{page_size}` max_related: `{max_related}`"
+        )
+        since = parse_timeframe(timeframe)
+        limit = page_size
+        offset = (page - 1) * page_size
 
-    # Build context
-    context = await context_service.build_context(
-        types=types, depth=depth, since=since, limit=limit, offset=offset, max_related=max_related
-    )
-    recent_context = await to_graph_context(
-        context, entity_repository=entity_repository, page=page, page_size=page_size
-    )
-    logger.debug(f"V2 Recent context: {recent_context.model_dump_json()}")
-    return recent_context
+        with logfire.span(
+            "api.memory.recent_activity.build_context",
+            domain="memory",
+            action="recent_activity",
+            phase="build_context",
+            page=page,
+            page_size=page_size,
+        ):
+            context = await context_service.build_context(
+                types=types,
+                depth=depth,
+                since=since,
+                limit=limit,
+                offset=offset,
+                max_related=max_related,
+            )
+        with logfire.span(
+            "api.memory.recent_activity.shape_response",
+            domain="memory",
+            action="recent_activity",
+            phase="shape_response",
+            result_count=len(context.results),
+        ):
+            recent_context = await to_graph_context(
+                context, entity_repository=entity_repository, page=page, page_size=page_size
+            )
+        logger.debug(f"V2 Recent context: {recent_context.model_dump_json()}")
+        return recent_context
 
 
 # get_memory_context needs to be declared last so other paths can match
@@ -111,20 +137,46 @@ async def get_memory_context(
     Returns:
         GraphContext with the entity and its related context
     """
-    logger.debug(
-        f"V2 Getting context for project {project_id}, URI: `{uri}` depth: `{depth}` timeframe: `{timeframe}` page: `{page}` page_size: `{page_size}` max_related: `{max_related}`"
-    )
-    memory_url = normalize_memory_url(uri)
+    with logfire.span(
+        "api.request.memory.build_context",
+        entrypoint="api",
+        domain="memory",
+        action="build_context",
+        page=page,
+        page_size=page_size,
+    ):
+        logger.debug(
+            f"V2 Getting context for project {project_id}, URI: `{uri}` depth: `{depth}` timeframe: `{timeframe}` page: `{page}` page_size: `{page_size}` max_related: `{max_related}`"
+        )
+        memory_url = normalize_memory_url(uri)
 
-    # Parse timeframe
-    since = parse_timeframe(timeframe) if timeframe else None
-    limit = page_size
-    offset = (page - 1) * page_size
+        since = parse_timeframe(timeframe) if timeframe else None
+        limit = page_size
+        offset = (page - 1) * page_size
 
-    # Build context
-    context = await context_service.build_context(
-        memory_url, depth=depth, since=since, limit=limit, offset=offset, max_related=max_related
-    )
-    return await to_graph_context(
-        context, entity_repository=entity_repository, page=page, page_size=page_size
-    )
+        with logfire.span(
+            "api.memory.build_context.build_context",
+            domain="memory",
+            action="build_context",
+            phase="build_context",
+            page=page,
+            page_size=page_size,
+        ):
+            context = await context_service.build_context(
+                memory_url,
+                depth=depth,
+                since=since,
+                limit=limit,
+                offset=offset,
+                max_related=max_related,
+            )
+        with logfire.span(
+            "api.memory.build_context.shape_response",
+            domain="memory",
+            action="build_context",
+            phase="shape_response",
+            result_count=len(context.results),
+        ):
+            return await to_graph_context(
+                context, entity_repository=entity_repository, page=page, page_size=page_size
+            )

src/basic_memory/api/v2/routers/project_router.py

@@ -48,7 +48,7 @@ async def list_projects(
         A list of all projects with metadata
     """
     projects = await project_service.list_projects()
-    default_project = project_service.default_project
+    default_project = await project_service.get_default_project_name()
 
     project_items = [
         ProjectItem(

src/basic_memory/api/v2/routers/prompt_router.py

@@ -6,6 +6,7 @@ have entity IDs in URLs - they generate formatted prompts from queries.
 """
 
 from datetime import datetime, timezone
+from typing import Any
 from fastapi import APIRouter, HTTPException, status, Path
 from loguru import logger
 
@@ -59,6 +60,7 @@ async def continue_conversation(
 
     # Initialize search results
     search_results = []
+    hierarchical_results_for_count = []
 
     # Get data needed for template
     if request.topic:
@@ -91,7 +93,8 @@ async def continue_conversation(
         # Limit to a reasonable number of total results
         all_hierarchical_results = all_hierarchical_results[:10]
 
-        template_context = {
+        hierarchical_results_for_count = all_hierarchical_results
+        template_context: dict[str, Any] = {
             "topic": request.topic,
             "timeframe": request.timeframe,
             "hierarchical_results": all_hierarchical_results,
@@ -110,6 +113,7 @@ async def continue_conversation(
 
         hierarchical_results = recent_context.results[:5]  # Limit to top 5 recent items
 
+        hierarchical_results_for_count = hierarchical_results
         template_context = {
             "topic": f"Recent Activity from ({request.timeframe})",
             "timeframe": request.timeframe,
@@ -129,9 +133,6 @@ async def continue_conversation(
         relation_count = 0
         entity_count = 0
 
-        # Get the hierarchical results from the template context
-        hierarchical_results_for_count = template_context.get("hierarchical_results", [])
-
         # For topic-based search
         if request.topic:
             for item in hierarchical_results_for_count:
@@ -159,29 +160,24 @@ async def continue_conversation(
                             elif related.type == "entity":  # pragma: no cover
                                 entity_count += 1  # pragma: no cover
 
-        # Build metadata
-        metadata = {
-            "query": request.topic,
-            "timeframe": request.timeframe,
-            "search_count": len(search_results)
-            if request.topic
-            else 0,  # Original search results count
-            "context_count": len(hierarchical_results_for_count),
-            "observation_count": observation_count,
-            "relation_count": relation_count,
-            "total_items": (
+        prompt_metadata = PromptMetadata(
+            query=request.topic,
+            timeframe=request.timeframe,
+            search_count=len(search_results) if request.topic else 0,
+            context_count=len(hierarchical_results_for_count),
+            observation_count=observation_count,
+            relation_count=relation_count,
+            total_items=(
                 len(hierarchical_results_for_count)
                 + observation_count
                 + relation_count
                 + entity_count
             ),
-            "search_limit": request.search_items_limit,
-            "context_depth": request.depth,
-            "related_limit": request.related_items_limit,
-            "generated_at": datetime.now(timezone.utc).isoformat(),
-        }
-
-        prompt_metadata = PromptMetadata(**metadata)
+            search_limit=request.search_items_limit,
+            context_depth=request.depth,
+            related_limit=request.related_items_limit,
+            generated_at=datetime.now(timezone.utc).isoformat(),
+        )
 
         return PromptResponse(
             prompt=rendered_prompt, context=template_context, metadata=prompt_metadata
@@ -229,7 +225,7 @@ async def search_prompt(
     results = await search_service.search(query, limit=limit, offset=offset)
     search_results = await to_search_results(entity_service, results)
 
-    template_context = {
+    template_context: dict[str, Any] = {
         "query": request.query,
         "timeframe": request.timeframe,
         "results": search_results,
@@ -241,22 +237,19 @@ async def search_prompt(
         # Render template
         rendered_prompt = await template_loader.render("prompts/search.hbs", template_context)
 
-        # Build metadata
-        metadata = {
-            "query": request.query,
-            "timeframe": request.timeframe,
-            "search_count": len(search_results),
-            "context_count": len(search_results),
-            "observation_count": 0,  # Search results don't include observations
-            "relation_count": 0,  # Search results don't include relations
-            "total_items": len(search_results),
-            "search_limit": limit,
-            "context_depth": 0,  # No context depth for basic search
-            "related_limit": 0,  # No related items for basic search
-            "generated_at": datetime.now(timezone.utc).isoformat(),
-        }
-
-        prompt_metadata = PromptMetadata(**metadata)
+        prompt_metadata = PromptMetadata(
+            query=request.query,
+            timeframe=request.timeframe,
+            search_count=len(search_results),
+            context_count=len(search_results),
+            observation_count=0,
+            relation_count=0,
+            total_items=len(search_results),
+            search_limit=limit,
+            context_depth=0,
+            related_limit=0,
+            generated_at=datetime.now(timezone.utc).isoformat(),
+        )
 
         return PromptResponse(
             prompt=rendered_prompt, context=template_context, metadata=prompt_metadata

src/basic_memory/api/v2/routers/resource_router.py

@@ -15,6 +15,7 @@ from pathlib import Path as PathLib
 from fastapi import APIRouter, HTTPException, Response, Path
 from loguru import logger
 
+import logfire
 from basic_memory.deps import (
     ProjectConfigV2ExternalDep,
     FileServiceV2ExternalDep,
@@ -55,36 +56,62 @@ async def get_resource_content(
     Raises:
         HTTPException: 404 if entity or file not found
     """
-    logger.debug(f"V2 Getting content for project {project_id}, entity_id: {entity_id}")
+    with logfire.span(
+        "api.request.resource.get_content",
+        entrypoint="api",
+        domain="resource",
+        action="get_content",
+    ):
+        logger.debug(f"V2 Getting content for project {project_id}, entity_id: {entity_id}")
 
-    # Get entity by external_id
-    entity = await entity_repository.get_by_external_id(entity_id)
-    if not entity:
-        raise HTTPException(status_code=404, detail=f"Entity {entity_id} not found")
+        with logfire.span(
+            "api.resource.get_content.load_entity",
+            domain="resource",
+            action="get_content",
+            phase="load_entity",
+        ):
+            entity = await entity_repository.get_by_external_id(entity_id)
+        if not entity:
+            raise HTTPException(status_code=404, detail=f"Entity {entity_id} not found")
 
-    # Validate entity file path to prevent path traversal
-    project_path = PathLib(config.home)
-    if not validate_project_path(entity.file_path, project_path):
-        logger.error(  # pragma: no cover
-            f"Invalid file path in entity {entity.id}: {entity.file_path}"
-        )
-        raise HTTPException(  # pragma: no cover
-            status_code=500,
-            detail="Entity contains invalid file path",
-        )
+        with logfire.span(
+            "api.resource.get_content.validate_path",
+            domain="resource",
+            action="get_content",
+            phase="validate_path",
+        ):
+            project_path = PathLib(config.home)
+            if not validate_project_path(entity.file_path, project_path):
+                logger.error(  # pragma: no cover
+                    f"Invalid file path in entity {entity.id}: {entity.file_path}"
+                )
+                raise HTTPException(  # pragma: no cover
+                    status_code=500,
+                    detail="Entity contains invalid file path",
+                )
 
-    # Check file exists via file_service (for cloud compatibility)
-    if not await file_service.exists(entity.file_path):
-        raise HTTPException(  # pragma: no cover
-            status_code=404,
-            detail=f"File not found: {entity.file_path}",
-        )
+        with logfire.span(
+            "api.resource.get_content.ensure_exists",
+            domain="resource",
+            action="get_content",
+            phase="ensure_exists",
+        ):
+            if not await file_service.exists(entity.file_path):
+                raise HTTPException(  # pragma: no cover
+                    status_code=404,
+                    detail=f"File not found: {entity.file_path}",
+                )
 
-    # Read content via file_service as bytes (works with both local and S3)
-    content = await file_service.read_file_bytes(entity.file_path)
-    content_type = file_service.content_type(entity.file_path)
+        with logfire.span(
+            "api.resource.get_content.read_content",
+            domain="resource",
+            action="get_content",
+            phase="read_content",
+        ):
+            content = await file_service.read_file_bytes(entity.file_path)
+            content_type = file_service.content_type(entity.file_path)
 
-    return Response(content=content, media_type=content_type)
+        return Response(content=content, media_type=content_type)
 
 
 @router.post("", response_model=ResourceResponse)
@@ -112,74 +139,94 @@ async def create_resource(
     Raises:
         HTTPException: 400 for invalid file paths, 409 if file already exists
     """
-    try:
-        # Validate path to prevent path traversal attacks
-        project_path = PathLib(config.home)
-        if not validate_project_path(data.file_path, project_path):
-            logger.warning(
-                f"Invalid file path attempted: {data.file_path} in project {config.name}"
+    with logfire.span(
+        "api.request.resource.create",
+        entrypoint="api",
+        domain="resource",
+        action="create",
+    ):
+        try:
+            # Validate path to prevent path traversal attacks
+            project_path = PathLib(config.home)
+            if not validate_project_path(data.file_path, project_path):
+                logger.warning(
+                    f"Invalid file path attempted: {data.file_path} in project {config.name}"
+                )
+                raise HTTPException(
+                    status_code=400,
+                    detail=f"Invalid file path: {data.file_path}. "
+                    "Path must be relative and stay within project boundaries.",
+                )
+
+            existing_entity = await entity_repository.get_by_file_path(data.file_path)
+            if existing_entity:
+                raise HTTPException(
+                    status_code=409,
+                    detail=f"Resource already exists at {data.file_path} with entity_id {existing_entity.external_id}. "
+                    f"Use PUT /resource/{existing_entity.external_id} to update it.",
+                )
+
+            with logfire.span(
+                "api.resource.create.write_file",
+                domain="resource",
+                action="create",
+                phase="write_file",
+            ):
+                await file_service.ensure_directory(PathLib(data.file_path).parent)
+                checksum = await file_service.write_file(data.file_path, data.content)
+
+            with logfire.span(
+                "api.resource.create.read_metadata",
+                domain="resource",
+                action="create",
+                phase="read_metadata",
+            ):
+                file_metadata = await file_service.get_file_metadata(data.file_path)
+
+            file_name = PathLib(data.file_path).name
+            content_type = file_service.content_type(data.file_path)
+            note_type = "canvas" if data.file_path.endswith(".canvas") else "file"
+
+            entity = EntityModel(
+                external_id=str(uuid.uuid4()),
+                title=file_name,
+                note_type=note_type,
+                content_type=content_type,
+                file_path=data.file_path,
+                checksum=checksum,
+                created_at=file_metadata.created_at,
+                updated_at=file_metadata.modified_at,
             )
-            raise HTTPException(
-                status_code=400,
-                detail=f"Invalid file path: {data.file_path}. "
-                "Path must be relative and stay within project boundaries.",
+            with logfire.span(
+                "api.resource.create.upsert_entity",
+                domain="resource",
+                action="create",
+                phase="upsert_entity",
+            ):
+                entity = await entity_repository.add(entity)
+
+            with logfire.span(
+                "api.resource.create.search_index",
+                domain="resource",
+                action="create",
+                phase="search_index",
+            ):
+                await search_service.index_entity(entity)
+
+            return ResourceResponse(
+                entity_id=entity.id,
+                external_id=entity.external_id,
+                file_path=data.file_path,
+                checksum=checksum,
+                size=file_metadata.size,
+                created_at=file_metadata.created_at.timestamp(),
+                modified_at=file_metadata.modified_at.timestamp(),
             )
-
-        # Check if entity already exists
-        existing_entity = await entity_repository.get_by_file_path(data.file_path)
-        if existing_entity:
-            raise HTTPException(
-                status_code=409,
-                detail=f"Resource already exists at {data.file_path} with entity_id {existing_entity.external_id}. "
-                f"Use PUT /resource/{existing_entity.external_id} to update it.",
-            )
-
-        # Cloud compatibility: avoid assuming a local filesystem path.
-        # Delegate directory creation + writes to FileService (local or S3).
-        await file_service.ensure_directory(PathLib(data.file_path).parent)
-        checksum = await file_service.write_file(data.file_path, data.content)
-
-        # Get file info
-        file_metadata = await file_service.get_file_metadata(data.file_path)
-
-        # Determine file details
-        file_name = PathLib(data.file_path).name
-        content_type = file_service.content_type(data.file_path)
-        entity_type = "canvas" if data.file_path.endswith(".canvas") else "file"
-
-        # Create a new entity model
-        # Explicitly set external_id to ensure NOT NULL constraint is satisfied (fixes #512)
-        entity = EntityModel(
-            external_id=str(uuid.uuid4()),
-            title=file_name,
-            entity_type=entity_type,
-            content_type=content_type,
-            file_path=data.file_path,
-            checksum=checksum,
-            created_at=file_metadata.created_at,
-            updated_at=file_metadata.modified_at,
-        )
-        entity = await entity_repository.add(entity)
-
-        # Index the file for search
-        await search_service.index_entity(entity)  # pyright: ignore
-
-        # Return success response
-        return ResourceResponse(
-            entity_id=entity.id,
-            external_id=entity.external_id,
-            file_path=data.file_path,
-            checksum=checksum,
-            size=file_metadata.size,
-            created_at=file_metadata.created_at.timestamp(),
-            modified_at=file_metadata.modified_at.timestamp(),
-        )
-    except HTTPException:
-        # Re-raise HTTP exceptions without wrapping
-        raise
-    except Exception as e:  # pragma: no cover
-        logger.error(f"Error creating resource {data.file_path}: {e}")
-        raise HTTPException(status_code=500, detail=f"Failed to create resource: {str(e)}")
+        except HTTPException:
+            raise
+        except Exception as e:  # pragma: no cover
+            logger.error(f"Error creating resource {data.file_path}: {e}")
+            raise HTTPException(status_code=500, detail=f"Failed to create resource: {str(e)}")
 
 
 @router.put("/{entity_id}", response_model=ResourceResponse)
@@ -211,79 +258,96 @@ async def update_resource(
     Raises:
         HTTPException: 404 if entity not found, 400 for invalid paths
     """
-    try:
-        # Get existing entity by external_id
-        entity = await entity_repository.get_by_external_id(entity_id)
-        if not entity:
-            raise HTTPException(status_code=404, detail=f"Entity {entity_id} not found")
+    with logfire.span(
+        "api.request.resource.update",
+        entrypoint="api",
+        domain="resource",
+        action="update",
+    ):
+        try:
+            entity = await entity_repository.get_by_external_id(entity_id)
+            if not entity:
+                raise HTTPException(status_code=404, detail=f"Entity {entity_id} not found")
 
-        # Determine target file path
-        target_file_path = data.file_path if data.file_path else entity.file_path
+            target_file_path = data.file_path if data.file_path else entity.file_path
 
-        # Validate path to prevent path traversal attacks
-        project_path = PathLib(config.home)
-        if not validate_project_path(target_file_path, project_path):
-            logger.warning(
-                f"Invalid file path attempted: {target_file_path} in project {config.name}"
+            project_path = PathLib(config.home)
+            if not validate_project_path(target_file_path, project_path):
+                logger.warning(
+                    f"Invalid file path attempted: {target_file_path} in project {config.name}"
+                )
+                raise HTTPException(
+                    status_code=400,
+                    detail=f"Invalid file path: {target_file_path}. "
+                    "Path must be relative and stay within project boundaries.",
+                )
+
+            with logfire.span(
+                "api.resource.update.write_file",
+                domain="resource",
+                action="update",
+                phase="write_file",
+            ):
+                if data.file_path and data.file_path != entity.file_path:
+                    await file_service.ensure_directory(PathLib(target_file_path).parent)
+                    if await file_service.exists(entity.file_path):
+                        await file_service.delete_file(entity.file_path)
+                else:
+                    await file_service.ensure_directory(PathLib(target_file_path).parent)
+
+                checksum = await file_service.write_file(target_file_path, data.content)
+
+            with logfire.span(
+                "api.resource.update.read_metadata",
+                domain="resource",
+                action="update",
+                phase="read_metadata",
+            ):
+                file_metadata = await file_service.get_file_metadata(target_file_path)
+
+            file_name = PathLib(target_file_path).name
+            content_type = file_service.content_type(target_file_path)
+            note_type = "canvas" if target_file_path.endswith(".canvas") else "file"
+
+            with logfire.span(
+                "api.resource.update.update_entity",
+                domain="resource",
+                action="update",
+                phase="update_entity",
+            ):
+                updated_entity = await entity_repository.update(
+                    entity.id,
+                    {
+                        "title": file_name,
+                        "note_type": note_type,
+                        "content_type": content_type,
+                        "file_path": target_file_path,
+                        "checksum": checksum,
+                        "updated_at": file_metadata.modified_at,
+                    },
+                )
+            if updated_entity is None:
+                raise HTTPException(status_code=404, detail=f"Entity {entity_id} not found")
+
+            with logfire.span(
+                "api.resource.update.search_index",
+                domain="resource",
+                action="update",
+                phase="search_index",
+            ):
+                await search_service.index_entity(updated_entity)
+
+            return ResourceResponse(
+                entity_id=entity.id,
+                external_id=entity.external_id,
+                file_path=target_file_path,
+                checksum=checksum,
+                size=file_metadata.size,
+                created_at=file_metadata.created_at.timestamp(),
+                modified_at=file_metadata.modified_at.timestamp(),
             )
-            raise HTTPException(
-                status_code=400,
-                detail=f"Invalid file path: {target_file_path}. "
-                "Path must be relative and stay within project boundaries.",
-            )
-
-        # If moving file, handle the move
-        if data.file_path and data.file_path != entity.file_path:
-            # Ensure new parent directory exists (no-op for S3)
-            await file_service.ensure_directory(PathLib(target_file_path).parent)
-
-            # If old file exists, remove it via file_service (for cloud compatibility)
-            if await file_service.exists(entity.file_path):
-                await file_service.delete_file(entity.file_path)
-        else:
-            # Ensure directory exists for in-place update
-            await file_service.ensure_directory(PathLib(target_file_path).parent)
-
-        # Write content to target file
-        checksum = await file_service.write_file(target_file_path, data.content)
-
-        # Get file info
-        file_metadata = await file_service.get_file_metadata(target_file_path)
-
-        # Determine file details
-        file_name = PathLib(target_file_path).name
-        content_type = file_service.content_type(target_file_path)
-        entity_type = "canvas" if target_file_path.endswith(".canvas") else "file"
-
-        # Update entity using internal ID
-        updated_entity = await entity_repository.update(
-            entity.id,
-            {
-                "title": file_name,
-                "entity_type": entity_type,
-                "content_type": content_type,
-                "file_path": target_file_path,
-                "checksum": checksum,
-                "updated_at": file_metadata.modified_at,
-            },
-        )
-
-        # Index the updated file for search
-        await search_service.index_entity(updated_entity)  # pyright: ignore
-
-        # Return success response
-        return ResourceResponse(
-            entity_id=entity.id,
-            external_id=entity.external_id,
-            file_path=target_file_path,
-            checksum=checksum,
-            size=file_metadata.size,
-            created_at=file_metadata.created_at.timestamp(),
-            modified_at=file_metadata.modified_at.timestamp(),
-        )
-    except HTTPException:
-        # Re-raise HTTP exceptions without wrapping
-        raise
-    except Exception as e:  # pragma: no cover
-        logger.error(f"Error updating resource {entity_id}: {e}")
-        raise HTTPException(status_code=500, detail=f"Failed to update resource: {str(e)}")
+        except HTTPException:
+            raise
+        except Exception as e:  # pragma: no cover
+            logger.error(f"Error updating resource {entity_id}: {e}")
+            raise HTTPException(status_code=500, detail=f"Failed to update resource: {str(e)}")

src/basic_memory/api/v2/routers/schema_router.py

@@ -10,9 +10,15 @@ Flow: Entity loaded with eager observations/relations -> convert to tuples -> co
 
 from pathlib import Path as FilePath
 
+import frontmatter
 from fastapi import APIRouter, Path, Query
+from loguru import logger
 
-from basic_memory.deps import EntityRepositoryV2ExternalDep
+from basic_memory.deps import (
+    EntityRepositoryV2ExternalDep,
+    FileServiceV2ExternalDep,
+    LinkResolverV2ExternalDep,
+)
 from basic_memory.models.knowledge import Entity
 from basic_memory.schemas.schema import (
     ValidationReport,
@@ -51,7 +57,7 @@ def _entity_relations(entity: Entity) -> list[RelationData]:
         RelationData(
             relation_type=rel.relation_type,
             target_name=rel.to_name,
-            target_entity_type=rel.to_entity.entity_type if rel.to_entity else None,
+            target_note_type=rel.to_entity.note_type if rel.to_entity else None,
         )
         for rel in entity.outgoing_relations
     ]
@@ -67,11 +73,54 @@ def _entity_to_note_data(entity: Entity) -> NoteData:
 
 
 def _entity_frontmatter(entity: Entity) -> dict:
-    """Build a frontmatter dict from an entity for schema resolution."""
-    frontmatter = dict(entity.entity_metadata) if entity.entity_metadata else {}
-    if entity.entity_type:
-        frontmatter.setdefault("type", entity.entity_type)
-    return frontmatter
+    """Build a frontmatter dict from an entity's database metadata.
+
+    Used for the notes being validated — their type and schema ref are
+    unlikely to change between syncs.
+    """
+    fm = dict(entity.entity_metadata) if entity.entity_metadata else {}
+    if entity.note_type:
+        fm.setdefault("type", entity.note_type)
+    return fm
+
+
+async def _schema_frontmatter_from_file(
+    file_service: FileServiceV2ExternalDep,
+    entity: Entity,
+) -> dict:
+    """Read a schema entity's frontmatter directly from its file.
+
+    Schema definitions (field declarations, validation mode) are the source
+    of truth for validation. Reading from the file ensures schema-validate
+    always uses the latest settings, even when the file watcher hasn't
+    synced changes to entity_metadata in the database.
+    """
+    try:
+        content = await file_service.read_file_content(entity.file_path)
+        post = frontmatter.loads(content)
+        metadata = dict(post.metadata)
+
+        # Trigger: file is mid-edit and missing required schema fields
+        # Why: parse_schema_note() raises ValueError for missing entity/schema,
+        #   which would turn validation into a 500 response
+        # Outcome: fall back to last-known-good database metadata
+        if not metadata.get("entity") or not isinstance(metadata.get("schema"), dict):
+            logger.warning(
+                "Schema file has incomplete frontmatter, falling back to database metadata",
+                file_path=entity.file_path,
+            )
+            return _entity_frontmatter(entity)
+
+        return metadata
+    except Exception:
+        # Trigger: file is missing, unreadable, or has malformed frontmatter
+        # Why: fall back to database metadata rather than failing validation entirely
+        # Outcome: behaves like before this change — uses potentially stale data
+        logger.warning(
+            "Failed to read schema file, falling back to database metadata",
+            file_path=entity.file_path,
+        )
+        return _entity_frontmatter(entity)
 
 
 # --- Validation ---
@@ -80,22 +129,30 @@ def _entity_frontmatter(entity: Entity) -> dict:
 @router.post("/schema/validate", response_model=ValidationReport)
 async def validate_schema(
     entity_repository: EntityRepositoryV2ExternalDep,
+    file_service: FileServiceV2ExternalDep,
+    link_resolver: LinkResolverV2ExternalDep,
     project_id: str = Path(..., description="Project external UUID"),
-    entity_type: str | None = Query(None, description="Entity type to validate"),
+    note_type: str | None = Query(None, description="Note type to validate"),
     identifier: str | None = Query(None, description="Specific note identifier"),
 ):
     """Validate notes against their resolved schemas.
 
     Validates a specific note (by identifier) or all notes of a given type.
     Returns warnings/errors based on the schema's validation mode.
+
+    Schema definitions are read directly from their files to ensure the
+    latest settings (validation mode, field declarations) are always used,
+    even when file changes haven't been synced to the database yet.
     """
     results: list[NoteValidationResponse] = []
 
     # --- Single note validation ---
     if identifier:
-        entity = await entity_repository.get_by_permalink(identifier)
+        # Resolve identifier flexibly (permalink, title, path, fuzzy)
+        # to match how read_note and other tools resolve identifiers
+        entity = await link_resolver.resolve_link(identifier)
         if not entity:
-            return ValidationReport(entity_type=entity_type, total_notes=0, results=[])
+            return ValidationReport(note_type=note_type, total_notes=0, total_entities=0)
 
         frontmatter = _entity_frontmatter(entity)
         schema_ref = frontmatter.get("schema")
@@ -106,29 +163,31 @@ async def validate_schema(
                 query,
                 allow_reference_match=isinstance(schema_ref, str) and query == schema_ref,
             )
-            return [_entity_frontmatter(e) for e in entities]
+            return [await _schema_frontmatter_from_file(file_service, e) for e in entities]
 
         schema_def = await resolve_schema(frontmatter, search_fn)
         if schema_def:
             result = validate_note(
-                entity.permalink or identifier,
+                entity.title or entity.permalink or identifier,
                 schema_def,
                 _entity_observations(entity),
                 _entity_relations(entity),
+                frontmatter=frontmatter,
             )
             results.append(_to_note_validation_response(result))
 
         return ValidationReport(
-            entity_type=entity_type or entity.entity_type,
-            total_notes=1,
+            note_type=note_type or entity.note_type,
+            total_notes=len(results),
+            total_entities=1,
             valid_count=1 if (results and results[0].passed) else 0,
             warning_count=sum(len(r.warnings) for r in results),
             error_count=sum(len(r.errors) for r in results),
             results=results,
         )
 
-    # --- Batch validation by entity type ---
-    entities = await _find_by_entity_type(entity_repository, entity_type) if entity_type else []
+    # --- Batch validation by note type ---
+    entities = await _find_by_note_type(entity_repository, note_type) if note_type else []
 
     for entity in entities:
         frontmatter = _entity_frontmatter(entity)
@@ -140,21 +199,22 @@ async def validate_schema(
                 query,
                 allow_reference_match=isinstance(schema_ref, str) and query == schema_ref,
             )
-            return [_entity_frontmatter(e) for e in entities]
+            return [await _schema_frontmatter_from_file(file_service, e) for e in entities]
 
         schema_def = await resolve_schema(frontmatter, search_fn)
         if schema_def:
             result = validate_note(
-                entity.permalink or entity.file_path,
+                entity.title or entity.permalink or entity.file_path,
                 schema_def,
                 _entity_observations(entity),
                 _entity_relations(entity),
+                frontmatter=frontmatter,
             )
             results.append(_to_note_validation_response(result))
 
     valid = sum(1 for r in results if r.passed)
     return ValidationReport(
-        entity_type=entity_type,
+        note_type=note_type,
         total_notes=len(results),
         total_entities=len(entities),
         valid_count=valid,
@@ -171,7 +231,7 @@ async def validate_schema(
 async def infer_schema_endpoint(
     entity_repository: EntityRepositoryV2ExternalDep,
     project_id: str = Path(..., description="Project external UUID"),
-    entity_type: str = Query(..., description="Entity type to analyze"),
+    note_type: str = Query(..., description="Note type to analyze"),
     threshold: float = Query(0.25, description="Minimum frequency for optional fields"),
 ):
     """Infer a schema from existing notes of a given type.
@@ -179,13 +239,13 @@ async def infer_schema_endpoint(
     Examines observation categories and relation types across all notes
     of the given type. Returns frequency analysis and suggested Picoschema.
     """
-    entities = await _find_by_entity_type(entity_repository, entity_type)
+    entities = await _find_by_note_type(entity_repository, note_type)
     notes_data = [_entity_to_note_data(entity) for entity in entities]
 
-    result = infer_schema(entity_type, notes_data, optional_threshold=threshold)
+    result = infer_schema(note_type, notes_data, optional_threshold=threshold)
 
     return InferenceReport(
-        entity_type=result.entity_type,
+        note_type=result.note_type,
         notes_analyzed=result.notes_analyzed,
         field_frequencies=[
             FieldFrequencyResponse(
@@ -210,10 +270,11 @@ async def infer_schema_endpoint(
 # --- Drift Detection ---
 
 
-@router.get("/schema/diff/{entity_type}", response_model=DriftReport)
+@router.get("/schema/diff/{note_type}", response_model=DriftReport)
 async def diff_schema_endpoint(
     entity_repository: EntityRepositoryV2ExternalDep,
-    entity_type: str = Path(..., description="Entity type to check for drift"),
+    file_service: FileServiceV2ExternalDep,
+    note_type: str = Path(..., description="Note type to check for drift"),
     project_id: str = Path(..., description="Project external UUID"),
 ):
     """Show drift between a schema definition and actual note usage.
@@ -225,23 +286,23 @@ async def diff_schema_endpoint(
 
     async def search_fn(query: str) -> list[dict]:
         entities = await _find_schema_entities(entity_repository, query)
-        return [_entity_frontmatter(e) for e in entities]
+        return [await _schema_frontmatter_from_file(file_service, e) for e in entities]
 
-    # Resolve schema by entity type
-    schema_frontmatter = {"type": entity_type}
+    # Resolve schema by note type
+    schema_frontmatter = {"type": note_type}
     schema_def = await resolve_schema(schema_frontmatter, search_fn)
 
     if not schema_def:
-        return DriftReport(entity_type=entity_type, schema_found=False)
+        return DriftReport(note_type=note_type, schema_found=False)
 
     # Collect all notes of this type
-    entities = await _find_by_entity_type(entity_repository, entity_type)
+    entities = await _find_by_note_type(entity_repository, note_type)
     notes_data = [_entity_to_note_data(entity) for entity in entities]
 
     result = diff_schema(schema_def, notes_data)
 
     return DriftReport(
-        entity_type=entity_type,
+        note_type=note_type,
         new_fields=[
             DriftFieldResponse(
                 name=f.name,
@@ -269,19 +330,19 @@ async def diff_schema_endpoint(
 # --- Helpers ---
 
 
-async def _find_by_entity_type(
+async def _find_by_note_type(
     entity_repository: EntityRepositoryV2ExternalDep,
-    entity_type: str,
+    note_type: str,
 ) -> list[Entity]:
     """Find all entities of a given type using the repository's select pattern."""
-    query = entity_repository.select().where(Entity.entity_type == entity_type)
+    query = entity_repository.select().where(Entity.note_type == note_type)
     result = await entity_repository.execute_query(query)
     return list(result.scalars().all())
 
 
 async def _find_schema_entities(
     entity_repository: EntityRepositoryV2ExternalDep,
-    target_entity_type: str,
+    target_note_type: str,
     *,
     allow_reference_match: bool = False,
 ) -> list[Entity]:
@@ -293,11 +354,11 @@ async def _find_schema_entities(
     2) Only when allow_reference_match=True and no entity match was found, try
        exact reference matching by title/permalink (explicit schema references)
     """
-    query = entity_repository.select().where(Entity.entity_type == "schema")
+    query = entity_repository.select().where(Entity.note_type == "schema")
     result = await entity_repository.execute_query(query)
     entities = list(result.scalars().all())
 
-    normalized_target = generate_permalink(target_entity_type)
+    normalized_target = generate_permalink(target_note_type)
 
     entity_matches = [
         e

src/basic_memory/api/v2/routers/search_router.py

@@ -4,14 +4,17 @@ This router uses external_id UUIDs for stable, API-friendly routing.
 V1 uses string-based project names which are less efficient and less stable.
 """
 
+import asyncio
+
 from fastapi import APIRouter, HTTPException, Path
 
+import logfire
 from basic_memory.api.v2.utils import to_search_results
 from basic_memory.repository.semantic_errors import (
     SemanticDependenciesMissingError,
     SemanticSearchDisabledError,
 )
-from basic_memory.schemas.search import SearchQuery, SearchResponse
+from basic_memory.schemas.search import SearchQuery, SearchResponse, SearchRetrievalMode
 from basic_memory.deps import (
     SearchServiceV2ExternalDep,
     EntityServiceV2ExternalDep,
@@ -47,22 +50,87 @@ async def search(
     Returns:
         SearchResponse with paginated search results
     """
-    limit = page_size
-    offset = (page - 1) * page_size
-    try:
-        results = await search_service.search(query, limit=limit, offset=offset)
-    except SemanticSearchDisabledError as exc:
-        raise HTTPException(status_code=400, detail=str(exc)) from exc
-    except SemanticDependenciesMissingError as exc:
-        raise HTTPException(status_code=400, detail=str(exc)) from exc
-    except ValueError as exc:
-        raise HTTPException(status_code=400, detail=str(exc)) from exc
-    search_results = await to_search_results(entity_service, results)
-    return SearchResponse(
-        results=search_results,
-        current_page=page,
+    with logfire.span(
+        "api.request.search",
+        entrypoint="api",
+        domain="search",
+        action="search",
+        page=page,
         page_size=page_size,
-    )
+        retrieval_mode=query.retrieval_mode.value,
+        has_query=bool(
+            (query.text and query.text.strip())
+            or query.title
+            or query.permalink
+            or query.permalink_match
+        ),
+        has_filters=bool(query.note_types or query.entity_types or query.metadata_filters),
+    ):
+        offset = (page - 1) * page_size
+        exact_count_available = query.retrieval_mode == SearchRetrievalMode.FTS
+        try:
+            with logfire.span(
+                "api.search.search.execute_query",
+                domain="search",
+                action="search",
+                phase="execute_query",
+                page=page,
+                page_size=page_size,
+            ):
+                if exact_count_available:
+                    results, total = await asyncio.gather(
+                        search_service.search(query, limit=page_size, offset=offset),
+                        search_service.count(query),
+                    )
+                else:
+                    results = await search_service.search(query, limit=page_size + 1, offset=offset)
+                    total = 0
+        except SemanticSearchDisabledError as exc:
+            raise HTTPException(status_code=400, detail=str(exc)) from exc
+        except SemanticDependenciesMissingError as exc:
+            raise HTTPException(status_code=400, detail=str(exc)) from exc
+        except ValueError as exc:
+            raise HTTPException(status_code=400, detail=str(exc)) from exc
+
+        with logfire.span(
+            "api.search.search.paginate_results",
+            domain="search",
+            action="search",
+            phase="paginate_results",
+            result_count=len(results),
+        ):
+            if exact_count_available:
+                has_more = offset + len(results) < total
+            else:
+                # Trigger: semantic modes would need another vector/hybrid retrieval to count.
+                # Why: search requests should not pay for a second semantic pass.
+                # Outcome: preserve probe pagination for semantic search and leave total at 0.
+                has_more = len(results) > page_size
+                if has_more:
+                    results = results[:page_size]
+
+        with logfire.span(
+            "api.search.search.hydrate_results",
+            domain="search",
+            action="search",
+            phase="hydrate_results",
+            result_count=len(results),
+        ):
+            search_results = await to_search_results(entity_service, results)
+        with logfire.span(
+            "api.search.search.build_response",
+            domain="search",
+            action="search",
+            phase="build_response",
+            result_count=len(search_results),
+        ):
+            return SearchResponse(
+                results=search_results,
+                current_page=page,
+                page_size=page_size,
+                total=total,
+                has_more=has_more,
+            )
 
 
 @router.post("/search/reindex")

src/basic_memory/api/v2/utils.py

@@ -1,6 +1,6 @@
-from typing import Optional, List
+from typing import Any, Protocol, Optional, List, Sequence
 
-from basic_memory.repository import EntityRepository
+import logfire
 from basic_memory.repository.search_repository import SearchIndexRow
 from basic_memory.schemas.memory import (
     EntitySummary,
@@ -11,180 +11,266 @@ from basic_memory.schemas.memory import (
     ContextResult,
 )
 from basic_memory.schemas.search import SearchItemType, SearchResult
-from basic_memory.services import EntityService
 from basic_memory.services.context_service import (
     ContextResultRow,
     ContextResult as ServiceContextResult,
 )
 
 
+class EntityBatchLookup(Protocol):
+    async def find_by_ids(self, ids: List[int]) -> Sequence[Any]: ...
+
+
+class EntityServiceBatchLookup(Protocol):
+    async def get_entities_by_id(self, ids: List[int]) -> Sequence[Any]: ...
+
+
+def _required_str(value: str | None, field_name: str) -> str:
+    """Return a required search field or fail before producing invalid response data."""
+    if value is None:
+        raise ValueError(f"Search result is missing required field: {field_name}")
+    return value
+
+
+def _search_item_type(value: str | SearchItemType) -> SearchItemType:
+    """Normalize repository row type strings into the public search enum."""
+    return value if isinstance(value, SearchItemType) else SearchItemType(value)
+
+
 async def to_graph_context(
     context_result: ServiceContextResult,
-    entity_repository: EntityRepository,
+    entity_repository: EntityBatchLookup,
     page: Optional[int] = None,
     page_size: Optional[int] = None,
-):
-    # First pass: collect all entity IDs needed for external_id lookup
-    # This includes: entity primary results, observation parent entities, relation from/to entities
-    entity_ids_needed: set[int] = set()
-    for context_item in context_result.results:
-        for item in (
-            [context_item.primary_result] + context_item.observations + context_item.related_results
-        ):
-            if item.type == SearchItemType.ENTITY:
-                # Entity's own ID for its external_id
-                entity_ids_needed.add(item.id)
-            elif item.type == SearchItemType.OBSERVATION:
-                # Parent entity ID for entity_external_id
-                if item.entity_id:  # pyright: ignore
-                    entity_ids_needed.add(item.entity_id)  # pyright: ignore
-            elif item.type == SearchItemType.RELATION:
-                # Source and target entity IDs for external_ids
-                if item.from_id:  # pyright: ignore
-                    entity_ids_needed.add(item.from_id)  # pyright: ignore
-                if item.to_id:
-                    entity_ids_needed.add(item.to_id)
-
-    # Batch fetch all entities at once - get both title and external_id
-    entity_title_lookup: dict[int, str] = {}
-    entity_external_id_lookup: dict[int, str] = {}
-    if entity_ids_needed:
-        entities = await entity_repository.find_by_ids(list(entity_ids_needed))
-        for e in entities:
-            entity_title_lookup[e.id] = e.title
-            entity_external_id_lookup[e.id] = e.external_id
-
-    # Helper function to convert items to summaries
-    def to_summary(item: SearchIndexRow | ContextResultRow):
-        match item.type:
-            case SearchItemType.ENTITY:
-                return EntitySummary(
-                    external_id=entity_external_id_lookup.get(item.id, ""),
-                    entity_id=item.id,
-                    title=item.title,  # pyright: ignore
-                    permalink=item.permalink,
-                    content=item.content,
-                    file_path=item.file_path,
-                    created_at=item.created_at,
-                )
-            case SearchItemType.OBSERVATION:
-                entity_ext_id = None
-                if item.entity_id:  # pyright: ignore
-                    entity_ext_id = entity_external_id_lookup.get(item.entity_id)  # pyright: ignore
-                return ObservationSummary(
-                    observation_id=item.id,
-                    entity_id=item.entity_id,  # pyright: ignore
-                    entity_external_id=entity_ext_id,
-                    title=entity_title_lookup.get(item.entity_id),  # pyright: ignore
-                    file_path=item.file_path,
-                    category=item.category,  # pyright: ignore
-                    content=item.content,  # pyright: ignore
-                    permalink=item.permalink,  # pyright: ignore
-                    created_at=item.created_at,
-                )
-            case SearchItemType.RELATION:
-                from_title = entity_title_lookup.get(item.from_id) if item.from_id else None  # pyright: ignore
-                to_title = entity_title_lookup.get(item.to_id) if item.to_id else None
-                from_ext_id = entity_external_id_lookup.get(item.from_id) if item.from_id else None  # pyright: ignore
-                to_ext_id = entity_external_id_lookup.get(item.to_id) if item.to_id else None
-                return RelationSummary(
-                    relation_id=item.id,
-                    entity_id=item.entity_id,  # pyright: ignore
-                    title=item.title,  # pyright: ignore
-                    file_path=item.file_path,
-                    permalink=item.permalink,  # pyright: ignore
-                    relation_type=item.relation_type,  # pyright: ignore
-                    from_entity=from_title,
-                    from_entity_id=item.from_id,  # pyright: ignore
-                    from_entity_external_id=from_ext_id,
-                    to_entity=to_title,
-                    to_entity_id=item.to_id,
-                    to_entity_external_id=to_ext_id,
-                    created_at=item.created_at,
-                )
-            case _:  # pragma: no cover
-                raise ValueError(f"Unexpected type: {item.type}")
-
-    # Process the hierarchical results
-    hierarchical_results = []
-    for context_item in context_result.results:
-        # Process primary result
-        primary_result = to_summary(context_item.primary_result)
-
-        # Process observations (always ObservationSummary, validated by context_service)
-        observations = [to_summary(obs) for obs in context_item.observations]
-
-        # Process related results
-        related = [to_summary(rel) for rel in context_item.related_results]
-
-        # Add to hierarchical results
-        hierarchical_results.append(
-            ContextResult(
-                primary_result=primary_result,
-                observations=observations,  # pyright: ignore[reportArgumentType]
-                related_results=related,
-            )
-        )
-
-    # Create schema metadata from service metadata
-    metadata = MemoryMetadata(
-        uri=context_result.metadata.uri,
-        types=context_result.metadata.types,
-        depth=context_result.metadata.depth,
-        timeframe=context_result.metadata.timeframe,
-        generated_at=context_result.metadata.generated_at,
-        primary_count=context_result.metadata.primary_count,
-        related_count=context_result.metadata.related_count,
-        total_results=context_result.metadata.primary_count + context_result.metadata.related_count,
-        total_relations=context_result.metadata.total_relations,
-        total_observations=context_result.metadata.total_observations,
-    )
-
-    # Return new GraphContext with just hierarchical results
-    return GraphContext(
-        results=hierarchical_results,
-        metadata=metadata,
+) -> GraphContext:
+    with logfire.span(
+        "memory.hydrate_context",
+        domain="memory",
+        action="build_context",
+        phase="hydrate_context",
         page=page,
         page_size=page_size,
-    )
+        result_count=len(context_result.results),
+    ):
+        # First pass: collect all entity IDs needed for external_id lookup
+        # This includes: entity primary results, observation parent entities, relation from/to entities
+        entity_ids_needed: set[int] = set()
+        for context_item in context_result.results:
+            for item in (
+                [context_item.primary_result]
+                + context_item.observations
+                + context_item.related_results
+            ):
+                item_type = _search_item_type(item.type)
+                if item_type == SearchItemType.ENTITY:
+                    # Entity's own ID for its external_id
+                    entity_ids_needed.add(item.id)
+                elif item_type == SearchItemType.OBSERVATION:
+                    # Parent entity ID for entity_external_id
+                    if item.entity_id:
+                        entity_ids_needed.add(item.entity_id)
+                elif item_type == SearchItemType.RELATION:
+                    # Source and target entity IDs for external_ids
+                    if item.from_id:
+                        entity_ids_needed.add(item.from_id)
+                    if item.to_id:
+                        entity_ids_needed.add(item.to_id)
 
+        # Batch fetch all entities at once - get both title and external_id
+        entity_title_lookup: dict[int, str] = {}
+        entity_external_id_lookup: dict[int, str] = {}
+        if entity_ids_needed:
+            with logfire.span(
+                "memory.hydrate_context.lookup_entities",
+                domain="memory",
+                action="build_context",
+                phase="lookup_entities",
+                result_count=len(entity_ids_needed),
+            ):
+                entities = await entity_repository.find_by_ids(list(entity_ids_needed))
+            for e in entities:
+                entity_title_lookup[e.id] = e.title
+                entity_external_id_lookup[e.id] = e.external_id
 
-async def to_search_results(entity_service: EntityService, results: List[SearchIndexRow]):
-    search_results = []
-    for r in results:
-        entities = await entity_service.get_entities_by_id([r.entity_id, r.from_id, r.to_id])  # pyright: ignore
+        # Helper function to convert items to summaries
+        def to_summary(
+            item: SearchIndexRow | ContextResultRow,
+        ) -> EntitySummary | ObservationSummary | RelationSummary:
+            item_type = _search_item_type(item.type)
+            match item_type:
+                case SearchItemType.ENTITY:
+                    return EntitySummary(
+                        external_id=entity_external_id_lookup.get(item.id, ""),
+                        entity_id=item.id,
+                        title=_required_str(item.title, "title"),
+                        permalink=item.permalink,
+                        content=item.content,
+                        file_path=_required_str(item.file_path, "file_path"),
+                        created_at=item.created_at,
+                    )
+                case SearchItemType.OBSERVATION:
+                    entity_ext_id = None
+                    entity_title = None
+                    if item.entity_id:
+                        entity_ext_id = entity_external_id_lookup.get(item.entity_id)
+                        entity_title = entity_title_lookup.get(item.entity_id)
+                    return ObservationSummary(
+                        observation_id=item.id,
+                        entity_id=item.entity_id,
+                        entity_external_id=entity_ext_id,
+                        title=entity_title,
+                        file_path=_required_str(item.file_path, "file_path"),
+                        category=_required_str(item.category, "category"),
+                        content=_required_str(item.content, "content"),
+                        permalink=_required_str(item.permalink, "permalink"),
+                        created_at=item.created_at,
+                    )
+                case SearchItemType.RELATION:
+                    from_title = entity_title_lookup.get(item.from_id) if item.from_id else None
+                    to_title = entity_title_lookup.get(item.to_id) if item.to_id else None
+                    from_ext_id = (
+                        entity_external_id_lookup.get(item.from_id) if item.from_id else None
+                    )
+                    to_ext_id = entity_external_id_lookup.get(item.to_id) if item.to_id else None
+                    return RelationSummary(
+                        relation_id=item.id,
+                        entity_id=item.entity_id,
+                        title=_required_str(item.title, "title"),
+                        file_path=_required_str(item.file_path, "file_path"),
+                        permalink=_required_str(item.permalink, "permalink"),
+                        relation_type=_required_str(item.relation_type, "relation_type"),
+                        from_entity=from_title,
+                        from_entity_id=item.from_id,
+                        from_entity_external_id=from_ext_id,
+                        to_entity=to_title,
+                        to_entity_id=item.to_id,
+                        to_entity_external_id=to_ext_id,
+                        created_at=item.created_at,
+                    )
 
-        # Determine which IDs to set based on type
-        entity_id = None
-        observation_id = None
-        relation_id = None
+        with logfire.span(
+            "memory.hydrate_context.shape_results",
+            domain="memory",
+            action="build_context",
+            phase="shape_results",
+            result_count=len(context_result.results),
+        ):
+            hierarchical_results = []
+            for context_item in context_result.results:
+                primary_result = to_summary(context_item.primary_result)
+                observations = [
+                    summary
+                    for summary in (to_summary(obs) for obs in context_item.observations)
+                    if isinstance(summary, ObservationSummary)
+                ]
+                related = [to_summary(rel) for rel in context_item.related_results]
+                hierarchical_results.append(
+                    ContextResult(
+                        primary_result=primary_result,
+                        observations=observations,
+                        related_results=related,
+                    )
+                )
 
-        if r.type == SearchItemType.ENTITY:
-            entity_id = r.id
-        elif r.type == SearchItemType.OBSERVATION:
-            observation_id = r.id
-            entity_id = r.entity_id  # Parent entity
-        elif r.type == SearchItemType.RELATION:
-            relation_id = r.id
-            entity_id = r.entity_id  # Parent entity
-
-        search_results.append(
-            SearchResult(
-                title=r.title,  # pyright: ignore
-                type=r.type,  # pyright: ignore
-                permalink=r.permalink,
-                score=r.score,  # pyright: ignore
-                entity=entities[0].permalink if entities else None,
-                content=r.content,
-                file_path=r.file_path,
-                metadata=r.metadata,
-                entity_id=entity_id,
-                observation_id=observation_id,
-                relation_id=relation_id,
-                category=r.category,
-                from_entity=entities[0].permalink if entities else None,
-                to_entity=entities[1].permalink if len(entities) > 1 else None,
-                relation_type=r.relation_type,
-            )
+        metadata = MemoryMetadata(
+            uri=context_result.metadata.uri,
+            types=context_result.metadata.types,
+            depth=context_result.metadata.depth,
+            timeframe=context_result.metadata.timeframe,
+            generated_at=context_result.metadata.generated_at,
+            primary_count=context_result.metadata.primary_count,
+            related_count=context_result.metadata.related_count,
+            total_results=context_result.metadata.primary_count
+            + context_result.metadata.related_count,
+            total_relations=context_result.metadata.total_relations,
+            total_observations=context_result.metadata.total_observations,
         )
-    return search_results
+
+        return GraphContext(
+            results=hierarchical_results,
+            metadata=metadata,
+            page=page,
+            page_size=page_size,
+            has_more=context_result.metadata.has_more,
+        )
+
+
+async def to_search_results(
+    entity_service: EntityServiceBatchLookup, results: List[SearchIndexRow]
+) -> list[SearchResult]:
+    with logfire.span(
+        "search.hydrate_results",
+        domain="search",
+        action="search",
+        phase="hydrate_results",
+        result_count=len(results),
+    ):
+        # Collect all unique entity IDs across all results in a single pass
+        # This avoids N+1 queries — one batch fetch instead of one per result
+        all_entity_ids: set[int] = set()
+        for result in results:
+            for eid in (result.entity_id, result.from_id, result.to_id):
+                if eid is not None:
+                    all_entity_ids.add(eid)
+
+        # Single batch fetch for all entities
+        entities_by_id: dict[int, Any] = {}
+        with logfire.span(
+            "search.hydrate_results.fetch_entities",
+            domain="search",
+            action="search",
+            phase="fetch_entities",
+            result_count=len(all_entity_ids),
+        ):
+            if all_entity_ids:
+                entities = await entity_service.get_entities_by_id(list(all_entity_ids))
+                entities_by_id = {e.id: e for e in entities}
+
+        search_results = []
+        with logfire.span(
+            "search.hydrate_results.shape_results",
+            domain="search",
+            action="search",
+            phase="shape_results",
+            result_count=len(results),
+        ):
+            for result in results:
+                entity_id = None
+                observation_id = None
+                relation_id = None
+
+                if result.type == SearchItemType.ENTITY:
+                    entity_id = result.id
+                elif result.type == SearchItemType.OBSERVATION:
+                    observation_id = result.id
+                    entity_id = result.entity_id
+                elif result.type == SearchItemType.RELATION:
+                    relation_id = result.id
+                    entity_id = result.entity_id
+
+                # Look up entities by their specific IDs
+                parent_entity = entities_by_id.get(result.entity_id) if result.entity_id else None
+                from_entity = entities_by_id.get(result.from_id) if result.from_id else None
+                to_entity = entities_by_id.get(result.to_id) if result.to_id else None
+
+                search_results.append(
+                    SearchResult(
+                        title=_required_str(result.title, "title"),
+                        type=_search_item_type(result.type),
+                        permalink=result.permalink,
+                        score=result.score if result.score is not None else 0.0,
+                        entity=parent_entity.permalink if parent_entity else None,
+                        content=result.content,
+                        matched_chunk=result.matched_chunk_text,
+                        file_path=_required_str(result.file_path, "file_path"),
+                        metadata=result.metadata,
+                        entity_id=entity_id,
+                        observation_id=observation_id,
+                        relation_id=relation_id,
+                        category=result.category,
+                        from_entity=from_entity.permalink if from_entity else None,
+                        to_entity=to_entity.permalink if to_entity else None,
+                        relation_type=result.relation_type,
+                    )
+                )
+        return search_results

src/basic_memory/cli/analytics.py

@@ -0,0 +1,114 @@
+"""Lightweight CLI analytics via Umami event collector.
+
+Sends anonymous, non-blocking usage events to help understand how the
+CLI-to-cloud conversion funnel performs. No PII, no fingerprinting,
+no cookies. Respects the same opt-out mechanisms as promo messaging.
+
+Events are fire-and-forget — analytics never blocks or breaks the CLI.
+
+Defaults point to the Basic Memory Umami Cloud instance. Override via:
+    BASIC_MEMORY_UMAMI_HOST     — Custom Umami instance URL
+    BASIC_MEMORY_UMAMI_SITE_ID  — Custom Website ID
+Opt out entirely with BASIC_MEMORY_NO_PROMOS=1.
+"""
+
+import json
+import os
+import threading
+import urllib.request
+from typing import Optional
+
+import basic_memory
+
+
+# ---------------------------------------------------------------------------
+# Configuration — defaults baked in, overridable via environment
+# ---------------------------------------------------------------------------
+
+_DEFAULT_UMAMI_HOST = "https://api-gateway.umami.dev"
+_DEFAULT_UMAMI_SITE_ID = "f6479898-ebaf-4e60-bce2-6dc60a3f6c5c"
+
+
+def _umami_host() -> Optional[str]:
+    return os.getenv("BASIC_MEMORY_UMAMI_HOST", "").strip() or _DEFAULT_UMAMI_HOST
+
+
+def _umami_site_id() -> Optional[str]:
+    return os.getenv("BASIC_MEMORY_UMAMI_SITE_ID", "").strip() or _DEFAULT_UMAMI_SITE_ID
+
+
+def _analytics_disabled() -> bool:
+    """True when analytics should not fire."""
+    value = os.getenv("BASIC_MEMORY_NO_PROMOS", "").strip().lower()
+    return value in {"1", "true", "yes"}
+
+
+def _is_configured() -> bool:
+    """True when both host and site ID are available."""
+    return _umami_host() is not None and _umami_site_id() is not None
+
+
+# ---------------------------------------------------------------------------
+# Public API
+# ---------------------------------------------------------------------------
+
+# Well-known event names for the promo/cloud funnel
+EVENT_PROMO_SHOWN = "cli-promo-shown"
+EVENT_PROMO_OPTED_OUT = "cli-promo-opted-out"
+EVENT_CLOUD_LOGIN_STARTED = "cli-cloud-login-started"
+EVENT_CLOUD_LOGIN_SUCCESS = "cli-cloud-login-success"
+EVENT_CLOUD_LOGIN_SUB_REQUIRED = "cli-cloud-login-sub-required"
+
+
+def track(event_name: str, data: Optional[dict] = None) -> None:
+    """Send an analytics event to Umami. Non-blocking, silent on failure.
+
+    Parameters
+    ----------
+    event_name:
+        Short kebab-case name (e.g. "cli-promo-shown").
+    data:
+        Optional dict of event properties (all values should be strings/numbers).
+    """
+    if _analytics_disabled() or not _is_configured():
+        return
+
+    host = _umami_host()
+    site_id = _umami_site_id()
+
+    # Umami v2 /api/send requires "type" at top level alongside "payload"
+    payload = {
+        "type": "event",
+        "payload": {
+            "hostname": "cli.basicmemory.com",
+            "language": "en",
+            "url": f"/cli/{event_name}",
+            "website": site_id,
+            "name": event_name,
+            "data": {
+                "version": basic_memory.__version__,
+                **(data or {}),
+            },
+        },
+    }
+
+    def _send():
+        try:
+            req = urllib.request.Request(
+                f"{host}/api/send",
+                data=json.dumps(payload).encode("utf-8"),
+                headers={
+                    "Content-Type": "application/json",
+                    # Umami's bot detection rejects non-browser User-Agents
+                    "User-Agent": "Mozilla/5.0 (compatible; BasicMemoryCLI/"
+                    f"{basic_memory.__version__})",
+                },
+            )
+            urllib.request.urlopen(req, timeout=3)
+        except Exception:
+            pass  # Never break the CLI for analytics
+
+    # Non-daemon so the process waits for the request to complete.
+    # The 3s urllib timeout caps the worst-case exit delay.
+    t = threading.Thread(target=_send)
+    t.start()

src/basic_memory/cli/app.py

@@ -8,9 +8,11 @@ from typing import Optional  # noqa: E402
 
 import typer  # noqa: E402
 
+from basic_memory.cli.auto_update import maybe_run_periodic_auto_update  # noqa: E402
 from basic_memory.cli.container import CliContainer, set_container  # noqa: E402
 from basic_memory.cli.promo import maybe_show_cloud_promo, maybe_show_init_line  # noqa: E402
 from basic_memory.config import init_cli_logging  # noqa: E402
+import logfire  # noqa: E402
 
 
 def version_callback(value: bool) -> None:
@@ -41,6 +43,14 @@ def app_callback(
 
     # Initialize logging for CLI (file only, no stdout)
     init_cli_logging()
+    command_name = ctx.invoked_subcommand or "root"
+    ctx.with_resource(
+        logfire.span(
+            f"cli.command.{command_name}",
+            entrypoint="cli",
+            command_name=command_name,
+        )
+    )
 
     # --- Composition Root ---
     # Create container and read config (single point of config access)
@@ -52,10 +62,14 @@ def app_callback(
     # Outcome: one-time plain line printed before the subcommand runs.
     maybe_show_init_line(ctx.invoked_subcommand)
 
-    # Trigger: register promo as a post-command callback.
-    # Why: promo output should appear after the command's own output, not before.
-    # Outcome: promo panel renders below the command results (status tree, table, etc.).
-    ctx.call_on_close(lambda: maybe_show_cloud_promo(ctx.invoked_subcommand))
+    # Trigger: register post-command messaging callbacks.
+    # Why: informational/promo/update output belongs below command results.
+    # Outcome: command output remains primary, with optional follow-up notices afterwards.
+    def _post_command_messages() -> None:
+        maybe_show_cloud_promo(ctx.invoked_subcommand)
+        maybe_run_periodic_auto_update(ctx.invoked_subcommand)
+
+    ctx.call_on_close(_post_command_messages)
 
     # Run initialization for commands that don't use the API
     # Skip for 'mcp' command - it has its own lifespan that handles initialization
@@ -70,6 +84,7 @@ def app_callback(
         "tool",
         "reset",
         "reindex",
+        "update",
         "watch",
     }
     if (

src/basic_memory/cli/auto_update.py

@@ -0,0 +1,389 @@
+"""Automatic update checks and upgrades for the Basic Memory CLI."""
+
+from __future__ import annotations
+
+import json
+import subprocess
+import sys
+import urllib.error
+import urllib.request
+from dataclasses import dataclass
+from datetime import datetime, timedelta
+from enum import Enum
+
+from loguru import logger
+from packaging.version import InvalidVersion, Version
+from rich.console import Console
+
+import basic_memory
+from basic_memory.config import ConfigManager
+
+PACKAGE_NAME = "basic-memory"
+PYPI_JSON_URL = "https://pypi.org/pypi/basic-memory/json"
+
+PYPI_TIMEOUT_SECONDS = 5
+BREW_OUTDATED_TIMEOUT_SECONDS = 60
+UV_UPGRADE_TIMEOUT_SECONDS = 180
+BREW_UPGRADE_TIMEOUT_SECONDS = 600
+
+
+class InstallSource(str, Enum):
+    """How the running CLI appears to have been installed."""
+
+    HOMEBREW = "homebrew"
+    UV_TOOL = "uv_tool"
+    UVX = "uvx"
+    UNKNOWN = "unknown"
+
+
+class AutoUpdateStatus(str, Enum):
+    """Result classification for update checks and installs."""
+
+    SKIPPED = "skipped"
+    UP_TO_DATE = "up_to_date"
+    UPDATE_AVAILABLE = "update_available"
+    UPDATED = "updated"
+    FAILED = "failed"
+
+
+@dataclass(frozen=True)
+class AutoUpdateResult:
+    """Structured result for update checks/install attempts."""
+
+    status: AutoUpdateStatus
+    source: InstallSource
+    checked: bool
+    update_available: bool
+    updated: bool
+    latest_version: str | None = None
+    message: str | None = None
+    error: str | None = None
+    restart_recommended: bool = False
+
+
+def detect_install_source(executable: str | None = None) -> InstallSource:
+    """Infer installation source from the active interpreter path."""
+    active_executable = executable or sys.executable
+    normalized = active_executable.lower().replace("\\", "/")
+
+    if "cellar/basic-memory" in normalized:
+        return InstallSource.HOMEBREW
+    if "uv/tools/basic-memory" in normalized:
+        return InstallSource.UV_TOOL
+    if "/uv/archive-" in normalized:
+        return InstallSource.UVX
+    return InstallSource.UNKNOWN
+
+
+def _is_interactive_session() -> bool:
+    """Return whether stdin/stdout are interactive terminals."""
+    try:
+        return sys.stdin.isatty() and sys.stdout.isatty()
+    except ValueError:
+        # Trigger: stdin/stdout may be closed during transport teardown.
+        # Why: isatty() raises ValueError on closed descriptors.
+        # Outcome: treat as non-interactive and suppress periodic output.
+        return False
+
+
+def _run_subprocess(
+    command: list[str],
+    *,
+    timeout_seconds: int,
+    silent: bool,
+    capture_output: bool,
+) -> subprocess.CompletedProcess[str]:
+    """Run a subprocess with explicit stdio behavior for protocol safety."""
+    # Trigger: silent operation (MCP/background) with no need for subprocess output.
+    # Why: prevent protocol/terminal pollution from child process output.
+    # Outcome: stdout/stderr are discarded unless explicit capture is requested.
+    use_devnull = silent and not capture_output
+    stdout_target = subprocess.DEVNULL if use_devnull else subprocess.PIPE
+    stderr_target = subprocess.DEVNULL if use_devnull else subprocess.PIPE
+
+    return subprocess.run(
+        command,
+        stdin=subprocess.DEVNULL,
+        stdout=stdout_target,
+        stderr=stderr_target,
+        text=True,
+        timeout=timeout_seconds,
+        check=False,
+    )
+
+
+def _version_from_pypi() -> str:
+    """Fetch the latest published package version from PyPI."""
+    request = urllib.request.Request(
+        PYPI_JSON_URL,
+        headers={"User-Agent": f"basic-memory-cli/{basic_memory.__version__}"},
+    )
+    with urllib.request.urlopen(request, timeout=PYPI_TIMEOUT_SECONDS) as response:
+        payload = json.loads(response.read().decode("utf-8"))
+    latest = payload.get("info", {}).get("version")
+    if not latest:
+        raise RuntimeError("PyPI JSON response did not include info.version")
+    return str(latest)
+
+
+def _check_homebrew_update_available(silent: bool) -> tuple[bool, str | None]:
+    """Check whether Homebrew reports an outdated basic-memory formula."""
+    result = _run_subprocess(
+        ["brew", "outdated", "--quiet", PACKAGE_NAME],
+        timeout_seconds=BREW_OUTDATED_TIMEOUT_SECONDS,
+        silent=silent,
+        capture_output=True,
+    )
+    # Trigger: brew outdated exits 1 when the formula IS outdated (with name on stdout).
+    # Why: non-zero exit here means "outdated", not "error".
+    # Outcome: check stdout for the package name to determine outdated status.
+    stdout = (result.stdout or "").strip()
+    is_outdated = PACKAGE_NAME in stdout
+    return is_outdated, None
+
+
+def _check_pypi_update_available() -> tuple[bool, str]:
+    """Compare installed package version with PyPI latest version."""
+    latest = _version_from_pypi()
+    try:
+        current_version = Version(basic_memory.__version__)
+        latest_version = Version(latest)
+    except InvalidVersion as exc:
+        raise RuntimeError(
+            f"Could not compare versions (current={basic_memory.__version__}, latest={latest})"
+        ) from exc
+
+    return latest_version > current_version, latest
+
+
+def _manual_update_hint(source: InstallSource) -> str:
+    """Return manager-appropriate manual update instructions."""
+    if source == InstallSource.UV_TOOL:
+        return "Run `uv tool upgrade basic-memory`."
+    if source == InstallSource.HOMEBREW:
+        return "Run `brew upgrade basic-memory`."
+    return (
+        "Automatic install is not supported for this environment. "
+        "Update with your package manager (for pip: `python3 -m pip install -U basic-memory`)."
+    )
+
+
+def _save_last_checked_timestamp(config_manager: ConfigManager, checked_at: datetime) -> None:
+    """Persist the timestamp for the most recent attempted update check."""
+    config = config_manager.load_config()
+    config.auto_update_last_checked_at = checked_at
+    config_manager.save_config(config)
+
+
+def run_auto_update(
+    *,
+    force: bool = False,
+    check_only: bool = False,
+    silent: bool = False,
+    config_manager: ConfigManager | None = None,
+    now: datetime | None = None,
+    executable: str | None = None,
+) -> AutoUpdateResult:
+    """Run update check/install flow and return a structured result."""
+    manager = config_manager or ConfigManager()
+    config = manager.load_config()
+    source = detect_install_source(executable)
+    checked_at = now or datetime.now()
+
+    if source == InstallSource.UVX:
+        return AutoUpdateResult(
+            status=AutoUpdateStatus.SKIPPED,
+            source=source,
+            checked=False,
+            update_available=False,
+            updated=False,
+            message="uvx runtime detected; updates are managed by uvx cache resolution.",
+        )
+
+    if not force and not config.auto_update:
+        return AutoUpdateResult(
+            status=AutoUpdateStatus.SKIPPED,
+            source=source,
+            checked=False,
+            update_available=False,
+            updated=False,
+            message="Auto-update is disabled in config.",
+        )
+
+    if not force and config.auto_update_last_checked_at is not None:
+        try:
+            elapsed = checked_at - config.auto_update_last_checked_at
+        except TypeError:
+            # Trigger: mixed naive/aware datetimes from manual config edits.
+            # Why: datetime subtraction fails for mixed tz-awareness.
+            # Outcome: ignore the gate once and continue with a forced check path.
+            logger.warning("Auto-update interval gate skipped due to incompatible timestamp format")
+        else:
+            if elapsed < timedelta(seconds=config.update_check_interval):
+                return AutoUpdateResult(
+                    status=AutoUpdateStatus.SKIPPED,
+                    source=source,
+                    checked=False,
+                    update_available=False,
+                    updated=False,
+                    message="Update check interval has not elapsed.",
+                )
+
+    try:
+        # --- Availability check ---
+        latest_version: str | None = None
+        if source == InstallSource.HOMEBREW:
+            update_available, latest_version = _check_homebrew_update_available(silent=silent)
+        else:
+            update_available, latest_version = _check_pypi_update_available()
+
+        if not update_available:
+            return AutoUpdateResult(
+                status=AutoUpdateStatus.UP_TO_DATE,
+                source=source,
+                checked=True,
+                update_available=False,
+                updated=False,
+                latest_version=latest_version,
+                message=f"Basic Memory is up to date ({basic_memory.__version__}).",
+            )
+
+        if check_only:
+            return AutoUpdateResult(
+                status=AutoUpdateStatus.UPDATE_AVAILABLE,
+                source=source,
+                checked=True,
+                update_available=True,
+                updated=False,
+                latest_version=latest_version,
+                message=(
+                    f"Update available (latest: {latest_version or 'unknown'}). "
+                    f"{_manual_update_hint(source)}"
+                ),
+            )
+
+        if source == InstallSource.UNKNOWN:
+            return AutoUpdateResult(
+                status=AutoUpdateStatus.UPDATE_AVAILABLE,
+                source=source,
+                checked=True,
+                update_available=True,
+                updated=False,
+                latest_version=latest_version,
+                message=(
+                    f"Update available (latest: {latest_version or 'unknown'}). "
+                    f"{_manual_update_hint(source)}"
+                ),
+            )
+
+        # --- Automatic install ---
+        command = (
+            ["uv", "tool", "upgrade", PACKAGE_NAME]
+            if source == InstallSource.UV_TOOL
+            else ["brew", "upgrade", PACKAGE_NAME]
+        )
+        timeout = (
+            UV_UPGRADE_TIMEOUT_SECONDS
+            if source == InstallSource.UV_TOOL
+            else BREW_UPGRADE_TIMEOUT_SECONDS
+        )
+
+        install_result = _run_subprocess(
+            command,
+            timeout_seconds=timeout,
+            silent=silent,
+            capture_output=not silent,
+        )
+        if install_result.returncode != 0:
+            stderr = (install_result.stderr or "").strip() if install_result.stderr else ""
+            stdout = (install_result.stdout or "").strip() if install_result.stdout else ""
+            detail = stderr or stdout or "update command failed"
+            return AutoUpdateResult(
+                status=AutoUpdateStatus.FAILED,
+                source=source,
+                checked=True,
+                update_available=True,
+                updated=False,
+                latest_version=latest_version,
+                message="Automatic update failed.",
+                error=detail,
+            )
+
+        return AutoUpdateResult(
+            status=AutoUpdateStatus.UPDATED,
+            source=source,
+            checked=True,
+            update_available=True,
+            updated=True,
+            latest_version=latest_version,
+            message=(
+                "Basic Memory was updated successfully. "
+                "Restart running sessions to use the new version."
+            ),
+            restart_recommended=True,
+        )
+
+    except (
+        RuntimeError,
+        urllib.error.URLError,
+        ValueError,
+        TimeoutError,
+        subprocess.SubprocessError,
+        OSError,
+    ) as exc:
+        logger.warning(f"Auto-update check failed: {exc}")
+        return AutoUpdateResult(
+            status=AutoUpdateStatus.FAILED,
+            source=source,
+            checked=True,
+            update_available=False,
+            updated=False,
+            message="Automatic update check failed.",
+            error=str(exc),
+        )
+    finally:
+        # Trigger: we attempted a check path (including failures).
+        # Why: repeated failing checks on every command create noise and unnecessary network load.
+        # Outcome: next periodic check is gated by update_check_interval.
+        try:
+            _save_last_checked_timestamp(manager, checked_at)
+        except Exception as exc:  # pragma: no cover
+            logger.warning(f"Failed to persist auto-update timestamp: {exc}")
+
+
+def maybe_run_periodic_auto_update(
+    invoked_subcommand: str | None,
+    *,
+    config_manager: ConfigManager | None = None,
+    is_interactive: bool | None = None,
+    console: Console | None = None,
+) -> AutoUpdateResult | None:
+    """Run a periodic auto-update check for interactive CLI sessions."""
+    interactive = _is_interactive_session() if is_interactive is None else is_interactive
+    if not interactive:
+        return None
+    if invoked_subcommand in {None, "mcp", "update"}:
+        return None
+
+    result = run_auto_update(
+        force=False,
+        check_only=False,
+        silent=False,
+        config_manager=config_manager,
+    )
+
+    if result.status in {
+        AutoUpdateStatus.UPDATE_AVAILABLE,
+        AutoUpdateStatus.UPDATED,
+        AutoUpdateStatus.FAILED,
+    }:
+        out = console or Console()
+        if result.status == AutoUpdateStatus.UPDATED:
+            out.print(f"[green]{result.message}[/green]")
+        elif result.status == AutoUpdateStatus.FAILED:
+            error_detail = f" {result.error}" if result.error else ""
+            out.print(f"[yellow]{result.message}{error_detail}[/yellow]")
+        elif result.message:
+            out.print(f"[cyan]{result.message}[/cyan]")
+
+    return result

src/basic_memory/cli/commands/__init__.py

@@ -8,8 +8,7 @@ from . import (
     project,
     format,
     schema,
-    watch,
-    workspace,
+    update,
 )
 
 __all__ = [
@@ -25,6 +24,5 @@ __all__ = [
     "project",
     "format",
     "schema",
-    "watch",
-    "workspace",
+    "update",
 ]

src/basic_memory/cli/commands/cloud/__init__.py

@@ -6,11 +6,14 @@ from basic_memory.cli.app import cloud_app
 from basic_memory.cli.commands.cloud.core_commands import *  # noqa: F401,F403
 from basic_memory.cli.commands.cloud.api_client import get_authenticated_headers, get_cloud_config  # noqa: F401
 from basic_memory.cli.commands.cloud.upload_command import *  # noqa: F401,F403
+from basic_memory.cli.commands.cloud.project_sync import *  # noqa: F401,F403
 
 # Register snapshot sub-command group
 from basic_memory.cli.commands.cloud.snapshot import snapshot_app
+from basic_memory.cli.commands.cloud.workspace import workspace_app
 
 cloud_app.add_typer(snapshot_app, name="snapshot")
+cloud_app.add_typer(workspace_app, name="workspace")
 
 # Register restore command (directly on cloud_app via decorator)
 from basic_memory.cli.commands.cloud.restore import restore  # noqa: F401, E402

src/basic_memory/cli/commands/cloud/api_client.py

@@ -45,14 +45,26 @@ def get_cloud_config() -> tuple[str, str, str]:
 
 async def get_authenticated_headers(auth: CLIAuth | None = None) -> dict[str, str]:
     """
-    Get authentication headers with JWT token.
-    handles jwt refresh if needed.
+    Get authentication headers for cloud API requests.
+
+    Credential priority mirrors async_client._resolve_cloud_token():
+      1. API key (config.cloud_api_key) — fast, no refresh needed
+      2. OAuth token via CLIAuth — handles JWT refresh automatically
     """
+    # --- API key (preferred) ---
+    config_manager = ConfigManager()
+    api_key = config_manager.config.cloud_api_key
+    if api_key:
+        return {"Authorization": f"Bearer {api_key}"}
+
+    # --- OAuth fallback ---
     client_id, domain, _ = get_cloud_config()
     auth_obj = auth or CLIAuth(client_id=client_id, authkit_domain=domain)
     token = await auth_obj.get_valid_token()
     if not token:
-        console.print("[red]Not authenticated. Please run 'basic-memory cloud login' first.[/red]")
+        console.print(
+            "[red]Not authenticated. Run 'bm cloud set-key <key>' or 'bm cloud login' first.[/red]"
+        )
         raise typer.Exit(1)
 
     return {"Authorization": f"Bearer {token}"}
@@ -87,41 +99,39 @@ async def make_api_request(
             response = await client.request(method=method, url=url, headers=headers, json=json_data)
             response.raise_for_status()
             return response
+        except httpx.HTTPStatusError as e:
+            response = e.response
+
+            # Try to parse error detail from response
+            error_detail = None
+            try:
+                error_detail = response.json()
+            except Exception:
+                # If JSON parsing fails, we'll handle it as a generic error
+                pass
+
+            # Check for subscription_required error (403)
+            if response.status_code == 403 and isinstance(error_detail, dict):
+                # Handle both FastAPI HTTPException format (nested under "detail")
+                # and direct format
+                detail_obj = error_detail.get("detail", error_detail)
+                if (
+                    isinstance(detail_obj, dict)
+                    and detail_obj.get("error") == "subscription_required"
+                ):
+                    message = detail_obj.get("message", "Active subscription required")
+                    subscribe_url = detail_obj.get(
+                        "subscribe_url", "https://basicmemory.com/subscribe"
+                    )
+                    raise SubscriptionRequiredError(
+                        message=message, subscribe_url=subscribe_url
+                    ) from e
+
+            # Raise generic CloudAPIError with status code and detail
+            raise CloudAPIError(
+                f"API request failed: {e}",
+                status_code=response.status_code,
+                detail=error_detail if isinstance(error_detail, dict) else {},
+            ) from e
         except httpx.HTTPError as e:
-            # Check if this is a response error with response details
-            if hasattr(e, "response") and e.response is not None:  # pyright: ignore [reportAttributeAccessIssue]
-                response = e.response  # type: ignore
-
-                # Try to parse error detail from response
-                error_detail = None
-                try:
-                    error_detail = response.json()
-                except Exception:
-                    # If JSON parsing fails, we'll handle it as a generic error
-                    pass
-
-                # Check for subscription_required error (403)
-                if response.status_code == 403 and isinstance(error_detail, dict):
-                    # Handle both FastAPI HTTPException format (nested under "detail")
-                    # and direct format
-                    detail_obj = error_detail.get("detail", error_detail)
-                    if (
-                        isinstance(detail_obj, dict)
-                        and detail_obj.get("error") == "subscription_required"
-                    ):
-                        message = detail_obj.get("message", "Active subscription required")
-                        subscribe_url = detail_obj.get(
-                            "subscribe_url", "https://basicmemory.com/subscribe"
-                        )
-                        raise SubscriptionRequiredError(
-                            message=message, subscribe_url=subscribe_url
-                        ) from e
-
-                # Raise generic CloudAPIError with status code and detail
-                raise CloudAPIError(
-                    f"API request failed: {e}",
-                    status_code=response.status_code,
-                    detail=error_detail if isinstance(error_detail, dict) else {},
-                ) from e
-
             raise CloudAPIError(f"API request failed: {e}") from e

src/basic_memory/cli/commands/cloud/cloud_utils.py

@@ -2,10 +2,12 @@
 
 from basic_memory.cli.commands.cloud.api_client import make_api_request
 from basic_memory.config import ConfigManager
+from basic_memory.mcp.async_client import resolve_configured_workspace
 from basic_memory.schemas.cloud import (
     CloudProjectList,
     CloudProjectCreateRequest,
     CloudProjectCreateResponse,
+    ProjectVisibility,
 )
 from basic_memory.utils import generate_permalink
 
@@ -16,12 +18,33 @@ class CloudUtilsError(Exception):
     pass
 
 
+def _workspace_headers(
+    *,
+    project_name: str | None = None,
+    workspace: str | None = None,
+) -> dict[str, str]:
+    """Build optional workspace headers using the CLI config resolution chain."""
+    resolved_workspace = resolve_configured_workspace(
+        project_name=project_name,
+        workspace=workspace,
+    )
+    if resolved_workspace is None:
+        return {}
+    return {"X-Workspace-ID": resolved_workspace}
+
+
 async def fetch_cloud_projects(
     *,
+    project_name: str | None = None,
+    workspace: str | None = None,
     api_request=make_api_request,
 ) -> CloudProjectList:
     """Fetch list of projects from cloud API.
 
+    Args:
+        project_name: Optional project name for workspace resolution
+        workspace: Cloud workspace tenant_id to list projects from
+
     Returns:
         CloudProjectList with projects from cloud
     """
@@ -30,7 +53,11 @@ async def fetch_cloud_projects(
         config = config_manager.config
         host_url = config.cloud_host.rstrip("/")
 
-        response = await api_request(method="GET", url=f"{host_url}/proxy/v2/projects/")
+        response = await api_request(
+            method="GET",
+            url=f"{host_url}/proxy/v2/projects/",
+            headers=_workspace_headers(project_name=project_name, workspace=workspace),
+        )
 
         return CloudProjectList.model_validate(response.json())
     except Exception as e:
@@ -40,12 +67,16 @@ async def fetch_cloud_projects(
 async def create_cloud_project(
     project_name: str,
     *,
+    workspace: str | None = None,
+    visibility: ProjectVisibility = "workspace",
     api_request=make_api_request,
 ) -> CloudProjectCreateResponse:
     """Create a new project on cloud.
 
     Args:
         project_name: Name of project to create
+        workspace: Optional workspace override for tenant-scoped project creation
+        visibility: Visibility for the created cloud project
 
     Returns:
         CloudProjectCreateResponse with project details from API
@@ -62,12 +93,16 @@ async def create_cloud_project(
             name=project_name,
             path=project_path,
             set_default=False,
+            visibility=visibility,
         )
 
         response = await api_request(
             method="POST",
             url=f"{host_url}/proxy/v2/projects/",
-            headers={"Content-Type": "application/json"},
+            headers={
+                "Content-Type": "application/json",
+                **_workspace_headers(project_name=project_name, workspace=workspace),
+            },
             json_data=project_data.model_dump(),
         )
 
@@ -81,28 +116,38 @@ async def sync_project(project_name: str, force_full: bool = False) -> None:
 
     Args:
         project_name: Name of project to sync
-        force_full: If True, force a full scan bypassing watermark optimization
+        force_full: ignored, kept for backwards compatibility
     """
     try:
         from basic_memory.cli.commands.command_utils import run_sync
 
-        await run_sync(project=project_name, force_full=force_full)
+        await run_sync(project=project_name)
     except Exception as e:
         raise CloudUtilsError(f"Failed to sync project '{project_name}': {e}") from e
 
 
-async def project_exists(project_name: str, *, api_request=make_api_request) -> bool:
+async def project_exists(
+    project_name: str,
+    *,
+    workspace: str | None = None,
+    api_request=make_api_request,
+) -> bool:
     """Check if a project exists on cloud.
 
     Args:
         project_name: Name of project to check
+        workspace: Optional workspace override for tenant-scoped project lookup
 
     Returns:
         True if project exists, False otherwise
+
+    Raises:
+        CloudUtilsError: If the project list cannot be fetched from cloud
     """
-    try:
-        projects = await fetch_cloud_projects(api_request=api_request)
-        project_names = {p.name for p in projects.projects}
-        return project_name in project_names
-    except Exception:
-        return False
+    projects = await fetch_cloud_projects(
+        project_name=project_name,
+        workspace=workspace,
+        api_request=api_request,
+    )
+    project_names = {p.name for p in projects.projects}
+    return project_name in project_names

src/basic_memory/cli/commands/cloud/core_commands.py

@@ -6,6 +6,13 @@ from rich.console import Console
 from basic_memory.cli.app import cloud_app
 from basic_memory.cli.commands.command_utils import run_with_cleanup
 from basic_memory.cli.auth import CLIAuth
+from basic_memory.cli.analytics import (
+    track,
+    EVENT_CLOUD_LOGIN_STARTED,
+    EVENT_CLOUD_LOGIN_SUCCESS,
+    EVENT_CLOUD_LOGIN_SUB_REQUIRED,
+    EVENT_PROMO_OPTED_OUT,
+)
 from basic_memory.cli.promo import OSS_DISCOUNT_CODE
 from basic_memory.config import ConfigManager
 from basic_memory.cli.commands.cloud.api_client import (
@@ -33,6 +40,7 @@ def login():
     """Authenticate with WorkOS using OAuth Device Authorization flow."""
 
     async def _login():
+        track(EVENT_CLOUD_LOGIN_STARTED)
         client_id, domain, host_url = get_cloud_config()
         auth = CLIAuth(client_id=client_id, authkit_domain=domain)
 
@@ -46,10 +54,12 @@ def login():
             console.print("[dim]Verifying subscription access...[/dim]")
             await make_api_request("GET", f"{host_url.rstrip('/')}/proxy/health")
 
+            track(EVENT_CLOUD_LOGIN_SUCCESS)
             console.print("[green]Cloud authentication successful[/green]")
             console.print(f"[dim]Cloud host ready: {host_url}[/dim]")
 
         except SubscriptionRequiredError as e:
+            track(EVENT_CLOUD_LOGIN_SUB_REQUIRED)
             console.print("\n[red]Subscription Required[/red]\n")
             console.print(f"[yellow]{e.args[0]}[/yellow]\n")
             console.print(
@@ -66,22 +76,34 @@ def login():
 
 @cloud_app.command()
 def logout():
-    """Remove stored OAuth tokens."""
-    config = ConfigManager().config
+    """Remove stored OAuth tokens and clear cached workspace selection."""
+    config_manager = ConfigManager()
+    config = config_manager.config
     auth = CLIAuth(client_id=config.cloud_client_id, authkit_domain=config.cloud_domain)
     auth.logout()
+
+    # Trigger: ending a session must invalidate the cached workspace.
+    # Why: a follow-up `bm cloud login` (often as a different user, or returning
+    #      from an org workspace to personal) inherits the previous selection
+    #      and silently routes everything through the wrong tenant. See #755.
+    # Outcome: re-login starts from a clean slate; the user picks again via
+    #      `bm cloud workspace set-default` or per-project --workspace.
+    if config.default_workspace is not None:
+        config.default_workspace = None
+        config_manager.save_config(config)
+
     console.print("[dim]API key (if configured) remains available for cloud project routing.[/dim]")
 
 
 @cloud_app.command("status")
 def status() -> None:
-    """Check cloud authentication state and cloud instance health."""
+    """Check cloud authentication and connection status."""
     config_manager = ConfigManager()
     config = config_manager.load_config()
     auth = CLIAuth(client_id=config.cloud_client_id, authkit_domain=config.cloud_domain)
     tokens = auth.load_tokens()
 
-    console.print("[bold blue]Cloud Authentication Status[/bold blue]")
+    console.print("[bold blue]Cloud Status[/bold blue]")
     console.print(f"  Host: {config.cloud_host}")
     console.print(
         f"  API Key: {'[green]configured[/green]' if config.cloud_api_key else '[yellow]not set[/yellow]'}"
@@ -89,51 +111,33 @@ def status() -> None:
 
     oauth_status = "[yellow]not logged in[/yellow]"
     if tokens:
-        oauth_status = (
-            "[green]token valid[/green]"
-            if auth.is_token_valid(tokens)
-            else "[yellow]token expired[/yellow]"
-        )
+        if auth.is_token_valid(tokens):
+            oauth_status = "[green]token valid[/green]"
+        else:
+            oauth_status = "[yellow]token expired[/yellow]"
     console.print(f"  OAuth: {oauth_status}")
 
-    # Get cloud configuration
-    _, _, host_url = get_cloud_config()
-    host_url = host_url.rstrip("/")
-
     has_credentials = bool(config.cloud_api_key) or tokens is not None
     if not has_credentials:
         console.print(
-            "\n[dim]No cloud credentials found. Run: bm cloud login or bm cloud set-key <key>[/dim]"
+            "\n[dim]No cloud credentials found. Run: bm cloud login or bm cloud api-key save <key>[/dim]"
         )
         return
 
+    # Quick connection check — just verify we can reach the cloud
+    _, _, host_url = get_cloud_config()
+    host_url = host_url.rstrip("/")
+
     try:
-        console.print("\n[blue]Checking cloud instance health...[/blue]")
-
-        # Make API request to check health
-        response = run_with_cleanup(make_api_request(method="GET", url=f"{host_url}/proxy/health"))
-
-        health_data = response.json()
-
-        console.print("[green]Cloud instance is healthy[/green]")
-
-        # Display status details
-        if "status" in health_data:
-            console.print(f"  Status: {health_data['status']}")
-        if "version" in health_data:
-            console.print(f"  Version: {health_data['version']}")
-        if "timestamp" in health_data:
-            console.print(f"  Timestamp: {health_data['timestamp']}")
-
-        console.print("\n[dim]To sync projects, use: bm project bisync --name <project>[/dim]")
-
-    except CloudAPIError as e:
-        console.print(f"[yellow]Cloud health check failed: {e}[/yellow]")
+        run_with_cleanup(make_api_request(method="GET", url=f"{host_url}/proxy/health"))
+        console.print("\n[green]Cloud connected[/green]")
+    except CloudAPIError:
+        console.print("\n[yellow]Cloud not connected[/yellow]")
         console.print(
-            "[dim]Try re-authenticating with 'bm cloud login' or setting API key with 'bm cloud set-key'.[/dim]"
+            "[dim]Try re-authenticating with 'bm cloud login' or 'bm cloud api-key save'.[/dim]"
         )
-    except Exception as e:
-        console.print(f"[yellow]Unexpected health check error: {e}[/yellow]")
+    except Exception:
+        console.print("\n[yellow]Cloud not connected[/yellow]")
 
 
 @cloud_app.command("setup")
@@ -141,7 +145,7 @@ def setup() -> None:
     """Set up cloud sync by installing rclone and configuring credentials.
 
     After setup, use project commands for syncing:
-      bm project add <name> <path> --local-path ~/projects/<name>
+      bm project add <name> --cloud --local-path ~/projects/<name>
       bm project bisync --name <name> --resync  # First time
       bm project bisync --name <name>            # Subsequent syncs
     """
@@ -173,9 +177,9 @@ def setup() -> None:
         console.print("\n[bold green]Cloud setup completed successfully![/bold green]")
         console.print("\n[bold]Next steps:[/bold]")
         console.print("1. Add a project with local sync path:")
-        console.print("   bm project add research --local-path ~/Documents/research")
+        console.print("   bm project add research --cloud --local-path ~/Documents/research")
         console.print("\n   Or configure sync for an existing project:")
-        console.print("   bm project sync-setup research ~/Documents/research")
+        console.print("   bm cloud sync-setup research ~/Documents/research")
         console.print("\n2. Preview the initial sync (recommended):")
         console.print("   bm project bisync --name research --resync --dry-run")
         console.print("\n3. If all looks good, run the actual sync:")
@@ -205,20 +209,26 @@ def promo(enabled: bool = typer.Option(True, "--on/--off", help="Enable or disab
     if enabled:
         console.print("[green]Cloud promo messages enabled[/green]")
     else:
+        track(EVENT_PROMO_OPTED_OUT)
         console.print("[yellow]Cloud promo messages disabled[/yellow]")
 
 
-@cloud_app.command("set-key")
-def set_key(
+# --- API key management subcommand group ---
+
+api_key_app = typer.Typer(help="Manage cloud API keys")
+cloud_app.add_typer(api_key_app, name="api-key")
+
+
+@api_key_app.command("save")
+def api_key_save(
     api_key: str = typer.Argument(..., help="API key (bmc_ prefixed) for cloud access"),
 ) -> None:
-    """Save a cloud API key for per-project cloud routing.
+    """Save an existing API key to local config.
 
-    The API key is account-level and used by projects set to cloud mode.
-    Create a key in the web app or use 'bm cloud create-key'.
+    Use when you already have an API key (e.g., from the web app).
 
     Example:
-      bm cloud set-key bmc_abc123...
+      bm cloud api-key save bmc_abc123...
     """
     if not api_key.startswith("bmc_"):
         console.print("[red]Error: API key must start with 'bmc_'[/red]")
@@ -234,17 +244,16 @@ def set_key(
     console.print("[dim]Set a project to cloud mode: bm project set-cloud <name>[/dim]")
 
 
-@cloud_app.command("create-key")
-def create_key(
+@api_key_app.command("create")
+def api_key_create(
     name: str = typer.Argument(..., help="Human-readable name for the API key"),
 ) -> None:
-    """Create a new cloud API key and save it locally.
+    """Create a new API key via the cloud API and save it locally.
 
     Requires active OAuth session (run 'bm cloud login' first).
-    The key is created via the cloud API and saved to local config.
 
     Example:
-      bm cloud create-key "my-laptop"
+      bm cloud api-key create "my-laptop"
     """
 
     async def _create_key():

src/basic_memory/cli/commands/cloud/project_sync.py

@@ -0,0 +1,343 @@
+"""Cloud sync commands for Basic Memory projects.
+
+Commands for syncing, bisyncing, and checking integrity between local and cloud
+project instances. These were previously in project.py but belong here since
+they are cloud-specific operations.
+"""
+
+import os
+from datetime import datetime
+
+import typer
+from rich.console import Console
+
+from basic_memory.cli.app import cloud_app
+from basic_memory.cli.commands.cloud.bisync_commands import get_mount_info
+from basic_memory.cli.commands.cloud.rclone_commands import (
+    RcloneError,
+    SyncProject,
+    get_project_bisync_state,
+    project_bisync,
+    project_check,
+    project_sync,
+)
+from basic_memory.cli.commands.command_utils import run_with_cleanup
+from basic_memory.cli.commands.routing import force_routing
+from basic_memory.config import ConfigManager, ProjectEntry
+from basic_memory.mcp.async_client import get_client
+from basic_memory.mcp.clients import ProjectClient
+from basic_memory.schemas.project_info import ProjectItem
+from basic_memory.utils import generate_permalink, normalize_project_path
+
+console = Console()
+
+
+# --- Shared helpers ---
+
+
+def _has_cloud_credentials(config) -> bool:
+    """Return whether cloud credentials are available (API key or OAuth token)."""
+    from basic_memory.config import has_cloud_credentials
+
+    return has_cloud_credentials(config)
+
+
+def _require_cloud_credentials(config) -> None:
+    """Exit with actionable guidance when cloud credentials are missing."""
+    if _has_cloud_credentials(config):
+        return
+
+    console.print("[red]Error: cloud credentials are required for this command[/red]")
+    console.print("[dim]Run 'bm cloud login' or 'bm cloud api-key save <key>' first[/dim]")
+    raise typer.Exit(1)
+
+
+async def _get_cloud_project(name: str) -> ProjectItem | None:
+    """Fetch a project by name from the cloud API."""
+    async with get_client(project_name=name) as client:
+        projects_list = await ProjectClient(client).list_projects()
+        for proj in projects_list.projects:
+            if generate_permalink(proj.name) == generate_permalink(name):
+                return proj
+        return None
+
+
+def _get_sync_project(
+    name: str, config, project_data: ProjectItem
+) -> tuple[SyncProject, str | None]:
+    """Build a SyncProject and resolve local_sync_path from config.
+
+    Returns (sync_project, local_sync_path). Exits if no local_sync_path configured.
+    """
+    sync_entry = config.projects.get(name)
+    # Support both new (path) and legacy (local_sync_path) configs
+    local_sync_path = (sync_entry.local_sync_path or sync_entry.path) if sync_entry else None
+
+    if not local_sync_path or not os.path.isabs(local_sync_path):
+        console.print(f"[red]Error: Project '{name}' has no local sync path configured[/red]")
+        console.print(f"\nConfigure sync with: bm cloud sync-setup {name} ~/path/to/local")
+        raise typer.Exit(1)
+
+    sync_project = SyncProject(
+        name=project_data.name,
+        path=normalize_project_path(project_data.path),
+        local_sync_path=local_sync_path,
+    )
+    return sync_project, local_sync_path
+
+
+# --- Commands ---
+
+
+@cloud_app.command("sync")
+def sync_project_command(
+    name: str = typer.Option(..., "--name", help="Project name to sync"),
+    dry_run: bool = typer.Option(False, "--dry-run", help="Preview changes without syncing"),
+    verbose: bool = typer.Option(False, "--verbose", "-v", help="Show detailed output"),
+) -> None:
+    """One-way sync: local -> cloud (make cloud identical to local).
+
+    Example:
+      bm cloud sync --name research
+      bm cloud sync --name research --dry-run
+    """
+    config = ConfigManager().config
+    _require_cloud_credentials(config)
+
+    try:
+        # Get tenant info for bucket name
+        tenant_info = run_with_cleanup(get_mount_info())
+        bucket_name = tenant_info.bucket_name
+
+        # Get project info
+        with force_routing(cloud=True):
+            project_data = run_with_cleanup(_get_cloud_project(name))
+        if not project_data:
+            console.print(f"[red]Error: Project '{name}' not found[/red]")
+            raise typer.Exit(1)
+
+        sync_project, local_sync_path = _get_sync_project(name, config, project_data)
+
+        # Run sync
+        console.print(f"[blue]Syncing {name} (local -> cloud)...[/blue]")
+        success = project_sync(sync_project, bucket_name, dry_run=dry_run, verbose=verbose)
+
+        if success:
+            console.print(f"[green]{name} synced successfully[/green]")
+        else:
+            console.print(f"[red]{name} sync failed[/red]")
+            raise typer.Exit(1)
+
+    except RcloneError as e:
+        console.print(f"[red]Sync error: {e}[/red]")
+        raise typer.Exit(1)
+    except Exception as e:
+        console.print(f"[red]Error: {e}[/red]")
+        raise typer.Exit(1)
+
+
+@cloud_app.command("bisync")
+def bisync_project_command(
+    name: str = typer.Option(..., "--name", help="Project name to bisync"),
+    dry_run: bool = typer.Option(False, "--dry-run", help="Preview changes without syncing"),
+    resync: bool = typer.Option(False, "--resync", help="Force new baseline"),
+    verbose: bool = typer.Option(False, "--verbose", "-v", help="Show detailed output"),
+) -> None:
+    """Two-way sync: local <-> cloud (bidirectional sync).
+
+    Examples:
+      bm cloud bisync --name research --resync  # First time
+      bm cloud bisync --name research           # Subsequent syncs
+      bm cloud bisync --name research --dry-run # Preview changes
+    """
+    config = ConfigManager().config
+    _require_cloud_credentials(config)
+
+    try:
+        # Get tenant info for bucket name
+        tenant_info = run_with_cleanup(get_mount_info())
+        bucket_name = tenant_info.bucket_name
+
+        # Get project info
+        with force_routing(cloud=True):
+            project_data = run_with_cleanup(_get_cloud_project(name))
+        if not project_data:
+            console.print(f"[red]Error: Project '{name}' not found[/red]")
+            raise typer.Exit(1)
+
+        sync_project, local_sync_path = _get_sync_project(name, config, project_data)
+
+        # Run bisync
+        console.print(f"[blue]Bisync {name} (local <-> cloud)...[/blue]")
+        success = project_bisync(
+            sync_project, bucket_name, dry_run=dry_run, resync=resync, verbose=verbose
+        )
+
+        if success:
+            console.print(f"[green]{name} bisync completed successfully[/green]")
+
+            # Update config — sync_entry is guaranteed non-None because
+            # _get_sync_project validated local_sync_path (which comes from sync_entry)
+            sync_entry = config.projects.get(name)
+            if sync_entry is None:
+                raise RuntimeError(
+                    f"Sync entry for project '{name}' unexpectedly missing after validation"
+                )
+            sync_entry.last_sync = datetime.now()
+            sync_entry.bisync_initialized = True
+            ConfigManager().save_config(config)
+        else:
+            console.print(f"[red]{name} bisync failed[/red]")
+            raise typer.Exit(1)
+
+    except RcloneError as e:
+        console.print(f"[red]Bisync error: {e}[/red]")
+        raise typer.Exit(1)
+    except Exception as e:
+        console.print(f"[red]Error: {e}[/red]")
+        raise typer.Exit(1)
+
+
+@cloud_app.command("check")
+def check_project_command(
+    name: str = typer.Option(..., "--name", help="Project name to check"),
+    one_way: bool = typer.Option(False, "--one-way", help="Check one direction only (faster)"),
+) -> None:
+    """Verify file integrity between local and cloud.
+
+    Example:
+      bm cloud check --name research
+    """
+    config = ConfigManager().config
+    _require_cloud_credentials(config)
+
+    try:
+        # Get tenant info for bucket name
+        tenant_info = run_with_cleanup(get_mount_info())
+        bucket_name = tenant_info.bucket_name
+
+        # Get project info
+        with force_routing(cloud=True):
+            project_data = run_with_cleanup(_get_cloud_project(name))
+        if not project_data:
+            console.print(f"[red]Error: Project '{name}' not found[/red]")
+            raise typer.Exit(1)
+
+        sync_project, local_sync_path = _get_sync_project(name, config, project_data)
+
+        # Run check
+        console.print(f"[blue]Checking {name} integrity...[/blue]")
+        match = project_check(sync_project, bucket_name, one_way=one_way)
+
+        if match:
+            console.print(f"[green]{name} files match[/green]")
+        else:
+            console.print(f"[yellow]!{name} has differences[/yellow]")
+
+    except RcloneError as e:
+        console.print(f"[red]Check error: {e}[/red]")
+        raise typer.Exit(1)
+    except Exception as e:
+        console.print(f"[red]Error: {e}[/red]")
+        raise typer.Exit(1)
+
+
+@cloud_app.command("bisync-reset")
+def bisync_reset(
+    name: str = typer.Argument(..., help="Project name to reset bisync state for"),
+) -> None:
+    """Clear bisync state for a project.
+
+    This removes the bisync metadata files, forcing a fresh --resync on next bisync.
+    Useful when bisync gets into an inconsistent state or when remote path changes.
+    """
+    import shutil
+
+    try:
+        state_path = get_project_bisync_state(name)
+
+        if not state_path.exists():
+            console.print(f"[yellow]No bisync state found for project '{name}'[/yellow]")
+            return
+
+        # Remove the entire state directory
+        shutil.rmtree(state_path)
+        console.print(f"[green]Cleared bisync state for project '{name}'[/green]")
+        console.print("\nNext steps:")
+        console.print(f"  1. Preview: bm cloud bisync --name {name} --resync --dry-run")
+        console.print(f"  2. Sync: bm cloud bisync --name {name} --resync")
+
+    except Exception as e:
+        console.print(f"[red]Error clearing bisync state: {str(e)}[/red]")
+        raise typer.Exit(1)
+
+
+@cloud_app.command("sync-setup")
+def setup_project_sync(
+    name: str = typer.Argument(..., help="Project name"),
+    local_path: str = typer.Argument(..., help="Local sync directory"),
+) -> None:
+    """Configure local sync for an existing cloud project.
+
+    Example:
+      bm cloud sync-setup research ~/Documents/research
+    """
+    import os
+    from pathlib import Path
+
+    config_manager = ConfigManager()
+    config = config_manager.config
+    _require_cloud_credentials(config)
+
+    async def _verify_project_exists():
+        """Verify the project exists on cloud by listing all projects."""
+        async with get_client(project_name=name) as client:
+            projects_list = await ProjectClient(client).list_projects()
+            project_names = [p.name for p in projects_list.projects]
+            if name not in project_names:
+                raise ValueError(f"Project '{name}' not found on cloud")
+            return True
+
+    try:
+        # Verify project exists on cloud
+        with force_routing(cloud=True):
+            run_with_cleanup(_verify_project_exists())
+
+        # Resolve and create local path
+        resolved_path = Path(os.path.abspath(os.path.expanduser(local_path)))
+        resolved_path.mkdir(parents=True, exist_ok=True)
+
+        # Update project entry with sync path — path is always the local directory
+        entry = config.projects.get(name)
+        if entry:
+            entry.path = resolved_path.as_posix()
+            entry.local_sync_path = resolved_path.as_posix()
+            entry.bisync_initialized = False
+            entry.last_sync = None
+        else:
+            config.projects[name] = ProjectEntry(
+                path=resolved_path.as_posix(),
+                local_sync_path=resolved_path.as_posix(),
+            )
+        config_manager.save_config(config)
+
+        # Create the project in the local DB so the MCP server can immediately use it
+        async def _create_local_project():
+            async with get_client() as client:
+                data = {"name": name, "path": resolved_path.as_posix(), "set_default": False}
+                return await ProjectClient(client).create_project(data)
+
+        with force_routing(local=True):
+            try:
+                run_with_cleanup(_create_local_project())
+            except Exception:
+                pass  # Project may already exist locally; reconcile on next startup
+
+        console.print(f"[green]Sync configured for project '{name}'[/green]")
+        console.print(f"\nLocal sync path: {resolved_path}")
+        console.print("\nNext steps:")
+        console.print(f"  1. Preview: bm cloud bisync --name {name} --resync --dry-run")
+        console.print(f"  2. Sync: bm cloud bisync --name {name} --resync")
+    except Exception as e:
+        console.print(f"[red]Error configuring sync: {str(e)}[/red]")
+        raise typer.Exit(1)

src/basic_memory/cli/commands/cloud/rclone_commands.py

@@ -20,6 +20,7 @@ from loguru import logger
 from rich.console import Console
 
 from basic_memory.cli.commands.cloud.rclone_installer import is_rclone_installed
+from basic_memory.config import resolve_data_dir
 from basic_memory.utils import normalize_project_path
 
 console = Console()
@@ -138,13 +139,16 @@ def get_bmignore_filter_path() -> Path:
 def get_project_bisync_state(project_name: str) -> Path:
     """Get path to project's bisync state directory.
 
+    Honors ``BASIC_MEMORY_CONFIG_DIR`` so isolated instances each keep their
+    own bisync state alongside their config.
+
     Args:
         project_name: Name of the project
 
     Returns:
         Path to bisync state directory for this project
     """
-    return Path.home() / ".basic-memory" / "bisync-state" / project_name
+    return resolve_data_dir() / "bisync-state" / project_name
 
 
 def bisync_initialized(project_name: str) -> bool:
@@ -223,6 +227,9 @@ def project_sync(
         *TIGRIS_CONSISTENCY_HEADERS,
         "--filter-from",
         str(filter_path),
+        # Prevent NUL byte padding on virtual filesystems (e.g. Google Drive File Stream)
+        # See: rclone/rclone#6801
+        "--local-no-preallocate",
     ]
 
     if verbose:
@@ -299,6 +306,9 @@ def project_bisync(
         str(filter_path),
         "--workdir",
         str(state_path),
+        # Prevent NUL byte padding on virtual filesystems (e.g. Google Drive File Stream)
+        # See: rclone/rclone#6801
+        "--local-no-preallocate",
     ]
 
     # Add --create-empty-src-dirs if rclone version supports it (v1.64+)

src/basic_memory/cli/commands/cloud/upload.py

@@ -10,7 +10,6 @@ import httpx
 
 from basic_memory.ignore_utils import load_gitignore_patterns, should_ignore_path
 from basic_memory.mcp.async_client import get_client
-from basic_memory.mcp.tools.utils import call_put
 
 # Archive file extensions that should be skipped during upload
 ARCHIVE_EXTENSIONS = {".zip", ".tar", ".gz", ".bz2", ".xz", ".7z", ".rar", ".tgz", ".tbz2"}
@@ -24,7 +23,7 @@ async def upload_path(
     dry_run: bool = False,
     *,
     client_cm_factory: Callable[[], AbstractAsyncContextManager[httpx.AsyncClient]] | None = None,
-    put_func=call_put,
+    put_func: Callable | None = None,
 ) -> bool:
     """
     Upload a file or directory to cloud project via WebDAV.
@@ -117,9 +116,20 @@ async def upload_path(
 
                     # Upload via HTTP PUT to WebDAV endpoint with mtime header
                     # Using X-OC-Mtime (ownCloud/Nextcloud standard)
-                    response = await put_func(
-                        client, remote_path, content=content, headers={"X-OC-Mtime": str(mtime)}
-                    )
+                    if put_func is not None:
+                        # Test injection path
+                        response = await put_func(
+                            client,
+                            remote_path,
+                            content=content,
+                            headers={"X-OC-Mtime": str(mtime)},
+                        )
+                    else:
+                        response = await client.put(
+                            remote_path,
+                            content=content,
+                            headers={"X-OC-Mtime": str(mtime)},
+                        )
                     response.raise_for_status()
 
         # Format total size based on magnitude

src/basic_memory/cli/commands/cloud/upload_command.py

@@ -1,5 +1,6 @@
 """Upload CLI commands for basic-memory projects."""
 
+from functools import partial
 from pathlib import Path
 
 import typer
@@ -8,11 +9,16 @@ from rich.console import Console
 from basic_memory.cli.app import cloud_app
 from basic_memory.cli.commands.command_utils import run_with_cleanup
 from basic_memory.cli.commands.cloud.cloud_utils import (
+    CloudUtilsError,
     create_cloud_project,
     project_exists,
     sync_project,
 )
 from basic_memory.cli.commands.cloud.upload import upload_path
+from basic_memory.mcp.async_client import (
+    get_cloud_control_plane_client,
+    resolve_configured_workspace,
+)
 
 console = Console()
 
@@ -72,12 +78,20 @@ def upload(
     """
 
     async def _upload():
+        resolved_workspace = resolve_configured_workspace(project_name=project)
+
+        try:
+            project_already_exists = await project_exists(project, workspace=resolved_workspace)
+        except CloudUtilsError as e:
+            console.print(f"[red]Failed to check cloud project '{project}': {e}[/red]")
+            raise typer.Exit(1)
+
         # Check if project exists
-        if not await project_exists(project):
+        if not project_already_exists:
             if create_project:
                 console.print(f"[blue]Creating cloud project '{project}'...[/blue]")
                 try:
-                    await create_cloud_project(project)
+                    await create_cloud_project(project, workspace=resolved_workspace)
                     console.print(f"[green]Created project '{project}'[/green]")
                 except Exception as e:
                     console.print(f"[red]Failed to create project: {e}[/red]")
@@ -86,12 +100,14 @@ def upload(
                 console.print(
                     f"[red]Project '{project}' does not exist.[/red]\n"
                     f"[yellow]Options:[/yellow]\n"
-                    f"  1. Create it first: bm project add {project}\n"
+                    f"  1. Create it first: bm project add {project} --cloud\n"
                     f"  2. Use --create-project flag to create automatically"
                 )
                 raise typer.Exit(1)
 
         # Perform upload (or dry run)
+        if resolved_workspace:
+            console.print(f"[dim]Using workspace: {resolved_workspace}[/dim]")
         if dry_run:
             console.print(
                 f"[yellow]DRY RUN: Showing what would be uploaded to '{project}'[/yellow]"
@@ -100,7 +116,15 @@ def upload(
             console.print(f"[blue]Uploading {path} to project '{project}'...[/blue]")
 
         success = await upload_path(
-            path, project, verbose=verbose, use_gitignore=not no_gitignore, dry_run=dry_run
+            path,
+            project,
+            verbose=verbose,
+            use_gitignore=not no_gitignore,
+            dry_run=dry_run,
+            client_cm_factory=partial(
+                get_cloud_control_plane_client,
+                workspace=resolved_workspace,
+            ),
         )
         if not success:
             console.print("[red]Upload failed[/red]")
@@ -111,12 +135,14 @@ def upload(
         else:
             console.print(f"[green]Successfully uploaded to '{project}'[/green]")
 
-        # Sync project if requested (skip on dry run)
-        # Force full scan after bisync to ensure database is up-to-date with synced files
+        # Sync project if requested (skip on dry run).
+        # Trigger: upload adds new files the watcher has not observed locally.
+        # Why: force_full ensures those freshly uploaded files are indexed immediately.
+        # Outcome: upload keeps its eager reindex while sync/bisync stay incremental.
         if sync and not dry_run:
             console.print(f"[blue]Syncing project '{project}'...[/blue]")
             try:
-                await sync_project(project, force_full=True)
+                await sync_project(project)
             except Exception as e:
                 console.print(f"[yellow]Warning: Sync failed: {e}[/yellow]")
                 console.print("[dim]Files uploaded but may not be indexed yet[/dim]")

src/basic_memory/cli/commands/cloud/workspace.py

@@ -0,0 +1,113 @@
+"""Workspace commands for Basic Memory cloud workspaces."""
+
+import typer
+from rich.console import Console
+from rich.table import Table
+
+from basic_memory.cli.commands.command_utils import run_with_cleanup
+from basic_memory.config import ConfigManager
+from basic_memory.mcp.project_context import (
+    _workspace_choices,
+    _workspace_matches_identifier,
+    get_available_workspaces,
+)
+
+console = Console()
+
+workspace_app = typer.Typer(help="Manage cloud workspaces")
+
+
+@workspace_app.command("list")
+def list_workspaces() -> None:
+    """List cloud workspaces available to the current OAuth session."""
+
+    async def _list():
+        return await get_available_workspaces()
+
+    try:
+        workspaces = run_with_cleanup(_list())
+    except RuntimeError as exc:
+        console.print(f"[red]Error: {exc}[/red]")
+        raise typer.Exit(1)
+    except Exception as exc:  # pragma: no cover
+        console.print(f"[red]Error listing workspaces: {exc}[/red]")
+        raise typer.Exit(1)
+
+    if not workspaces:
+        console.print("[yellow]No accessible workspaces found.[/yellow]")
+        return
+
+    config = ConfigManager().config
+    default_ws = config.default_workspace
+
+    table = Table(title="Available Workspaces")
+    table.add_column("Name", style="cyan")
+    table.add_column("Type", style="blue")
+    table.add_column("Role", style="green")
+    table.add_column("Tenant ID", style="yellow")
+    table.add_column("Default", style="magenta")
+
+    for workspace in workspaces:
+        is_default = "[X]" if workspace.tenant_id == default_ws else ""
+        table.add_row(
+            workspace.name,
+            workspace.workspace_type,
+            workspace.role,
+            workspace.tenant_id,
+            is_default,
+        )
+
+    console.print(table)
+
+
+@workspace_app.command("set-default")
+def set_default_workspace(
+    identifier: str = typer.Argument(..., help="Workspace name or tenant_id to set as default"),
+) -> None:
+    """Set the default cloud workspace.
+
+    The default workspace is used as fallback when no per-project workspace
+    is configured. Resolves the identifier against available workspaces.
+
+    Examples:
+      bm cloud workspace set-default Personal
+      bm cloud workspace set-default 11111111-1111-1111-1111-111111111111
+    """
+
+    async def _list():
+        return await get_available_workspaces()
+
+    try:
+        workspaces = run_with_cleanup(_list())
+    except RuntimeError as exc:
+        console.print(f"[red]Error: {exc}[/red]")
+        raise typer.Exit(1)
+
+    if not workspaces:
+        console.print("[yellow]No accessible workspaces found.[/yellow]")
+        raise typer.Exit(1)
+
+    matches = [ws for ws in workspaces if _workspace_matches_identifier(ws, identifier)]
+
+    if not matches:
+        console.print(f"[red]Error: Workspace '{identifier}' not found[/red]")
+        console.print(f"[dim]Available:\n{_workspace_choices(workspaces)}[/dim]")
+        raise typer.Exit(1)
+
+    if len(matches) > 1:
+        console.print(
+            f"[red]Error: Workspace name '{identifier}' matches multiple workspaces. "
+            f"Use tenant_id instead.[/red]"
+        )
+        console.print(f"[dim]Available:\n{_workspace_choices(workspaces)}[/dim]")
+        raise typer.Exit(1)
+
+    selected = matches[0]
+    config_manager = ConfigManager()
+    config = config_manager.config
+    config.default_workspace = selected.tenant_id
+    config_manager.save_config(config)
+
+    console.print(
+        f"[green]Default workspace set to '{selected.name}' ({selected.tenant_id})[/green]"
+    )

src/basic_memory/cli/commands/command_utils.py

@@ -11,9 +11,8 @@ from rich.console import Console
 from basic_memory import db
 from basic_memory.config import ConfigManager
 from basic_memory.mcp.async_client import get_client
-from basic_memory.mcp.tools.utils import call_post, call_get
+from basic_memory.mcp.clients import ProjectClient
 from basic_memory.mcp.project_context import get_active_project
-from basic_memory.schemas import ProjectInfoResponse
 
 console = Console()
 
@@ -61,16 +60,12 @@ async def run_sync(
     try:
         async with get_client(project_name=project) as client:
             project_item = await get_active_project(client, project, None)
-            url = f"/v2/projects/{project_item.external_id}/sync"
-            params = []
-            if force_full:
-                params.append("force_full=true")
-            if not run_in_background:
-                params.append("run_in_background=false")
-            if params:
-                url += "?" + "&".join(params)
-            response = await call_post(client, url)
-            data = response.json()
+            project_client = ProjectClient(client)
+            data = await project_client.sync(
+                project_item.external_id,
+                force_full=force_full,
+                run_in_background=run_in_background,
+            )
             # Background mode returns {"message": "..."}, foreground returns SyncReportResponse
             if "message" in data:
                 console.print(f"[green]{data['message']}[/green]")
@@ -94,8 +89,21 @@ async def get_project_info(project: str):
     try:
         async with get_client(project_name=project) as client:
             project_item = await get_active_project(client, project, None)
-            response = await call_get(client, f"/v2/projects/{project_item.external_id}/info")
-            return ProjectInfoResponse.model_validate(response.json())
+            return await ProjectClient(client).get_info(project_item.external_id)
     except (ToolError, ValueError) as e:
-        console.print(f"[red]Sync failed: {e}[/red]")
+        error_text = str(e)
+        if "internal proxy error" in error_text.lower() and "not found in configuration" in (
+            error_text.lower()
+        ):
+            console.print(
+                "[red]Project info failed: cloud returned an internal configuration error for "
+                "this project.[/red]"
+            )
+            console.print(
+                "[yellow]This is a cloud backend issue for detailed info lookups. "
+                "Use `bm project list --cloud` for project metadata until the service is updated."
+                "[/yellow]"
+            )
+        else:
+            console.print(f"[red]Project info failed: {e}[/red]")
         raise typer.Exit(1)

src/basic_memory/cli/commands/db.py

@@ -1,7 +1,10 @@
 """Database management commands."""
 
-from pathlib import Path
+import os
+from dataclasses import dataclass
+from pathlib import Path, PurePosixPath, PureWindowsPath
 
+import psutil
 import typer
 from loguru import logger
 from rich.console import Console
@@ -11,7 +14,8 @@ from sqlalchemy.exc import OperationalError
 from basic_memory import db
 from basic_memory.cli.app import app
 from basic_memory.cli.commands.command_utils import run_with_cleanup
-from basic_memory.config import ConfigManager
+from basic_memory.config import ConfigManager, ProjectMode
+from basic_memory.indexing import IndexProgress
 from basic_memory.repository import ProjectRepository
 from basic_memory.services.initialization import reconcile_projects_with_config
 from basic_memory.sync.sync_service import get_sync_service
@@ -19,6 +23,136 @@ from basic_memory.sync.sync_service import get_sync_service
 console = Console()
 
 
+def _is_basic_memory_mcp(cmdline: list[str]) -> bool:
+    """Heuristic: does this argv represent a `basic-memory mcp` server?
+
+    The MCP server can be launched any of:
+      basic-memory mcp
+      bm mcp                                  # entrypoint alias from pyproject.toml
+      python -m basic_memory.cli.main mcp     # module form
+      uv run basic-memory mcp / uv run bm mcp # uv wrappers
+      /abs/path/to/{bm,basic-memory}[.exe] mcp
+
+    A reliable match needs both signals:
+      1. "mcp" appears as an exact argv token (not "mcp-foo").
+      2. Some argv token names the basic-memory entrypoint — either by
+         hyphen/underscore form, or as a `bm` script (covers `/usr/local/bin/bm`,
+         `bm.exe`, etc. via Path.stem).
+    """
+    if "mcp" not in cmdline:
+        return False
+    for arg in cmdline:
+        if "basic-memory" in arg or "basic_memory" in arg:
+            return True
+        # Try both POSIX and Windows path interpretations so a test on
+        # macOS still recognizes `C:\\...\\bm.exe`, and a real Windows
+        # run still recognizes `/usr/local/bin/bm`. Path() alone uses
+        # the host OS, which gives wrong stems for foreign separators.
+        if PurePosixPath(arg).stem == "bm" or PureWindowsPath(arg).stem == "bm":
+            return True
+    return False
+
+
+def _find_live_mcp_processes() -> list[tuple[int, str]]:
+    """Return (pid, joined_cmdline) for live `basic-memory mcp` processes.
+
+    Why this exists (issue #765):
+        On POSIX, `Path.unlink()` removes the directory entry but the inode
+        survives as long as any process holds the file open. A `bm reset`
+        run while Claude Desktop (or another MCP client) is alive will
+        therefore "succeed" — but the still-running MCP keeps reading the
+        old, now-invisible memory.db inode and returns phantom rows. On
+        Windows the OS naturally raises PermissionError on `unlink()`, so
+        the bug is POSIX-specific. We detect proactively to give the same
+        error experience on every platform before doing damage.
+
+    The current process is excluded so this can be called from inside a
+    `bm reset` invocation. NoSuchProcess / AccessDenied are swallowed
+    because process tables race with the scan and we don't want a
+    transient permission error to mask a real zombie.
+    """
+    me = os.getpid()
+    matches: list[tuple[int, str]] = []
+    for proc in psutil.process_iter(["pid", "cmdline"]):
+        try:
+            pid = proc.info.get("pid")
+            if pid is None or pid == me:
+                continue
+            cmdline = proc.info.get("cmdline") or []
+            if not cmdline:
+                continue
+            if _is_basic_memory_mcp(cmdline):
+                matches.append((pid, " ".join(cmdline)))
+        except (psutil.NoSuchProcess, psutil.AccessDenied):
+            continue
+    return matches
+
+
+def _abort_if_mcp_processes_alive() -> None:
+    """Refuse `bm reset` while basic-memory MCP processes are still running.
+
+    See _find_live_mcp_processes for the underlying POSIX-vs-Windows
+    rationale. Prints a per-PID list and platform-appropriate cleanup
+    instructions, then exits non-zero so destructive work never starts.
+    """
+    zombies = _find_live_mcp_processes()
+    if not zombies:
+        return
+
+    console.print("[red]Refusing to reset:[/red] basic-memory MCP processes are still running.")
+    console.print(
+        "[yellow]On macOS/Linux these would keep reading the deleted memory.db inode "
+        "and return phantom search results (see #765).[/yellow]"
+    )
+    for pid, cmd in zombies:
+        console.print(f"  PID {pid}: {cmd}")
+    console.print("\n[bold]How to clean up:[/bold]")
+    console.print("  1. Quit Claude Desktop and any other MCP clients.")
+    if os.name == "nt":
+        console.print(
+            "  2. Verify nothing remains: "
+            "[green]Get-CimInstance Win32_Process | "
+            "Where-Object {$_.CommandLine -like '*basic-memory*mcp*'}[/green]"
+        )
+    else:
+        console.print("  2. Verify nothing remains: [green]pgrep -fa 'basic-memory mcp'[/green]")
+    console.print("  3. Re-run [green]bm reset[/green].")
+    raise typer.Exit(1)
+
+
+@dataclass(slots=True)
+class EmbeddingProgress:
+    """Typed CLI progress payload for embedding backfills."""
+
+    entity_id: int
+    completed: int
+    total: int
+
+
+def _format_eta(seconds: float | None) -> str:
+    """Render a compact ETA string for CLI progress descriptions."""
+    if seconds is None:
+        return "--:--"
+
+    whole_seconds = max(int(seconds), 0)
+    minutes, remaining_seconds = divmod(whole_seconds, 60)
+    hours, remaining_minutes = divmod(minutes, 60)
+    if hours:
+        return f"{hours:d}:{remaining_minutes:02d}:{remaining_seconds:02d}"
+    return f"{remaining_minutes:02d}:{remaining_seconds:02d}"
+
+
+def _format_index_progress(progress: IndexProgress) -> str:
+    """Render typed index progress as a compact Rich task description."""
+    files_per_minute = int(progress.files_per_minute) if progress.files_per_minute else 0
+    return (
+        "  Indexing files... "
+        f"{progress.files_processed}/{progress.files_total} files | "
+        f"{progress.batches_completed}/{progress.batches_total} batches | "
+        f"{files_per_minute}/min | ETA {_format_eta(progress.eta_seconds)}"
+    )
+
+
 async def _reindex_projects(app_config):
     """Reindex all projects in a single async context.
 
@@ -51,6 +185,16 @@ async def _reindex_projects(app_config):
 @app.command()
 def reset(
     reindex: bool = typer.Option(False, "--reindex", help="Rebuild db index from filesystem"),
+    force: bool = typer.Option(
+        False,
+        "--force",
+        help=(
+            "Skip the pre-flight check that refuses to reset while "
+            "basic-memory MCP processes are running. Use only in "
+            "automated workflows where you've already ensured no MCP "
+            "clients are attached to the database."
+        ),
+    ),
 ):  # pragma: no cover
     """Reset database (drop all tables and recreate)."""
     console.print(
@@ -59,6 +203,14 @@ def reset(
         "Use [green]bm reset --reindex[/green] to automatically rebuild the index afterward."
     )
     if typer.confirm("Reset the database index?"):
+        # Pre-flight: refuse to proceed if MCP processes still hold the DB
+        # file open. POSIX would silently let us unlink the inode while
+        # they keep reading it; Windows would error here anyway. See
+        # _find_live_mcp_processes for the full story. --force is the
+        # documented escape hatch for scripted/CI runs.
+        if not force:
+            _abort_if_mcp_processes_alive()
+
         logger.info("Resetting database...")
         config_manager = ConfigManager()
         app_config = config_manager.config
@@ -112,20 +264,30 @@ def reindex(
         False, "--embeddings", "-e", help="Rebuild vector embeddings (requires semantic search)"
     ),
     search: bool = typer.Option(False, "--search", "-s", help="Rebuild full-text search index"),
+    full: bool = typer.Option(
+        False,
+        "--full",
+        help="Force a full filesystem scan and file reindex instead of the default incremental scan",
+    ),
     project: str = typer.Option(
         None, "--project", "-p", help="Reindex a specific project (default: all)"
     ),
 ):  # pragma: no cover
     """Rebuild search indexes and/or vector embeddings without dropping the database.
 
-    By default rebuilds everything (search + embeddings if semantic is enabled).
-    Use --search or --embeddings to rebuild only one.
+    By default runs incremental search + embeddings (if semantic search is enabled).
+    Use --full to bypass incremental scan optimization, rebuild all file-backed search rows,
+    and re-embed all eligible notes.
+    Use --search or --embeddings to rebuild only one side.
 
     Examples:
-        bm reindex                  # Rebuild everything
+        bm reindex                  # Incremental search + embeddings
+        bm reindex --full           # Full search + full re-embed
         bm reindex --embeddings     # Only rebuild vector embeddings
         bm reindex --search         # Only rebuild FTS index
-        bm reindex -p claw          # Reindex only the 'claw' project
+        bm reindex --full --search  # Full search only
+        bm reindex --full --embeddings  # Full re-embed only
+        bm reindex -p claw --full   # Full reindex for only the 'claw' project
     """
     # If neither flag is set, do both
     if not embeddings and not search:
@@ -144,10 +306,19 @@ def reindex(
         if not search:
             raise typer.Exit(0)
 
-    run_with_cleanup(_reindex(app_config, search=search, embeddings=embeddings, project=project))
+    run_with_cleanup(
+        _reindex(app_config, search=search, embeddings=embeddings, full=full, project=project)
+    )
 
 
-async def _reindex(app_config, search: bool, embeddings: bool, project: str | None):
+async def _reindex(
+    app_config,
+    *,
+    search: bool,
+    embeddings: bool,
+    full: bool,
+    project: str | None,
+):
     """Run reindex operations."""
     from basic_memory.repository import EntityRepository
     from basic_memory.repository.search_repository import create_search_repository
@@ -169,21 +340,63 @@ async def _reindex(app_config, search: bool, embeddings: bool, project: str | No
         if project:
             projects = [p for p in projects if p.name == project]
             if not projects:
-                console.print(f"[red]Project '{project}' not found.[/red]")
+                # Check if it's a cloud-only project — those can't be reindexed locally
+                project_mode = app_config.get_project_mode(project)
+                if project_mode == ProjectMode.CLOUD:
+                    console.print(
+                        f"[yellow]Project '{project}' is a cloud project.[/yellow]\n"
+                        "Reindexing is a local operation — cloud projects are "
+                        "indexed on the server."
+                    )
+                else:
+                    console.print(f"[red]Project '{project}' not found.[/red]")
                 raise typer.Exit(1)
 
         for proj in projects:
             console.print(f"\n[bold]Project: [cyan]{proj.name}[/cyan][/bold]")
 
             if search:
-                console.print("  Rebuilding full-text search index...")
+                search_mode_label = "full scan" if full else "incremental scan"
+                console.print(
+                    f"  Rebuilding full-text search index ([cyan]{search_mode_label}[/cyan])..."
+                )
                 sync_service = await get_sync_service(proj)
                 sync_dir = Path(proj.path)
-                await sync_service.sync(sync_dir, project_name=proj.name)
-                console.print("  [green]✓[/green] Full-text search index rebuilt")
+                with Progress(
+                    SpinnerColumn(),
+                    TextColumn("[progress.description]{task.description}"),
+                    BarColumn(),
+                    TaskProgressColumn(),
+                    console=console,
+                ) as progress:
+                    task = progress.add_task("  Indexing files... scanning changes", total=1)
+
+                    async def on_index_progress(update: IndexProgress) -> None:
+                        total = update.files_total or 1
+                        completed = update.files_processed if update.files_total else 1
+                        progress.update(
+                            task,
+                            description=_format_index_progress(update),
+                            total=total,
+                            completed=min(completed, total),
+                        )
+
+                    await sync_service.sync(
+                        sync_dir,
+                        project_name=proj.name,
+                        force_full=full,
+                        sync_embeddings=False,
+                        progress_callback=on_index_progress,
+                    )
+                    progress.update(task, completed=progress.tasks[task].total or 1)
+
+                console.print("  [green]done[/green] Full-text search index rebuilt")
 
             if embeddings:
-                console.print("  Building vector embeddings...")
+                embedding_mode_label = "full rebuild" if full else "incremental sync"
+                console.print(
+                    f"  Building vector embeddings ([cyan]{embedding_mode_label}[/cyan])..."
+                )
                 entity_repository = EntityRepository(session_maker, project_id=proj.id)
                 search_repository = create_search_repository(
                     session_maker, project_id=proj.id, app_config=app_config
@@ -204,13 +417,29 @@ async def _reindex(app_config, search: bool, embeddings: bool, project: str | No
                     task = progress.add_task("  Embedding entities...", total=None)
 
                     def on_progress(entity_id, index, total):
-                        progress.update(task, total=total, completed=index)
+                        embedding_progress = EmbeddingProgress(
+                            entity_id=entity_id,
+                            completed=index,
+                            total=total,
+                        )
+                        # Trigger: repository progress now reports terminal entity completion.
+                        # Why: operators need to see finished embedding work rather than
+                        # entities merely entering prepare.
+                        # Outcome: the CLI bar advances steadily with real completed work.
+                        progress.update(
+                            task,
+                            total=embedding_progress.total,
+                            completed=embedding_progress.completed,
+                        )
 
-                    stats = await search_service.reindex_vectors(progress_callback=on_progress)
+                    stats = await search_service.reindex_vectors(
+                        progress_callback=on_progress,
+                        force_full=full,
+                    )
                     progress.update(task, completed=stats["total_entities"])
 
                 console.print(
-                    f"  [green]✓[/green] Embeddings complete: "
+                    f"  [green]done[/green] Embeddings complete: "
                     f"{stats['embedded']} entities embedded, "
                     f"{stats['skipped']} skipped, "
                     f"{stats['errors']} errors"

src/basic_memory/cli/commands/doctor.py

@@ -19,7 +19,6 @@ from basic_memory.markdown.markdown_processor import MarkdownProcessor
 from basic_memory.markdown.schemas import EntityFrontmatter, EntityMarkdown
 from basic_memory.mcp.async_client import get_client
 from basic_memory.mcp.clients import KnowledgeClient, ProjectClient, SearchClient
-from basic_memory.mcp.tools.utils import call_post
 from basic_memory.schemas.base import Entity
 from basic_memory.schemas.project_info import ProjectInfoRequest
 from basic_memory.schemas.search import SearchQuery
@@ -55,6 +54,9 @@ async def run_doctor() -> None:
                 if not status.new_project:
                     raise ValueError("Failed to create doctor project")
                 project_id = status.new_project.external_id
+                # Use the resolved path from the server — when project_root is configured,
+                # the actual project directory differs from the requested temp_path
+                project_path = Path(status.new_project.path)
                 console.print(f"[green]OK[/green] Created doctor project: {project_name}")
 
                 # --- DB -> File: create an entity via API ---
@@ -62,14 +64,14 @@ async def run_doctor() -> None:
                 api_note = Entity(
                     title=api_note_title,
                     directory="doctor",
-                    entity_type="note",
+                    note_type="note",
                     content_type="text/markdown",
                     content=f"# {api_note_title}\n\n- [note] API to file check",
                     entity_metadata={"tags": ["doctor"]},
                 )
-                api_result = await knowledge_client.create_entity(api_note.model_dump(), fast=False)
+                api_result = await knowledge_client.create_entity(api_note.model_dump())
 
-                api_file = temp_path / api_result.file_path
+                api_file = project_path / api_result.file_path
                 if not api_file.exists():
                     raise ValueError(f"API note file missing: {api_result.file_path}")
 
@@ -80,7 +82,7 @@ async def run_doctor() -> None:
                 console.print("[green]OK[/green] API write created file")
 
                 # --- File -> DB: write markdown file directly, then sync ---
-                parser = EntityParser(temp_path)
+                parser = EntityParser(project_path)
                 processor = MarkdownProcessor(parser)
                 manual_markdown = EntityMarkdown(
                     frontmatter=EntityFrontmatter(
@@ -94,15 +96,14 @@ async def run_doctor() -> None:
                     content=f"# {manual_note_title}\n\n- [note] File to DB check",
                 )
 
-                manual_path = temp_path / "doctor" / "manual-note.md"
+                manual_path = project_path / "doctor" / "manual-note.md"
                 await processor.write_file(manual_path, manual_markdown)
                 console.print("[green]OK[/green] Manual file written")
 
-                sync_response = await call_post(
-                    client,
-                    f"/v2/projects/{project_id}/sync?force_full=true&run_in_background=false",
+                sync_data = await project_client.sync(
+                    project_id, force_full=False, run_in_background=False
                 )
-                sync_report = SyncReportResponse.model_validate(sync_response.json())
+                sync_report = SyncReportResponse.model_validate(sync_data)
                 if sync_report.total == 0:
                     raise ValueError("Sync did not detect any changes")
 
@@ -118,8 +119,7 @@ async def run_doctor() -> None:
 
                 console.print("[green]OK[/green] Search confirmed manual file")
 
-                status_response = await call_post(client, f"/v2/projects/{project_id}/status")
-                status_report = SyncReportResponse.model_validate(status_response.json())
+                status_report = await project_client.get_status(project_id)
                 if status_report.total != 0:
                     raise ValueError("Project status not clean after sync")
 
@@ -142,6 +142,9 @@ def doctor(
     """Run local consistency checks to verify file/database sync."""
     try:
         validate_routing_flags(local, cloud)
+        # Doctor runs local filesystem checks — always default to local routing
+        if not local and not cloud:
+            local = True
         with force_routing(local=local, cloud=cloud):
             run_with_cleanup(run_doctor())
     except (ToolError, ValueError) as e:

src/basic_memory/cli/commands/format.py

@@ -183,10 +183,10 @@ def format(
     By default, formats all .md, .json, and .canvas files in the current project.
 
     Examples:
-        basic-memory format                    # Format all files in current project
-        basic-memory format --project research # Format files in specific project
-        basic-memory format notes/meeting.md   # Format a specific file
-        basic-memory format notes/             # Format all files in directory
+        bm format                    # Format all files in current project
+        bm format --project research # Format files in specific project
+        bm format notes/meeting.md   # Format a specific file
+        bm format notes/             # Format all files in directory
     """
     try:
         run_with_cleanup(run_format(path, project))

src/basic_memory/cli/commands/import_chatgpt.py

@@ -44,7 +44,7 @@ def import_chatgpt(
     2. Convert them to linear markdown conversations
     3. Save as clean, readable markdown files
 
-    After importing, run 'basic-memory sync' to index the new files.
+    After importing, run 'bm reindex --search' to index the new files.
     """
 
     try:
@@ -81,7 +81,7 @@ def import_chatgpt(
             )
         )
 
-        console.print("\nRun 'basic-memory sync' to index the new files.")
+        console.print("\nRun 'bm reindex --search' to index the new files.")
 
     except Exception as e:
         logger.error("Import failed")

src/basic_memory/cli/commands/import_claude_conversations.py

@@ -44,7 +44,7 @@ def import_claude(
     2. Create markdown files for each conversation
     3. Format content in clean, readable markdown
 
-    After importing, run 'basic-memory sync' to index the new files.
+    After importing, run 'bm reindex --search' to index the new files.
     """
 
     config = get_project_config()
@@ -84,7 +84,7 @@ def import_claude(
             )
         )
 
-        console.print("\nRun 'basic-memory sync' to index the new files.")
+        console.print("\nRun 'bm reindex --search' to index the new files.")
 
     except Exception as e:
         logger.error("Import failed")

src/basic_memory/cli/commands/import_claude_projects.py

@@ -44,7 +44,7 @@ def import_projects(
     2. Store docs in a docs/ subdirectory
     3. Place prompt template in project root
 
-    After importing, run 'basic-memory sync' to index the new files.
+    After importing, run 'bm reindex --search' to index the new files.
     """
     config = get_project_config()
     try:
@@ -83,7 +83,7 @@ def import_projects(
             )
         )
 
-        console.print("\nRun 'basic-memory sync' to index the new files.")
+        console.print("\nRun 'bm reindex --search' to index the new files.")
 
     except Exception as e:
         logger.error("Import failed")

src/basic_memory/cli/commands/mcp.py

@@ -1,12 +1,14 @@
 """MCP server command with streamable HTTP transport."""
 
 import os
+import threading
 from typing import Any, Optional
 
 import typer
 from loguru import logger
 
 from basic_memory.cli.app import app
+from basic_memory.cli.auto_update import AutoUpdateStatus, run_auto_update
 from basic_memory.config import ConfigManager, init_mcp_logging
 
 
@@ -36,7 +38,7 @@ def mcp(
     This command starts an MCP server using one of three transport options:
 
     - stdio: Standard I/O (good for local usage)
-    - streamable-http: Recommended for web deployments (default)
+    - streamable-http: Recommended for web deployments
     - sse: Server-Sent Events (for compatibility with existing clients)
 
     Initialization, file sync, and cleanup are handled by the MCP server's lifespan.
@@ -45,14 +47,20 @@ def mcp(
     Users who have cloud mode enabled can still use local MCP for Claude Code
     and Claude Desktop while using cloud MCP for web and mobile access.
     """
-    # Force local routing for local MCP server.
-    # Trigger: MCP server command invocation (all transports).
-    # Why: local MCP must never route through cloud; stdio in particular must
-    #      remain local-only to avoid cross-environment ambiguity.
-    # Outcome: explicit local override disables per-project cloud routing.
-    os.environ["BASIC_MEMORY_FORCE_LOCAL"] = "true"
-    os.environ.pop("BASIC_MEMORY_FORCE_CLOUD", None)
-    os.environ["BASIC_MEMORY_EXPLICIT_ROUTING"] = "true"
+    # --- Routing setup ---
+    # Trigger: MCP server command invocation.
+    # Why: HTTP/SSE transports serve as local API endpoints and must never
+    #      route through cloud. Stdio is a client-facing protocol that
+    #      should honor per-project routing (local or cloud).
+    # Outcome: HTTP/SSE get explicit local override; stdio passes through
+    #          whatever env vars are already set (honoring external overrides)
+    #          and defaults to per-project routing resolution.
+    if transport in ("streamable-http", "sse"):
+        os.environ["BASIC_MEMORY_FORCE_LOCAL"] = "true"
+        os.environ.pop("BASIC_MEMORY_FORCE_CLOUD", None)
+        os.environ["BASIC_MEMORY_EXPLICIT_ROUTING"] = "true"
+    # stdio: no env var manipulation — per-project routing applies by default,
+    # and externally-set env vars (e.g. BASIC_MEMORY_FORCE_CLOUD) are honored.
 
     # Import mcp tools/prompts to register them with the server
     import basic_memory.mcp.tools  # noqa: F401  # pragma: no cover
@@ -74,6 +82,22 @@ def mcp(
         os.environ["BASIC_MEMORY_MCP_PROJECT"] = project_name
         logger.info(f"MCP server constrained to project: {project_name}")
 
+    def _run_background_auto_update() -> None:
+        result = run_auto_update(force=False, check_only=False, silent=True)
+        if result.restart_recommended:
+            logger.info(
+                "A newer Basic Memory version was installed and will apply on next restart."
+            )
+        elif result.status == AutoUpdateStatus.FAILED and result.error:
+            logger.warning(f"MCP background auto-update failed: {result.error}")
+
+    # Trigger: stdio transport corresponds to local user installs.
+    # Why: server transports (HTTP/SSE) run in managed environments where
+    # package-manager self-upgrades are inappropriate.
+    # Outcome: background auto-update runs only for local stdio MCP sessions.
+    if transport == "stdio":
+        threading.Thread(target=_run_background_auto_update, daemon=True).start()
+
     # Run the MCP server (blocks)
     # Lifespan handles: initialization, migrations, file sync, cleanup
     logger.info(f"Starting MCP server with {transport.upper()} transport")

src/basic_memory/cli/commands/schema.py

@@ -2,6 +2,10 @@
 
 Provides CLI access to schema validation, inference, and drift detection.
 Registered as a subcommand group: `bm schema validate`, `bm schema infer`, `bm schema diff`.
+
+Each command calls the corresponding MCP tool with output_format="json" and
+renders the result as Rich tables — same code path as `bm tool schema-*` but
+with human-friendly formatting.
 """
 
 import json
@@ -16,8 +20,9 @@ from basic_memory.cli.app import app
 from basic_memory.cli.commands.command_utils import run_with_cleanup
 from basic_memory.cli.commands.routing import force_routing, validate_routing_flags
 from basic_memory.config import ConfigManager
-from basic_memory.mcp.async_client import get_client
-from basic_memory.mcp.project_context import get_active_project
+from basic_memory.mcp.tools import schema_diff as mcp_schema_diff
+from basic_memory.mcp.tools import schema_infer as mcp_schema_infer
+from basic_memory.mcp.tools import schema_validate as mcp_schema_validate
 
 console = Console()
 
@@ -37,77 +42,124 @@ def _resolve_project_name(project: Optional[str]) -> Optional[str]:
     return config_manager.default_project
 
 
-# --- Validate ---
+# --- Rendering helpers ---
 
 
-async def _run_validate(
-    target: Optional[str] = None,
-    project: Optional[str] = None,
-    strict: bool = False,
-):
-    """Run schema validation via the API."""
-    from basic_memory.mcp.clients.schema import SchemaClient
+def _render_validate_table(data: dict) -> None:
+    """Render a validation report dict as a Rich table."""
+    note_type = data.get("note_type")
+    title_label = note_type or "all"
 
-    async with get_client(project_name=project) as client:
-        active_project = await get_active_project(client, project, None)
-        schema_client = SchemaClient(client, active_project.external_id)
+    table = Table(title=f"Schema Validation: {title_label}")
+    table.add_column("Note", style="cyan")
+    table.add_column("Status", justify="center")
+    table.add_column("Warnings", justify="right")
+    table.add_column("Errors", justify="right")
 
-        # Determine if target is a note identifier or note type
-        # Heuristic: if target contains / or ., treat as identifier
-        entity_type = None
-        identifier = None
-        if target:
-            if "/" in target or "." in target:
-                identifier = target
-            else:
-                entity_type = target
+    for result in data.get("results", []):
+        warnings = result.get("warnings", [])
+        errors = result.get("errors", [])
+        passed = result.get("passed", True)
 
-        report = await schema_client.validate(
-            entity_type=entity_type,
-            identifier=identifier,
+        if passed and not warnings:
+            status = "[green]pass[/green]"
+        elif passed:
+            status = "[yellow]warn[/yellow]"
+        else:
+            status = "[red]fail[/red]"
+
+        table.add_row(
+            result.get("note_identifier", ""),
+            status,
+            str(len(warnings)),
+            str(len(errors)),
         )
 
-        # --- Display results ---
-        if report.total_notes == 0:
-            if report.total_entities == 0:
-                console.print(f"[yellow]No notes of type '{entity_type}' found.[/yellow]")
-            else:
-                console.print(
-                    f"[yellow]Found {report.total_entities} notes but no schema "
-                    f"defined for '{entity_type}'.[/yellow]"
-                )
-            return
+    console.print(table)
+    console.print(
+        f"\nSummary: {data.get('valid_count', 0)}/{data.get('total_notes', 0)} valid, "
+        f"{data.get('warning_count', 0)} warnings, {data.get('error_count', 0)} errors"
+    )
 
-        table = Table(title=f"Schema Validation: {entity_type or identifier or 'all'}")
-        table.add_column("Note", style="cyan")
-        table.add_column("Status", justify="center")
-        table.add_column("Warnings", justify="right")
-        table.add_column("Errors", justify="right")
 
-        for result in report.results:
-            if result.passed and not result.warnings:
-                status = "[green]pass[/green]"
-            elif result.passed:
-                status = "[yellow]warn[/yellow]"
-            else:
-                status = "[red]fail[/red]"
+def _render_infer_table(data: dict) -> None:
+    """Render an inference report dict as a Rich table."""
+    note_type = data.get("note_type", "")
+    notes_analyzed = data.get("notes_analyzed", 0)
+    suggested_required = data.get("suggested_required", [])
+    suggested_optional = data.get("suggested_optional", [])
 
-            table.add_row(
-                result.note_identifier,
-                status,
-                str(len(result.warnings)),
-                str(len(result.errors)),
+    console.print(f"\n[bold]Analyzing {notes_analyzed} notes with type: {note_type}...[/bold]\n")
+
+    table = Table(title="Field Frequencies")
+    table.add_column("Field", style="cyan")
+    table.add_column("Source")
+    table.add_column("Count", justify="right")
+    table.add_column("Percentage", justify="right")
+    table.add_column("Suggested")
+
+    for freq in data.get("field_frequencies", []):
+        pct = f"{freq.get('percentage', 0):.0%}"
+        name = freq.get("name", "")
+        if name in suggested_required:
+            suggested = "[green]required[/green]"
+        elif name in suggested_optional:
+            suggested = "[yellow]optional[/yellow]"
+        else:
+            suggested = "[dim]excluded[/dim]"
+
+        table.add_row(
+            name,
+            freq.get("source", ""),
+            str(freq.get("count", 0)),
+            pct,
+            suggested,
+        )
+
+    console.print(table)
+
+    suggested_schema = data.get("suggested_schema", {})
+    if suggested_schema:
+        console.print("\n[bold]Suggested schema:[/bold]")
+        console.print(json.dumps(suggested_schema, indent=2))
+
+
+def _render_diff_output(data: dict) -> None:
+    """Render a drift report dict as Rich output."""
+    note_type = data.get("note_type", "")
+    new_fields = data.get("new_fields", [])
+    dropped_fields = data.get("dropped_fields", [])
+    cardinality_changes = data.get("cardinality_changes", [])
+
+    has_drift = new_fields or dropped_fields or cardinality_changes
+
+    if not has_drift:
+        console.print(f"[green]No drift detected for {note_type} schema.[/green]")
+        return
+
+    console.print(f"\n[bold]Schema drift detected for {note_type}:[/bold]\n")
+
+    if new_fields:
+        console.print("[green]+ New fields (common in notes, not in schema):[/green]")
+        for f in new_fields:
+            console.print(
+                f"  + {f['name']}: {f.get('percentage', 0):.0%} of notes ({f.get('source', '')})"
             )
 
-        console.print(table)
-        console.print(
-            f"\nSummary: {report.valid_count}/{report.total_notes} valid, "
-            f"{report.warning_count} warnings, {report.error_count} errors"
-        )
+    if dropped_fields:
+        console.print("[red]- Dropped fields (in schema, rare in notes):[/red]")
+        for f in dropped_fields:
+            console.print(
+                f"  - {f['name']}: {f.get('percentage', 0):.0%} of notes ({f.get('source', '')})"
+            )
 
-        # Exit with error code in strict mode if there are failures
-        if strict and report.error_count > 0:
-            raise typer.Exit(1)
+    if cardinality_changes:
+        console.print("[yellow]~ Cardinality changes:[/yellow]")
+        for change in cardinality_changes:
+            console.print(f"  ~ {change}")
+
+
+# --- Commands ---
 
 
 @schema_app.command()
@@ -121,6 +173,7 @@ def validate(
         typer.Option(help="The project name."),
     ] = None,
     strict: bool = typer.Option(False, "--strict", help="Exit with error on validation failures"),
+    json_output: bool = typer.Option(False, "--json", help="Output in JSON format"),
     local: bool = typer.Option(
         False, "--local", help="Force local API routing (ignore cloud mode)"
     ),
@@ -131,6 +184,7 @@ def validate(
     TARGET can be a note path (e.g., people/ada-lovelace.md) or a note type
     (e.g., person). If omitted, validates all notes that have schemas.
 
+    Use --json for machine-readable output.
     Use --strict to exit with error code 1 if any validation errors are found.
     Use --local to force local routing when cloud mode is enabled.
     Use --cloud to force cloud routing when cloud mode is disabled.
@@ -138,8 +192,43 @@ def validate(
     try:
         validate_routing_flags(local, cloud)
         project_name = _resolve_project_name(project)
+
+        # Heuristic: if target contains / or ., treat as identifier; otherwise as note type
+        note_type, identifier = None, None
+        if target:
+            if "/" in target or "." in target:
+                identifier = target
+            else:
+                note_type = target
+
         with force_routing(local=local, cloud=cloud):
-            run_with_cleanup(_run_validate(target, project_name, strict))
+            result = run_with_cleanup(
+                mcp_schema_validate(
+                    note_type=note_type,
+                    identifier=identifier,
+                    project=project_name,
+                    output_format="json",
+                )
+            )
+
+        # Handle error responses
+        if isinstance(result, dict) and "error" in result:
+            if json_output:
+                print(json.dumps(result, indent=2, default=str))
+            else:
+                console.print(f"[yellow]{result['error']}[/yellow]")
+            return
+
+        # output_format="json" guarantees a dict return
+        assert isinstance(result, dict)
+
+        if json_output:
+            print(json.dumps(result, indent=2, default=str))
+        else:
+            _render_validate_table(result)
+
+        if strict and result.get("error_count", 0) > 0:
+            raise typer.Exit(1)
     except ValueError as e:
         console.print(f"[red]Error: {e}[/red]")
         raise typer.Exit(1)
@@ -151,94 +240,9 @@ def validate(
         raise
 
 
-# --- Infer ---
-
-
-async def _run_infer(
-    entity_type: str,
-    project: Optional[str] = None,
-    threshold: float = 0.25,
-    save: bool = False,
-):
-    """Run schema inference via the API."""
-    from basic_memory.mcp.clients.schema import SchemaClient
-
-    async with get_client(project_name=project) as client:
-        active_project = await get_active_project(client, project, None)
-        schema_client = SchemaClient(client, active_project.external_id)
-
-        report = await schema_client.infer(entity_type, threshold=threshold)
-
-        if report.notes_analyzed == 0:
-            console.print(f"[yellow]No notes found with type: {entity_type}[/yellow]")
-            return
-
-        # --- Empty schema guard ---
-        # Trigger: notes were analyzed but no fields met the threshold
-        # Why: dumping hundreds of excluded fields is not useful output
-        # Outcome: show count and suggest a more specific type
-        if not report.suggested_schema:
-            console.print(
-                f"\n[yellow]Analyzed {report.notes_analyzed} notes of type '{entity_type}', "
-                f"but no fields met the {threshold:.0%} threshold.[/yellow]\n"
-            )
-            console.print(
-                f"This usually means '{entity_type}' is too broad — "
-                f"the notes don't share a consistent structure.\n"
-            )
-            console.print("[bold]Suggestions:[/bold]")
-            console.print("  1. Use a more specific type")
-            console.print(
-                f"  2. Lower the threshold: bm schema infer {entity_type} --threshold 0.1"
-            )
-            console.print("  3. Create typed notes with write_note using a specific note_type")
-            return
-
-        # --- Display frequency analysis ---
-        console.print(
-            f"\n[bold]Analyzing {report.notes_analyzed} notes with type: {entity_type}...[/bold]\n"
-        )
-
-        table = Table(title="Field Frequencies")
-        table.add_column("Field", style="cyan")
-        table.add_column("Source")
-        table.add_column("Count", justify="right")
-        table.add_column("Percentage", justify="right")
-        table.add_column("Suggested")
-
-        for freq in report.field_frequencies:
-            pct = f"{freq.percentage:.0%}"
-            if freq.name in report.suggested_required:
-                suggested = "[green]required[/green]"
-            elif freq.name in report.suggested_optional:
-                suggested = "[yellow]optional[/yellow]"
-            else:
-                suggested = "[dim]excluded[/dim]"
-
-            table.add_row(
-                freq.name,
-                freq.source,
-                str(freq.count),
-                pct,
-                suggested,
-            )
-
-        console.print(table)
-
-        # --- Display suggested schema ---
-        console.print("\n[bold]Suggested schema:[/bold]")
-        console.print(json.dumps(report.suggested_schema, indent=2))
-
-        if save:
-            console.print(
-                f"\n[yellow]--save not yet implemented. "
-                f"Copy the schema above into schema/{entity_type}.md[/yellow]"
-            )
-
-
 @schema_app.command()
 def infer(
-    entity_type: Annotated[
+    note_type: Annotated[
         str,
         typer.Argument(help="Note type to analyze (e.g., person, meeting)"),
     ],
@@ -250,6 +254,7 @@ def infer(
         0.25, "--threshold", help="Minimum frequency for optional fields (0-1)"
     ),
     save: bool = typer.Option(False, "--save", help="Save inferred schema to schema/ directory"),
+    json_output: bool = typer.Option(False, "--json", help="Output in JSON format"),
     local: bool = typer.Option(
         False, "--local", help="Force local API routing (ignore cloud mode)"
     ),
@@ -263,14 +268,53 @@ def infer(
     Fields present in 95%+ of notes become required. Fields above the
     threshold (default 25%) become optional. Fields below threshold are excluded.
 
+    Use --json for machine-readable output.
     Use --local to force local routing when cloud mode is enabled.
     Use --cloud to force cloud routing when cloud mode is disabled.
     """
     try:
         validate_routing_flags(local, cloud)
         project_name = _resolve_project_name(project)
+
         with force_routing(local=local, cloud=cloud):
-            run_with_cleanup(_run_infer(entity_type, project_name, threshold, save))
+            result = run_with_cleanup(
+                mcp_schema_infer(
+                    note_type=note_type,
+                    threshold=threshold,
+                    project=project_name,
+                    output_format="json",
+                )
+            )
+
+        # Handle error responses
+        if isinstance(result, dict) and "error" in result:
+            if json_output:
+                print(json.dumps(result, indent=2, default=str))
+            else:
+                console.print(f"[yellow]{result['error']}[/yellow]")
+            return
+
+        # output_format="json" guarantees a dict return
+        assert isinstance(result, dict)
+
+        # Handle zero notes
+        if result.get("notes_analyzed", 0) == 0:
+            if json_output:
+                print(json.dumps(result, indent=2, default=str))
+            else:
+                console.print(f"[yellow]No notes found with type: {note_type}[/yellow]")
+            return
+
+        if json_output:
+            print(json.dumps(result, indent=2, default=str))
+        else:
+            _render_infer_table(result)
+
+        if save:
+            console.print(
+                f"\n[yellow]--save not yet implemented. "
+                f"Copy the schema above into schema/{note_type}.md[/yellow]"
+            )
     except ValueError as e:
         console.print(f"[red]Error: {e}[/red]")
         raise typer.Exit(1)
@@ -282,49 +326,9 @@ def infer(
         raise
 
 
-# --- Diff ---
-
-
-async def _run_diff(
-    entity_type: str,
-    project: Optional[str] = None,
-):
-    """Run schema drift detection via the API."""
-    from basic_memory.mcp.clients.schema import SchemaClient
-
-    async with get_client(project_name=project) as client:
-        active_project = await get_active_project(client, project, None)
-        schema_client = SchemaClient(client, active_project.external_id)
-
-        report = await schema_client.diff(entity_type)
-
-        has_drift = report.new_fields or report.dropped_fields or report.cardinality_changes
-
-        if not has_drift:
-            console.print(f"[green]No drift detected for {entity_type} schema.[/green]")
-            return
-
-        console.print(f"\n[bold]Schema drift detected for {entity_type}:[/bold]\n")
-
-        if report.new_fields:
-            console.print("[green]+ New fields (common in notes, not in schema):[/green]")
-            for f in report.new_fields:
-                console.print(f"  + {f.name}: {f.percentage:.0%} of notes ({f.source})")
-
-        if report.dropped_fields:
-            console.print("[red]- Dropped fields (in schema, rare in notes):[/red]")
-            for f in report.dropped_fields:
-                console.print(f"  - {f.name}: {f.percentage:.0%} of notes ({f.source})")
-
-        if report.cardinality_changes:
-            console.print("[yellow]~ Cardinality changes:[/yellow]")
-            for change in report.cardinality_changes:
-                console.print(f"  ~ {change}")
-
-
 @schema_app.command()
 def diff(
-    entity_type: Annotated[
+    note_type: Annotated[
         str,
         typer.Argument(help="Note type to check for drift"),
     ],
@@ -332,6 +336,7 @@ def diff(
         Optional[str],
         typer.Option(help="The project name."),
     ] = None,
+    json_output: bool = typer.Option(False, "--json", help="Output in JSON format"),
     local: bool = typer.Option(
         False, "--local", help="Force local API routing (ignore cloud mode)"
     ),
@@ -343,14 +348,38 @@ def diff(
     are actually structured. Identifies new fields,
     dropped fields, and cardinality changes.
 
+    Use --json for machine-readable output.
     Use --local to force local routing when cloud mode is enabled.
     Use --cloud to force cloud routing when cloud mode is disabled.
     """
     try:
         validate_routing_flags(local, cloud)
         project_name = _resolve_project_name(project)
+
         with force_routing(local=local, cloud=cloud):
-            run_with_cleanup(_run_diff(entity_type, project_name))
+            result = run_with_cleanup(
+                mcp_schema_diff(
+                    note_type=note_type,
+                    project=project_name,
+                    output_format="json",
+                )
+            )
+
+        # Handle error responses
+        if isinstance(result, dict) and "error" in result:
+            if json_output:
+                print(json.dumps(result, indent=2, default=str))
+            else:
+                console.print(f"[yellow]{result['error']}[/yellow]")
+            return
+
+        # output_format="json" guarantees a dict return
+        assert isinstance(result, dict)
+
+        if json_output:
+            print(json.dumps(result, indent=2, default=str))
+        else:
+            _render_diff_output(result)
     except ValueError as e:
         console.print(f"[red]Error: {e}[/red]")
         raise typer.Exit(1)

src/basic_memory/cli/commands/status.py

@@ -1,5 +1,6 @@
 """Status command for basic-memory CLI."""
 
+import json
 from typing import Set, Dict
 from typing import Annotated, Optional
 
@@ -14,7 +15,7 @@ from basic_memory.cli.app import app
 from basic_memory.cli.commands.routing import force_routing, validate_routing_flags
 from basic_memory.config import ConfigManager
 from basic_memory.mcp.async_client import get_client
-from basic_memory.mcp.tools.utils import call_post
+from basic_memory.mcp.clients import ProjectClient
 from basic_memory.schemas import SyncReportResponse
 from basic_memory.mcp.project_context import get_active_project
 
@@ -141,22 +142,20 @@ def display_changes(
     console.print(Panel(tree, expand=False))
 
 
-async def run_status(project: Optional[str] = None, verbose: bool = False):  # pragma: no cover
-    """Check sync status of files vs database."""
+async def run_status(
+    project: Optional[str] = None,
+) -> tuple[str, SyncReportResponse]:
+    """Fetch sync status of files vs database.
+
+    Returns (project_name, sync_report) for the caller to render.
+    """
     # Resolve default project so get_client() can route per-project
     project = project or ConfigManager().default_project
 
-    try:
-        async with get_client(project_name=project) as client:
-            project_item = await get_active_project(client, project, None)
-            response = await call_post(client, f"/v2/projects/{project_item.external_id}/status")
-            sync_report = SyncReportResponse.model_validate(response.json())
-
-            display_changes(project_item.name, "Status", sync_report, verbose)
-
-    except (ValueError, ToolError) as e:
-        console.print(f"[red]Error: {e}[/red]")
-        raise typer.Exit(1)
+    async with get_client(project_name=project) as client:
+        project_item = await get_active_project(client, project, None)
+        sync_report = await ProjectClient(client).get_status(project_item.external_id)
+        return project_item.name, sync_report
 
 
 @app.command()
@@ -166,6 +165,7 @@ def status(
         typer.Option(help="The project name."),
     ] = None,
     verbose: bool = typer.Option(False, "--verbose", "-v", help="Show detailed file information"),
+    json_output: bool = typer.Option(False, "--json", help="Output in JSON format"),
     local: bool = typer.Option(
         False, "--local", help="Force local API routing (ignore cloud mode)"
     ),
@@ -173,6 +173,7 @@ def status(
 ):
     """Show sync status between files and database.
 
+    Use --json for machine-readable output.
     Use --local to force local routing when cloud mode is enabled.
     Use --cloud to force cloud routing when cloud mode is disabled.
     """
@@ -180,12 +181,32 @@ def status(
 
     try:
         validate_routing_flags(local, cloud)
+        # Trigger: no explicit routing flag provided
+        # Why: status scans the local filesystem — cloud routing would use the
+        #      Docker-internal path stored in the cloud database, which doesn't
+        #      exist locally.
+        # Outcome: default to local routing unless --cloud was explicitly requested.
+        if not local and not cloud:
+            local = True
         with force_routing(local=local, cloud=cloud):
-            run_with_cleanup(run_status(project, verbose))  # pragma: no cover
-    except ValueError as e:
-        console.print(f"[red]Error: {e}[/red]")
+            project_name, sync_report = run_with_cleanup(run_status(project))
+
+        if json_output:
+            print(json.dumps(sync_report.model_dump(mode="json"), indent=2, default=str))
+        else:
+            display_changes(project_name, "Status", sync_report, verbose)
+    except (ValueError, ToolError) as e:
+        if json_output:
+            print(json.dumps({"error": str(e)}, indent=2))
+        else:
+            console.print(f"[red]Error: {e}[/red]")
         raise typer.Exit(code=1)
+    except typer.Exit:
+        raise
     except Exception as e:
         logger.error(f"Error checking status: {e}")
-        typer.echo(f"Error checking status: {e}", err=True)
+        if json_output:
+            print(json.dumps({"error": str(e)}, indent=2))
+        else:
+            typer.echo(f"Error checking status: {e}", err=True)
         raise typer.Exit(code=1)  # pragma: no cover

src/basic_memory/cli/commands/update.py

@@ -0,0 +1,40 @@
+"""Manual update command for Basic Memory CLI."""
+
+import typer
+from rich.console import Console
+
+from basic_memory.cli.app import app
+from basic_memory.cli.auto_update import AutoUpdateStatus, run_auto_update
+
+console = Console()
+
+
+@app.command("update")
+def update(
+    check: bool = typer.Option(
+        False,
+        "--check",
+        help="Check for updates only (do not install).",
+    ),
+) -> None:
+    """Check for updates and install when supported."""
+    result = run_auto_update(force=True, check_only=check, silent=False)
+
+    if result.status == AutoUpdateStatus.FAILED:
+        detail = f" {result.error}" if result.error else ""
+        console.print(f"[red]{result.message or 'Update failed.'}{detail}[/red]")
+        raise typer.Exit(1)
+
+    if result.status == AutoUpdateStatus.UPDATED:
+        console.print(f"[green]{result.message or 'Basic Memory updated successfully.'}[/green]")
+        return
+
+    if result.status == AutoUpdateStatus.UP_TO_DATE:
+        console.print(f"[green]{result.message or 'Basic Memory is up to date.'}[/green]")
+        return
+
+    if result.status == AutoUpdateStatus.UPDATE_AVAILABLE:
+        console.print(f"[cyan]{result.message or 'Update available.'}[/cyan]")
+        return
+
+    console.print(f"[dim]{result.message or 'No update action was performed.'}[/dim]")

src/basic_memory/cli/commands/watch.py

@@ -1,97 +0,0 @@
-"""Watch command - run file watcher as a standalone long-running process."""
-
-import asyncio
-import os
-import signal
-import sys
-from typing import Optional
-
-import typer
-from loguru import logger
-
-from basic_memory import db
-from basic_memory.cli.app import app
-from basic_memory.cli.container import get_container
-from basic_memory.config import ConfigManager
-from basic_memory.services.initialization import initialize_app
-from basic_memory.sync.coordinator import SyncCoordinator
-
-
-async def run_watch(project: Optional[str] = None) -> None:
-    """Run the file watcher as a long-running process.
-
-    This is the async core of the watch command. It:
-    1. Initializes the app (DB migrations + project reconciliation)
-    2. Validates and sets project constraint if --project given
-    3. Creates a SyncCoordinator with quiet=False for Rich console output
-    4. Blocks until SIGINT/SIGTERM, then shuts down cleanly
-    """
-    container = get_container()
-    config = container.config
-
-    # --- Initialization ---
-    # Wrapped in try/finally so DB resources are cleaned up on all exit paths,
-    # including early exits from invalid --project names.
-    await initialize_app(config)
-    sync_coordinator = None
-
-    try:
-        # --- Project constraint ---
-        if project:
-            config_manager = ConfigManager()
-            project_name, _ = config_manager.get_project(project)
-            if not project_name:
-                typer.echo(f"No project found named: {project}", err=True)
-                raise typer.Exit(1)
-
-            os.environ["BASIC_MEMORY_MCP_PROJECT"] = project_name
-            logger.info(f"Watch constrained to project: {project_name}")
-
-        # --- Sync coordinator ---
-        # quiet=False so file change events are printed to the terminal
-        sync_coordinator = SyncCoordinator(config=config, should_sync=True, quiet=False)
-
-        # --- Signal handling ---
-        shutdown_event = asyncio.Event()
-
-        def _signal_handler() -> None:
-            logger.info("Shutdown signal received")
-            shutdown_event.set()
-
-        loop = asyncio.get_running_loop()
-
-        # Windows ProactorEventLoop does not support add_signal_handler;
-        # fall back to the stdlib signal module which works cross-platform.
-        try:
-            for sig in (signal.SIGINT, signal.SIGTERM):
-                loop.add_signal_handler(sig, _signal_handler)
-        except NotImplementedError:
-            for sig in (signal.SIGINT, signal.SIGTERM):
-                signal.signal(sig, lambda _signum, _frame: _signal_handler())
-
-        # --- Run ---
-        await sync_coordinator.start()
-        logger.info("Watch service running, press Ctrl+C to stop")
-        await shutdown_event.wait()
-    finally:
-        if sync_coordinator is not None:
-            await sync_coordinator.stop()
-        await db.shutdown_db()
-        logger.info("Watch service stopped")
-
-
-@app.command()
-def watch(
-    project: Optional[str] = typer.Option(None, help="Restrict watcher to a single project"),
-) -> None:
-    """Run file watcher as a long-running process (no MCP server).
-
-    Watches for file changes in project directories and syncs them to the
-    database. Useful for running Basic Memory sync alongside external tools
-    that don't use the MCP server.
-    """
-    # On Windows, use SelectorEventLoop to avoid ProactorEventLoop cleanup issues
-    if sys.platform == "win32":  # pragma: no cover
-        asyncio.set_event_loop_policy(asyncio.WindowsSelectorEventLoopPolicy())
-
-    asyncio.run(run_watch(project=project))

src/basic_memory/cli/commands/workspace.py

@@ -1,57 +0,0 @@
-"""Workspace commands for Basic Memory cloud workspaces."""
-
-import typer
-from rich.console import Console
-from rich.table import Table
-
-from basic_memory.cli.app import app
-from basic_memory.cli.commands.command_utils import run_with_cleanup
-from basic_memory.mcp.project_context import get_available_workspaces
-
-console = Console()
-
-workspace_app = typer.Typer(help="Manage cloud workspaces")
-app.add_typer(workspace_app, name="workspace")
-
-
-@workspace_app.command("list")
-def list_workspaces() -> None:
-    """List cloud workspaces available to the current OAuth session."""
-
-    async def _list():
-        return await get_available_workspaces()
-
-    try:
-        workspaces = run_with_cleanup(_list())
-    except RuntimeError as exc:
-        console.print(f"[red]Error: {exc}[/red]")
-        raise typer.Exit(1)
-    except Exception as exc:  # pragma: no cover
-        console.print(f"[red]Error listing workspaces: {exc}[/red]")
-        raise typer.Exit(1)
-
-    if not workspaces:
-        console.print("[yellow]No accessible workspaces found.[/yellow]")
-        return
-
-    table = Table(title="Available Workspaces")
-    table.add_column("Name", style="cyan")
-    table.add_column("Type", style="blue")
-    table.add_column("Role", style="green")
-    table.add_column("Tenant ID", style="yellow")
-
-    for workspace in workspaces:
-        table.add_row(
-            workspace.name,
-            workspace.workspace_type,
-            workspace.role,
-            workspace.tenant_id,
-        )
-
-    console.print(table)
-
-
-@app.command("workspaces")
-def workspaces_alias() -> None:
-    """Alias for `bm workspace list`."""
-    list_workspaces()

src/basic_memory/cli/main.py

@@ -28,7 +28,7 @@ if not _version_only_invocation(sys.argv[1:]):
         schema,
         status,
         tool,
-        workspace,
+        update,
     )
 
 warnings.filterwarnings("ignore")  # pragma: no cover

src/basic_memory/cli/promo.py

@@ -7,10 +7,13 @@ from rich.console import Console
 from rich.panel import Panel
 
 import basic_memory
+from basic_memory.cli.analytics import track, EVENT_PROMO_SHOWN
 from basic_memory.config import ConfigManager
 
 OSS_DISCOUNT_CODE = "BMFOSS"
-CLOUD_LEARN_MORE_URL = "https://basicmemory.com"
+CLOUD_LEARN_MORE_URL = (
+    "https://basicmemory.com?utm_source=bm-foss&utm_medium=promo&utm_campaign=cloud-upsell"
+)
 
 
 def _promos_disabled_by_env() -> bool:
@@ -21,7 +24,13 @@ def _promos_disabled_by_env() -> bool:
 
 def _is_interactive_session() -> bool:
     """Return whether stdin/stdout are interactive terminals."""
-    return sys.stdin.isatty() and sys.stdout.isatty()
+    try:
+        return sys.stdin.isatty() and sys.stdout.isatty()
+    except ValueError:
+        # Trigger: stdin/stdout already closed (e.g., MCP stdio transport shutdown)
+        # Why: isatty() raises ValueError on closed file descriptors
+        # Outcome: treat as non-interactive, suppressing promo output
+        return False
 
 
 def _build_cloud_promo_message() -> str:
@@ -113,6 +122,9 @@ def maybe_show_cloud_promo(
     out.print(f"Learn more at [link={CLOUD_LEARN_MORE_URL}]{CLOUD_LEARN_MORE_URL}[/link]")
     out.print("[dim]Disable with: bm cloud promo --off[/dim]")
 
+    trigger = "first_run" if show_first_run else "version_bump"
+    track(EVENT_PROMO_SHOWN, {"trigger": trigger})
+
     config.cloud_promo_first_run_shown = True
     config.cloud_promo_last_version_shown = basic_memory.__version__
     manager.save_config(config)

src/basic_memory/config.py

@@ -3,16 +3,19 @@
 import importlib.util
 import json
 import os
+import shutil
 from dataclasses import dataclass
 from datetime import datetime
-from pathlib import Path
-from typing import Any, Dict, Literal, Optional, List, Tuple
 from enum import Enum
+from pathlib import Path
+from typing import TYPE_CHECKING, Any, Dict, Literal, Optional, List, Tuple
 
 from loguru import logger
-from pydantic import BaseModel, Field, model_validator
+from pydantic import AliasChoices, BaseModel, Field, model_validator
 from pydantic_settings import BaseSettings, SettingsConfigDict
 
+from basic_memory import __version__
+from basic_memory.telemetry import configure_telemetry
 from basic_memory.utils import setup_logging, generate_permalink
 
 
@@ -40,8 +43,49 @@ class DatabaseBackend(str, Enum):
 
 
 def _default_semantic_search_enabled() -> bool:
-    """Enable semantic search by default when semantic extras are installed."""
-    return importlib.util.find_spec("fastembed") is not None
+    """Enable semantic search by default when required local semantic dependencies exist."""
+    required_modules = ("fastembed", "sqlite_vec")
+    return all(
+        importlib.util.find_spec(module_name) is not None for module_name in required_modules
+    )
+
+
+def resolve_data_dir() -> Path:
+    """Resolve the Basic Memory data directory.
+
+    Single source of truth for the per-user state directory. Honors
+    ``BASIC_MEMORY_CONFIG_DIR`` so each process/worktree can isolate config
+    and database state; otherwise falls back to ``<user home>/.basic-memory``.
+
+    Cross-platform: ``Path.home()`` reads ``$HOME`` on POSIX and
+    ``%USERPROFILE%`` on Windows, so there's no need to check ``$HOME``
+    explicitly here.
+    """
+    if config_dir := os.getenv("BASIC_MEMORY_CONFIG_DIR"):
+        return Path(config_dir)
+    return Path.home() / DATA_DIR_NAME
+
+
+def default_fastembed_cache_dir() -> str:
+    """Return the default cache directory used for FastEmbed model artifacts.
+
+    Resolution order:
+      1. ``FASTEMBED_CACHE_PATH`` env var — honors FastEmbed's own convention
+         so users who already configure it through the environment keep working.
+      2. ``<basic-memory data dir>/fastembed_cache`` — the same stable,
+         user-writable directory Basic Memory already uses for config and
+         the default SQLite database. Honors ``BASIC_MEMORY_CONFIG_DIR``.
+
+    Why not ``tempfile.gettempdir()``?
+      FastEmbed's own default is ``<system tmp>/fastembed_cache``, which is
+      ephemeral in many sandboxed MCP runtimes (e.g. Codex CLI wipes /tmp
+      between invocations). The model then disappears and every subsequent
+      ONNX load raises ``NO_SUCHFILE``. Persisting the cache under the
+      per-user data directory works identically on macOS, Linux, and Windows.
+    """
+    if env_override := os.getenv("FASTEMBED_CACHE_PATH"):
+        return env_override
+    return str(resolve_data_dir() / "fastembed_cache")
 
 
 @dataclass
@@ -93,10 +137,15 @@ class ProjectEntry(BaseModel):
         default=ProjectMode.LOCAL,
         description="Routing mode: local (in-process ASGI) or cloud (remote API)",
     )
-    # Cloud sync state (replaces CloudProjectConfig)
-    cloud_sync_path: Optional[str] = Field(
+    workspace_id: Optional[str] = Field(
         default=None,
-        description="Local working directory for bisync (formerly CloudProjectConfig.local_path)",
+        description="Cloud workspace tenant_id. Set by 'bm project set-cloud --workspace'.",
+    )
+    # Cloud sync state (replaces CloudProjectConfig)
+    local_sync_path: Optional[str] = Field(
+        default=None,
+        description="Local working directory for bisync",
+        validation_alias=AliasChoices("local_sync_path", "cloud_sync_path"),
     )
     bisync_initialized: bool = Field(
         default=False,
@@ -111,6 +160,11 @@ class ProjectEntry(BaseModel):
 class BasicMemoryConfig(BaseSettings):
     """Pydantic model for Basic Memory global configuration."""
 
+    if TYPE_CHECKING:
+        # Pydantic accepts raw constructor data and validates/coerces it at runtime.
+        # Model attributes remain strongly typed after initialization.
+        def __init__(self, **data: Any) -> None: ...
+
     env: Environment = Field(default="dev", description="Environment name")
 
     projects: Dict[str, ProjectEntry] = Field(
@@ -124,13 +178,31 @@ class BasicMemoryConfig(BaseSettings):
         description="Mapping of project names to their ProjectEntry configuration",
     )
     default_project: Optional[str] = Field(
-        default="main",
+        default=None,
         description="Name of the default project to use. When set, acts as fallback when no project parameter is specified. Set to null to disable automatic project resolution.",
     )
 
     # overridden by ~/.basic-memory/config.json
     log_level: str = "INFO"
 
+    # Optional Logfire telemetry (disabled by default)
+    logfire_enabled: bool = Field(
+        default=False,
+        description="Enable Logfire instrumentation for local development or managed deployments.",
+    )
+    logfire_send_to_logfire: bool = Field(
+        default=False,
+        description="When true, allow Logfire to export telemetry to the configured backend.",
+    )
+    logfire_service_name: str = Field(
+        default="basic-memory",
+        description="Base service name used when constructing entrypoint-specific Logfire service names.",
+    )
+    logfire_environment: str | None = Field(
+        default=None,
+        description="Optional override for Logfire environment. Defaults to env when unset.",
+    )
+
     # Database configuration
     database_backend: DatabaseBackend = Field(
         default=DatabaseBackend.SQLITE,
@@ -145,7 +217,7 @@ class BasicMemoryConfig(BaseSettings):
     # Semantic search configuration
     semantic_search_enabled: bool = Field(
         default_factory=_default_semantic_search_enabled,
-        description="Enable semantic search (vector/hybrid retrieval). Works on both SQLite and Postgres backends. Requires semantic extras.",
+        description="Enable semantic search (vector/hybrid retrieval). Works on both SQLite and Postgres backends. Requires semantic dependencies (included by default).",
     )
     semantic_embedding_provider: str = Field(
         default="fastembed",
@@ -159,11 +231,53 @@ class BasicMemoryConfig(BaseSettings):
         default=None,
         description="Embedding vector dimensions. Auto-detected from provider if not set (384 for FastEmbed, 1536 for OpenAI).",
     )
+    # Trigger: full local rebuilds spend most of their time waiting behind shared
+    # embed flushes, not constructing vectors themselves.
+    # Why: smaller FastEmbed batches cut queue wait far more than they increase
+    # write overhead on real-world projects, which makes full reindex materially faster.
+    # Outcome: default to the smaller local/cloud-safe batch size we benchmarked as
+    # the current best end-to-end setting in the shared vector sync pipeline.
     semantic_embedding_batch_size: int = Field(
-        default=64,
+        default=2,
         description="Batch size for embedding generation.",
         gt=0,
     )
+    semantic_embedding_request_concurrency: int = Field(
+        default=4,
+        description="Maximum number of concurrent provider requests for batched embedding generation when the active provider supports request-level concurrency.",
+        gt=0,
+    )
+    semantic_embedding_sync_batch_size: int = Field(
+        default=2,
+        description="Batch size for vector sync orchestration flushes.",
+        gt=0,
+    )
+    semantic_postgres_prepare_concurrency: int = Field(
+        default=4,
+        description="Number of Postgres entity prepare tasks to run concurrently during vector sync. Postgres only; keep this low to avoid overdriving the database connection pool.",
+        gt=0,
+        le=16,
+    )
+    semantic_embedding_cache_dir: str | None = Field(
+        default=None,
+        description=(
+            "Optional override for the FastEmbed model cache directory. "
+            "When unset, Basic Memory resolves this at runtime to "
+            "<basic-memory data dir>/fastembed_cache (or FASTEMBED_CACHE_PATH "
+            "when that env var is set) so the model persists across runs "
+            "without hardcoding a path into config.json."
+        ),
+    )
+    semantic_embedding_threads: int | None = Field(
+        default=None,
+        description="Optional FastEmbed runtime thread count override.",
+        gt=0,
+    )
+    semantic_embedding_parallel: int | None = Field(
+        default=None,
+        description="Optional FastEmbed embed() parallelism override.",
+        gt=0,
+    )
     semantic_vector_k: int = Field(
         default=100,
         description="Vector candidate count for vector and hybrid retrieval.",
@@ -175,6 +289,12 @@ class BasicMemoryConfig(BaseSettings):
         ge=0.0,
         le=1.0,
     )
+    default_search_type: Literal["text", "vector", "hybrid"] | None = Field(
+        default=None,
+        description="Default search type for search_notes when not specified per-query. "
+        "Valid values: text, vector, hybrid. "
+        "When unset, defaults to 'hybrid' if semantic search is enabled, otherwise 'text'.",
+    )
 
     # Database connection pool configuration (Postgres only)
     db_pool_size: int = Field(
@@ -226,6 +346,31 @@ class BasicMemoryConfig(BaseSettings):
         description="Maximum number of files to process concurrently during sync. Limits memory usage on large projects (2000+ files). Lower values reduce memory consumption.",
         gt=0,
     )
+    index_batch_size: int = Field(
+        default=32,
+        description="Maximum number of changed files to load into one indexing batch.",
+        gt=0,
+    )
+    index_batch_max_bytes: int = Field(
+        default=8 * 1024 * 1024,
+        description="Maximum total bytes to load into one indexing batch. Large files still run as single-file batches.",
+        gt=0,
+    )
+    index_parse_max_concurrent: int = Field(
+        default=8,
+        description="Maximum number of markdown parse tasks to run concurrently inside one indexing batch.",
+        gt=0,
+    )
+    index_entity_max_concurrent: int = Field(
+        default=4,
+        description="Maximum number of entity create/update tasks to run concurrently inside one indexing batch.",
+        gt=0,
+    )
+    index_metadata_update_max_concurrent: int = Field(
+        default=4,
+        description="Maximum number of metadata/search refresh tasks to run concurrently inside one indexing batch.",
+        gt=0,
+    )
 
     kebab_filenames: bool = Field(
         default=False,
@@ -237,8 +382,18 @@ class BasicMemoryConfig(BaseSettings):
         description="Disable automatic permalink generation in frontmatter. When enabled, new notes won't have permalinks added and sync won't update permalinks. Existing permalinks will still work for reading.",
     )
 
-    ensure_frontmatter_on_sync: bool = Field(
+    write_note_overwrite_default: bool = Field(
         default=False,
+        description=(
+            "Default value for write_note's overwrite parameter. "
+            "When False (default), write_note errors if note already exists. "
+            "Set to True to restore pre-v0.20 upsert behavior. "
+            "Env: BASIC_MEMORY_WRITE_NOTE_OVERWRITE_DEFAULT"
+        ),
+    )
+
+    ensure_frontmatter_on_sync: bool = Field(
+        default=True,
         description="Ensure markdown files have frontmatter during sync by adding derived title/type/permalink when missing. When combined with disable_permalinks=True, this setting takes precedence for missing-frontmatter files and still writes permalinks.",
     )
 
@@ -313,11 +468,32 @@ class BasicMemoryConfig(BaseSettings):
         description="Most recent cloud promo version shown in CLI.",
     )
 
+    auto_update: bool = Field(
+        default=True,
+        description="Enable automatic CLI update checks and installs when supported.",
+    )
+
+    update_check_interval: int = Field(
+        default=86400,
+        description="Seconds between automatic update checks.",
+        gt=0,
+    )
+
+    auto_update_last_checked_at: Optional[datetime] = Field(
+        default=None,
+        description="Timestamp of the last attempted automatic update check.",
+    )
+
     cloud_api_key: Optional[str] = Field(
         default=None,
         description="API key for cloud access (bmc_ prefixed). Account-level, not per-project.",
     )
 
+    default_workspace: Optional[str] = Field(
+        default=None,
+        description="Default cloud workspace tenant_id. Set by 'bm cloud workspace set-default'.",
+    )
+
     @model_validator(mode="before")
     @classmethod
     def migrate_legacy_projects(cls, data: Any) -> Any:
@@ -359,26 +535,27 @@ class BasicMemoryConfig(BaseSettings):
                 if name in cloud_projects:
                     cp = cloud_projects[name]
                     if isinstance(cp, dict):
-                        entry["cloud_sync_path"] = cp.get("local_path")
+                        entry["local_sync_path"] = cp.get("local_path")
                         entry["bisync_initialized"] = cp.get("bisync_initialized", False)
                         entry["last_sync"] = cp.get("last_sync")
                     else:
                         # Already a CloudProjectConfig-like object
-                        entry["cloud_sync_path"] = getattr(cp, "local_path", None)
+                        entry["local_sync_path"] = getattr(cp, "local_path", None)
                         entry["bisync_initialized"] = getattr(cp, "bisync_initialized", False)
                         entry["last_sync"] = getattr(cp, "last_sync", None)
                 new_projects[name] = entry
 
             # Pick up cloud_projects entries not already in projects
-            # These are cloud-only projects — path is the cloud permalink,
-            # local_path goes into cloud_sync_path for bisync
+            # These are cloud-only projects — path should be the local working
+            # directory (if one exists), local_path goes into local_sync_path for bisync
             for name, cp in cloud_projects.items():
                 if name not in new_projects:
                     if isinstance(cp, dict):
+                        local_path = cp.get("local_path", "")
                         new_projects[name] = {
-                            "path": generate_permalink(name),
+                            "path": local_path or "",
                             "mode": project_modes.get(name, "cloud"),
-                            "cloud_sync_path": cp.get("local_path"),
+                            "local_sync_path": local_path,
                             "bisync_initialized": cp.get("bisync_initialized", False),
                             "last_sync": cp.get("last_sync"),
                         }
@@ -389,6 +566,18 @@ class BasicMemoryConfig(BaseSettings):
             data.pop("project_modes", None)
             data.pop("cloud_projects", None)
 
+        # --- Promote local_sync_path into path for cloud projects with slug paths ---
+        # Trigger: project entry has local_sync_path set but path is a cloud slug (not absolute)
+        # Why: path must always be the local filesystem path; the cloud remote is derivable
+        # Outcome: path becomes the local directory, local_sync_path kept for backwards compat
+        projects = data.get("projects", {})
+        for name, entry in projects.items():
+            if isinstance(entry, dict):
+                lsp = entry.get("local_sync_path")
+                path = entry.get("path", "")
+                if lsp and not os.path.isabs(path):
+                    entry["path"] = lsp
+
         return data
 
     @property
@@ -411,10 +600,12 @@ class BasicMemoryConfig(BaseSettings):
     def get_project_mode(self, project_name: str) -> ProjectMode:
         """Get the routing mode for a project.
 
-        Returns the per-project mode if set, otherwise LOCAL.
+        Returns the per-project mode if set.
+        Unknown projects (not in local config) default to CLOUD —
+        local projects are always registered in config.
         """
         entry = self.projects.get(project_name)
-        return entry.mode if entry else ProjectMode.LOCAL
+        return entry.mode if entry else ProjectMode.CLOUD
 
     def set_project_mode(self, project_name: str, mode: ProjectMode) -> None:
         """Set the routing mode for a project.
@@ -477,18 +668,25 @@ class BasicMemoryConfig(BaseSettings):
         if self.database_backend == DatabaseBackend.POSTGRES:  # pragma: no cover
             return  # pragma: no cover
 
-        # Ensure at least one project exists; if none exist then create main
-        if not self.projects:  # pragma: no cover
+        # Trigger: no projects configured (fresh install or empty config)
+        # Why: every config needs at least one project to be functional
+        # Outcome: creates "main" project using BASIC_MEMORY_HOME or ~/basic-memory
+        if not self.projects:
             self.projects["main"] = ProjectEntry(
                 path=str(Path(os.getenv("BASIC_MEMORY_HOME", Path.home() / "basic-memory")))
             )
 
-        # Ensure default project is valid (i.e. points to an existing project)
-        # None means "no default" — intentionally left unset
-        if (
-            self.default_project is not None and self.default_project not in self.projects
-        ):  # pragma: no cover
-            # Set default to first available project
+        # Trigger: default_project was not explicitly provided in the input data
+        #          (config file omitted the key, or BasicMemoryConfig() called with no args)
+        # Why: callers like get_project_config() expect a valid project name;
+        #      but explicit None (discovery mode) must be preserved
+        # Outcome: sets default_project to the first available project
+        if "default_project" not in self.model_fields_set:
+            self.default_project = next(iter(self.projects.keys()))
+        # Trigger: default_project was explicitly set but references a non-existent project
+        # Why: project may have been removed or renamed since config was saved
+        # Outcome: corrects to the first available project
+        elif self.default_project is not None and self.default_project not in self.projects:
             self.default_project = next(iter(self.projects.keys()))
 
     @property
@@ -541,6 +739,9 @@ class BasicMemoryConfig(BaseSettings):
 
         for name, entry in self.projects.items():
             path = Path(entry.path)
+            # Skip cloud-only projects whose path is a slug, not a local directory
+            if not path.is_absolute():
+                continue
             if not path.exists():
                 try:
                     path.mkdir(parents=True)
@@ -552,15 +753,17 @@ class BasicMemoryConfig(BaseSettings):
     @property
     def data_dir_path(self) -> Path:
         """Get app state directory for config and default SQLite database."""
-        if config_dir := os.getenv("BASIC_MEMORY_CONFIG_DIR"):
-            return Path(config_dir)
-
-        home = os.getenv("HOME", Path.home())
-        return Path(home) / DATA_DIR_NAME
+        return resolve_data_dir()
 
 
 # Module-level cache for configuration
 _CONFIG_CACHE: Optional[BasicMemoryConfig] = None
+# Track config file mtime+size so cross-process changes (e.g. `bm project set-cloud`
+# in a separate terminal) invalidate the cache in long-lived processes like the
+# MCP stdio server. Using both mtime and size guards against coarse-granularity
+# filesystems where two writes within the same second share the same mtime.
+_CONFIG_MTIME: Optional[float] = None
+_CONFIG_SIZE: Optional[int] = None
 
 
 class ConfigManager:
@@ -568,16 +771,7 @@ class ConfigManager:
 
     def __init__(self) -> None:
         """Initialize the configuration manager."""
-        home = os.getenv("HOME", Path.home())
-        if isinstance(home, str):
-            home = Path(home)
-
-        # Allow override via environment variable
-        if config_dir := os.getenv("BASIC_MEMORY_CONFIG_DIR"):
-            self.config_dir = Path(config_dir)
-        else:
-            self.config_dir = home / DATA_DIR_NAME
-
+        self.config_dir = resolve_data_dir()
         self.config_file = self.config_dir / CONFIG_FILE_NAME
 
         # Ensure config directory exists
@@ -594,13 +788,38 @@ class ConfigManager:
         Environment variables take precedence over file config values,
         following Pydantic Settings best practices.
 
-        Uses module-level cache for performance across ConfigManager instances.
+        Uses module-level cache with file mtime validation so that
+        cross-process config changes (e.g. `bm project set-cloud` in a
+        separate terminal) are picked up by long-lived processes like
+        the MCP stdio server.
         """
-        global _CONFIG_CACHE
+        global _CONFIG_CACHE, _CONFIG_MTIME, _CONFIG_SIZE
 
-        # Return cached config if available
+        # Trigger: cached config exists but the on-disk file may have been
+        # modified by another process (CLI command in a different terminal).
+        # Why: the MCP server is long-lived; without this check it would
+        # serve stale project routing forever.
+        # Outcome: cheap os.stat() per access; re-read only when mtime or size differs.
         if _CONFIG_CACHE is not None:
-            return _CONFIG_CACHE
+            try:
+                st = self.config_file.stat()
+                current_mtime = st.st_mtime
+                current_size = st.st_size
+            except OSError:
+                current_mtime = None
+                current_size = None
+
+            if (
+                current_mtime is not None
+                and current_mtime == _CONFIG_MTIME
+                and current_size == _CONFIG_SIZE
+            ):
+                return _CONFIG_CACHE
+
+            # mtime/size changed or file gone — invalidate and fall through to re-read
+            _CONFIG_CACHE = None
+            _CONFIG_MTIME = None
+            _CONFIG_SIZE = None
 
         if self.config_file.exists():
             try:
@@ -622,6 +841,17 @@ class ConfigManager:
                     if isinstance(first_val, str):
                         needs_resave = True
 
+                # Check if any project has local_sync_path set but path is a cloud slug
+                # (will be migrated by migrate_legacy_projects validator)
+                if not needs_resave:
+                    for entry_data in projects_raw.values():
+                        if isinstance(entry_data, dict):
+                            lsp = entry_data.get("local_sync_path")
+                            p = entry_data.get("path", "")
+                            if lsp and not os.path.isabs(p):
+                                needs_resave = True
+                                break
+
                 # First, create config from environment variables (Pydantic will read them)
                 # Then overlay with file data for fields that aren't set via env vars
                 # This ensures env vars take precedence
@@ -644,15 +874,38 @@ class ConfigManager:
 
                 _CONFIG_CACHE = BasicMemoryConfig(**merged_data)
 
+                # Record mtime+size so subsequent calls detect cross-process changes
+                try:
+                    st = self.config_file.stat()
+                    _CONFIG_MTIME = st.st_mtime
+                    _CONFIG_SIZE = st.st_size
+                except OSError:
+                    _CONFIG_MTIME = None
+                    _CONFIG_SIZE = None
+
                 # Re-save to normalize legacy config into current format
                 if needs_resave:
-                    logger.info("Migrating config to current format")
+                    # Create backup before overwriting so users can revert if needed
+                    backup_path = self.config_file.with_suffix(".json.bak")
+                    shutil.copy2(self.config_file, backup_path)
+                    logger.info(f"Migrating config to current format (backup: {backup_path})")
                     save_basic_memory_config(self.config_file, _CONFIG_CACHE)
 
                 return _CONFIG_CACHE
+            except json.JSONDecodeError as e:  # pragma: no cover
+                logger.error(f"Invalid JSON in config file {self.config_file}: {e}")
+                raise SystemExit(
+                    f"Error: config file is not valid JSON: {self.config_file}\n"
+                    f"  {e}\n"
+                    f"Fix or delete the file and re-run."
+                )
             except Exception as e:  # pragma: no cover
-                logger.exception(f"Failed to load config: {e}")
-                raise e
+                logger.error(f"Failed to load config from {self.config_file}: {e}")
+                raise SystemExit(
+                    f"Error: failed to load config from {self.config_file}\n"
+                    f"  {e}\n"
+                    f"Fix or delete the file and re-run."
+                )
         else:
             config = BasicMemoryConfig()
             self.save_config(config)
@@ -660,10 +913,12 @@ class ConfigManager:
 
     def save_config(self, config: BasicMemoryConfig) -> None:
         """Save configuration to file and invalidate cache."""
-        global _CONFIG_CACHE
+        global _CONFIG_CACHE, _CONFIG_MTIME, _CONFIG_SIZE
         save_basic_memory_config(self.config_file, config)
         # Invalidate cache so next load_config() reads fresh data
         _CONFIG_CACHE = None
+        _CONFIG_MTIME = None
+        _CONFIG_SIZE = None
 
     @property
     def projects(self) -> Dict[str, str]:
@@ -685,11 +940,8 @@ class ConfigManager:
         if project_name:  # pragma: no cover
             raise ValueError(f"Project '{name}' already exists")
 
-        # Ensure the path exists
-        project_path = Path(path)
-        project_path.mkdir(parents=True, exist_ok=True)  # pragma: no cover
-
         # Load config, modify it, and save it
+        project_path = Path(path)
         config = self.load_config()
         config.projects[name] = ProjectEntry(path=str(project_path))
         self.save_config(config)
@@ -774,6 +1026,20 @@ def get_project_config(project_name: Optional[str] = None) -> ProjectConfig:
     raise ValueError(f"Project '{actual_project_name}' not found")  # pragma: no cover
 
 
+def has_cloud_credentials(config: BasicMemoryConfig) -> bool:
+    """Check if cloud credentials are available (API key or OAuth token).
+
+    Shared utility used by both MCP tools and CLI commands to determine
+    whether cloud project discovery is possible.
+    """
+    if config.cloud_api_key:
+        return True
+    from basic_memory.cli.auth import CLIAuth
+
+    auth = CLIAuth(client_id=config.cloud_client_id, authkit_domain=config.cloud_domain)
+    return auth.load_tokens() is not None
+
+
 def save_basic_memory_config(file_path: Path, config: BasicMemoryConfig) -> None:
     """Save configuration to file."""
     try:
@@ -787,33 +1053,50 @@ def save_basic_memory_config(file_path: Path, config: BasicMemoryConfig) -> None
 # Logging initialization functions for different entry points
 
 
-def init_cli_logging() -> None:  # pragma: no cover
+def _configure_logfire_for_entrypoint(entrypoint: str) -> None:
+    """Configure optional Logfire telemetry for a specific entrypoint."""
+    config = ConfigManager().config
+    service_name = f"{config.logfire_service_name}-{entrypoint}"
+    environment = config.logfire_environment or config.env
+    configure_telemetry(
+        service_name=service_name,
+        environment=environment,
+        service_version=__version__,
+        enable_logfire=config.logfire_enabled,
+        send_to_logfire=config.logfire_send_to_logfire,
+    )
+
+
+def init_cli_logging() -> None:
     """Initialize logging for CLI commands - file only.
 
     CLI commands should not log to stdout to avoid interfering with
     command output and shell integration.
     """
     log_level = os.getenv("BASIC_MEMORY_LOG_LEVEL", "INFO")
+    _configure_logfire_for_entrypoint("cli")
     setup_logging(log_level=log_level, log_to_file=True)
 
 
-def init_mcp_logging() -> None:  # pragma: no cover
+def init_mcp_logging() -> None:
     """Initialize logging for MCP server - file only.
 
     MCP server must not log to stdout as it would corrupt the
     JSON-RPC protocol communication.
     """
     log_level = os.getenv("BASIC_MEMORY_LOG_LEVEL", "INFO")
+    _configure_logfire_for_entrypoint("mcp")
     setup_logging(log_level=log_level, log_to_file=True)
 
 
-def init_api_logging() -> None:  # pragma: no cover
+def init_api_logging() -> None:
     """Initialize logging for API server.
 
     Cloud mode (BASIC_MEMORY_CLOUD_MODE=1): stdout with structured context
     Local mode: file only
     """
     log_level = os.getenv("BASIC_MEMORY_LOG_LEVEL", "INFO")
+    _configure_logfire_for_entrypoint("api")
     cloud_mode = os.getenv("BASIC_MEMORY_CLOUD_MODE", "").lower() in ("1", "true")
     if cloud_mode:
         setup_logging(log_level=log_level, log_to_stdout=True, structured_context=True)

src/basic_memory/db.py

@@ -383,6 +383,7 @@ async def run_migrations(
     so it's safe to call this multiple times - it will only run pending migrations.
     """
     logger.info("Running database migrations...")
+    temp_engine: AsyncEngine | None = None
     try:
         # Get the absolute path to the alembic directory relative to this file
         alembic_dir = Path(__file__).parent / "alembic"
@@ -407,7 +408,9 @@ async def run_migrations(
 
         # Get session maker - ensure we don't trigger recursive migration calls
         if _session_maker is None:
-            _, session_maker = _create_engine_and_session(app_config.database_path, database_type)
+            temp_engine, session_maker = _create_engine_and_session(
+                app_config.database_path, database_type, app_config
+            )
         else:
             session_maker = _session_maker
 
@@ -422,6 +425,15 @@ async def run_migrations(
             await PostgresSearchRepository(session_maker, 1).init_search_index()
         else:
             await SQLiteSearchRepository(session_maker, 1).init_search_index()
+
     except Exception as e:  # pragma: no cover
         logger.error(f"Error running migrations: {e}")
         raise
+    finally:
+        # Trigger: run_migrations() created a temporary engine while module-level
+        # session maker was not initialized.
+        # Why: temporary aiosqlite worker threads can outlive CLI command execution
+        # and block process shutdown if the engine is not disposed.
+        # Outcome: always dispose temporary engines after migration work completes.
+        if temp_engine is not None:
+            await temp_engine.dispose()

src/basic_memory/deps/services.py

@@ -9,6 +9,7 @@ This module provides service-layer dependencies:
 
 import asyncio
 import os
+from pathlib import Path
 from typing import Annotated, Any, Callable, Coroutine, Mapping, Protocol
 
 from fastapi import Depends
@@ -308,11 +309,13 @@ async def get_context_service(
     search_repository: SearchRepositoryDep,
     entity_repository: EntityRepositoryDep,
     observation_repository: ObservationRepositoryDep,
+    link_resolver: LinkResolverDep,
 ) -> ContextService:
     return ContextService(
         search_repository=search_repository,
         entity_repository=entity_repository,
         observation_repository=observation_repository,
+        link_resolver=link_resolver,
     )
 
 
@@ -323,12 +326,14 @@ async def get_context_service_v2(  # pragma: no cover
     search_repository: SearchRepositoryV2Dep,
     entity_repository: EntityRepositoryV2Dep,
     observation_repository: ObservationRepositoryV2Dep,
+    link_resolver: LinkResolverV2Dep,
 ) -> ContextService:
     """Create ContextService for v2 API."""
     return ContextService(
         search_repository=search_repository,
         entity_repository=entity_repository,
         observation_repository=observation_repository,
+        link_resolver=link_resolver,
     )
 
 
@@ -339,12 +344,14 @@ async def get_context_service_v2_external(
     search_repository: SearchRepositoryV2ExternalDep,
     entity_repository: EntityRepositoryV2ExternalDep,
     observation_repository: ObservationRepositoryV2ExternalDep,
+    link_resolver: LinkResolverV2ExternalDep,
 ) -> ContextService:
     """Create ContextService for v2 API (uses external_id)."""
     return ContextService(
         search_repository=search_repository,
         entity_repository=entity_repository,
         observation_repository=observation_repository,
+        link_resolver=link_resolver,
     )
 
 
@@ -485,7 +492,6 @@ class LocalTaskScheduler:
 
 
 async def get_task_scheduler(
-    entity_service: EntityServiceV2ExternalDep,
     sync_service: SyncServiceV2ExternalDep,
     search_service: SearchServiceV2ExternalDep,
     project_config: ProjectConfigV2ExternalDep,
@@ -493,28 +499,6 @@ async def get_task_scheduler(
 ) -> TaskScheduler:
     """Create a scheduler that maps task specs to coroutines."""
 
-    scheduler: LocalTaskScheduler | None = None
-
-    async def _reindex_entity(
-        entity_id: int,
-        resolve_relations: bool = False,
-        **_: Any,
-    ) -> None:
-        await entity_service.reindex_entity(entity_id)
-        # Trigger: caller requests relation resolution
-        # Why: resolve forward references created before the entity existed
-        # Outcome: updates unresolved relations pointing to this entity
-        if resolve_relations:
-            await sync_service.resolve_relations(entity_id=entity_id)
-        # Trigger: semantic search enabled in local config.
-        # Why: vector chunks are derived and should refresh after canonical reindex completes.
-        # Outcome: schedules out-of-band vector sync without extending write latency.
-        if app_config.semantic_search_enabled and scheduler is not None:
-            scheduler.schedule("sync_entity_vectors", entity_id=entity_id)
-
-    async def _resolve_relations(entity_id: int, **_: Any) -> None:
-        await sync_service.resolve_relations(entity_id=entity_id)
-
     async def _sync_entity_vectors(entity_id: int, **_: Any) -> None:
         await search_service.sync_entity_vectors(entity_id)
 
@@ -530,8 +514,6 @@ async def get_task_scheduler(
 
     scheduler = LocalTaskScheduler(
         {
-            "reindex_entity": _reindex_entity,
-            "resolve_relations": _resolve_relations,
             "sync_entity_vectors": _sync_entity_vectors,
             "sync_project": _sync_project,
             "reindex_project": _reindex_project,
@@ -549,9 +531,15 @@ TaskSchedulerDep = Annotated[TaskScheduler, Depends(get_task_scheduler)]
 
 async def get_project_service(
     project_repository: ProjectRepositoryDep,
+    app_config: AppConfigDep,
 ) -> ProjectService:
-    """Create ProjectService with repository."""
-    return ProjectService(repository=project_repository)
+    """Create ProjectService with repository and a system-level FileService for directory operations."""
+    # A system-level FileService for project directory creation (no project-specific base_path needed).
+    # ensure_directory() accepts absolute paths and ignores base_path for those, so Path.home() is safe.
+    entity_parser = EntityParser(Path.home())
+    markdown_processor = MarkdownProcessor(entity_parser, app_config=app_config)
+    file_service = FileService(Path.home(), markdown_processor, app_config=app_config)
+    return ProjectService(repository=project_repository, file_service=file_service)
 
 
 ProjectServiceDep = Annotated[ProjectService, Depends(get_project_service)]

src/basic_memory/file_utils.py

@@ -114,7 +114,13 @@ async def write_file_atomic(path: FilePath, content: str) -> None:
     temp_path = path_obj.with_suffix(".tmp")
 
     try:
-        # Use aiofiles for non-blocking write
+        # Trigger: callers hand us normalized Python text, but the final bytes are allowed
+        #          to use the host platform's native newline convention during the write.
+        # Why: preserving CRLF on Windows keeps local files aligned with editors like
+        #      Obsidian, while FileService now hashes the persisted file bytes instead of
+        #      the pre-write string.
+        # Outcome: this async write stays editor-friendly across platforms without
+        #          reintroducing checksum drift in sync or move detection.
         async with aiofiles.open(temp_path, mode="w", encoding="utf-8") as f:
             await f.write(content)
 
@@ -168,6 +174,13 @@ async def format_markdown_builtin(path: Path) -> Optional[str]:
 
         # Only write if content changed
         if formatted_content != content:
+            # Trigger: mdformat may rewrite markdown content, then the host platform
+            #          decides the newline bytes for the follow-up async text write.
+            # Why: we want formatter output to preserve native newlines instead of
+            #      forcing LF, and the authoritative checksum comes from rereading the
+            #      stored file bytes later in FileService.
+            # Outcome: formatting remains compatible with local editors on Windows while
+            #          checksum-based sync logic stays anchored to on-disk bytes.
             async with aiofiles.open(path, mode="w", encoding="utf-8") as f:
                 await f.write(formatted_content)
 
@@ -447,6 +460,11 @@ def sanitize_for_filename(text: str, replacement: str = "-") -> str:
     # compress multiple, repeated replacements
     text = re.sub(f"{re.escape(replacement)}+", replacement, text)
 
+    # Strip trailing periods — they cause "hi-everyone..md" double-dot filenames
+    # when ".md" is appended, which triggers path traversal false positives.
+    # Trailing periods are also invalid on Windows filesystems.
+    text = text.strip(".")
+
     return text.strip(replacement)
 
 

src/basic_memory/ignore_utils.py

@@ -4,6 +4,8 @@ import fnmatch
 from pathlib import Path
 from typing import Set
 
+from basic_memory.config import resolve_data_dir
+
 
 # Common directories and patterns to ignore by default
 # These are used as fallback if .bmignore doesn't exist
@@ -61,9 +63,11 @@ def get_bmignore_path() -> Path:
     """Get path to .bmignore file.
 
     Returns:
-        Path to ~/.basic-memory/.bmignore
+        Path to <basic-memory data dir>/.bmignore, honoring
+        ``BASIC_MEMORY_CONFIG_DIR`` so isolated instances each keep their
+        own ignore file.
     """
-    return Path.home() / ".basic-memory" / ".bmignore"
+    return resolve_data_dir() / ".bmignore"
 
 
 def create_default_bmignore() -> None:
@@ -176,7 +180,8 @@ def load_gitignore_patterns(base_path: Path, use_gitignore: bool = True) -> Set[
     """Load gitignore patterns from .gitignore file and .bmignore.
 
     Combines patterns from:
-    1. ~/.basic-memory/.bmignore (user's global ignore patterns)
+    1. <basic-memory data dir>/.bmignore (user's global ignore patterns, honors
+       BASIC_MEMORY_CONFIG_DIR)
     2. {base_path}/.gitignore (project-specific patterns, if use_gitignore=True)
 
     Args:

src/basic_memory/importers/utils.py

@@ -39,23 +39,24 @@ def format_timestamp(timestamp: Any) -> str:  # pragma: no cover
     Returns:
         A formatted string representation of the timestamp.
     """
+    parsed_timestamp = timestamp
     if isinstance(timestamp, str):
         try:
             # Try ISO format
-            timestamp = datetime.fromisoformat(timestamp.replace("Z", "+00:00"))
+            parsed_timestamp = datetime.fromisoformat(timestamp.replace("Z", "+00:00"))
         except ValueError:
             try:
                 # Try unix timestamp as string
-                timestamp = datetime.fromtimestamp(float(timestamp)).astimezone()
+                parsed_timestamp = datetime.fromtimestamp(float(timestamp)).astimezone()
             except ValueError:
                 # Return as is if we can't parse it
                 return timestamp
     elif isinstance(timestamp, (int, float)):
         # Unix timestamp
-        timestamp = datetime.fromtimestamp(timestamp).astimezone()
+        parsed_timestamp = datetime.fromtimestamp(timestamp).astimezone()
 
-    if isinstance(timestamp, datetime):
-        return timestamp.strftime("%Y-%m-%d %H:%M:%S")
+    if isinstance(parsed_timestamp, datetime):
+        return parsed_timestamp.strftime("%Y-%m-%d %H:%M:%S")
 
     # Return as is if we can't format it
-    return str(timestamp)  # pragma: no cover
+    return str(parsed_timestamp)  # pragma: no cover

src/basic_memory/indexing/__init__.py

@@ -0,0 +1,31 @@
+"""Reusable indexing primitives shared by local sync and future remote callers."""
+
+from basic_memory.indexing.batch_indexer import BatchIndexer
+from basic_memory.indexing.batching import build_index_batches
+from basic_memory.indexing.models import (
+    IndexedEntity,
+    IndexBatch,
+    IndexFileMetadata,
+    IndexFileWriter,
+    IndexFrontmatterUpdate,
+    IndexFrontmatterWriteResult,
+    IndexingBatchResult,
+    IndexInputFile,
+    IndexProgress,
+    SyncedMarkdownFile,
+)
+
+__all__ = [
+    "BatchIndexer",
+    "IndexedEntity",
+    "IndexBatch",
+    "IndexFileMetadata",
+    "IndexFileWriter",
+    "IndexFrontmatterUpdate",
+    "IndexFrontmatterWriteResult",
+    "IndexingBatchResult",
+    "IndexInputFile",
+    "IndexProgress",
+    "SyncedMarkdownFile",
+    "build_index_batches",
+]

src/basic_memory/indexing/batch_indexer.py

@@ -0,0 +1,710 @@
+"""Reusable batch executor for bounded-parallel file indexing."""
+
+from __future__ import annotations
+
+import asyncio
+from dataclasses import dataclass
+from datetime import datetime
+from pathlib import Path
+from typing import Awaitable, Callable, Mapping, TypeVar
+
+from loguru import logger
+from sqlalchemy.exc import IntegrityError
+
+import logfire
+from basic_memory.config import BasicMemoryConfig
+from basic_memory.file_utils import compute_checksum, has_frontmatter, remove_frontmatter
+from basic_memory.markdown.schemas import EntityMarkdown
+from basic_memory.indexing.models import (
+    IndexedEntity,
+    IndexFileWriter,
+    IndexFrontmatterUpdate,
+    IndexingBatchResult,
+    IndexInputFile,
+)
+from basic_memory.models import Entity, Relation
+from basic_memory.services import EntityService
+from basic_memory.services.exceptions import SyncFatalError
+from basic_memory.services.search_service import SearchService
+from basic_memory.repository import EntityRepository, RelationRepository
+
+T = TypeVar("T")
+
+
+@dataclass(slots=True)
+class _PreparedMarkdownFile:
+    file: IndexInputFile
+    content: str
+    final_checksum: str
+    markdown: EntityMarkdown
+    file_contains_frontmatter: bool
+
+
+@dataclass(slots=True)
+class _PreparedEntity:
+    path: str
+    entity_id: int
+    permalink: str | None
+    checksum: str
+    content_type: str | None
+    search_content: str | None
+    markdown_content: str | None = None
+
+
+@dataclass(slots=True)
+class _PersistedMarkdownFile:
+    prepared: _PreparedMarkdownFile
+    entity: Entity
+
+
+class BatchIndexer:
+    """Index already-loaded files without assuming where they came from."""
+
+    def __init__(
+        self,
+        *,
+        app_config: BasicMemoryConfig,
+        entity_service: EntityService,
+        entity_repository: EntityRepository,
+        relation_repository: RelationRepository,
+        search_service: SearchService,
+        file_writer: IndexFileWriter,
+    ) -> None:
+        self.app_config = app_config
+        self.entity_service = entity_service
+        self.entity_repository = entity_repository
+        self.relation_repository = relation_repository
+        self.search_service = search_service
+        self.file_writer = file_writer
+
+    async def index_files(
+        self,
+        files: Mapping[str, IndexInputFile],
+        *,
+        max_concurrent: int,
+        parse_max_concurrent: int | None = None,
+        existing_permalink_by_path: dict[str, str | None] | None = None,
+    ) -> IndexingBatchResult:
+        """Index one batch of loaded files with bounded concurrency."""
+        if max_concurrent <= 0:
+            raise ValueError("max_concurrent must be greater than zero")
+
+        ordered_paths = sorted(files)
+        if not ordered_paths:
+            return IndexingBatchResult()
+
+        parse_limit = parse_max_concurrent or max_concurrent
+        error_by_path: dict[str, str] = {}
+
+        markdown_paths = [path for path in ordered_paths if self._is_markdown(files[path])]
+        regular_paths = [path for path in ordered_paths if path not in markdown_paths]
+
+        prepared_markdown, parse_errors = await self._run_bounded(
+            markdown_paths,
+            limit=parse_limit,
+            worker=lambda path: self._prepare_markdown_file(files[path]),
+        )
+        error_by_path.update(parse_errors)
+
+        prepared_markdown, normalization_errors = await self._normalize_markdown_batch(
+            prepared_markdown,
+            existing_permalink_by_path=existing_permalink_by_path,
+        )
+        error_by_path.update(normalization_errors)
+
+        indexed_entities: list[IndexedEntity] = []
+        resolved_count = 0
+        unresolved_count = 0
+        search_indexed = 0
+
+        prepared_entities: dict[str, _PreparedEntity] = {}
+
+        markdown_upserts, markdown_errors = await self._run_bounded(
+            [path for path in markdown_paths if path not in error_by_path],
+            limit=max_concurrent,
+            worker=lambda path: self._upsert_markdown_file(prepared_markdown[path]),
+        )
+        error_by_path.update(markdown_errors)
+        prepared_entities.update(markdown_upserts)
+        if existing_permalink_by_path is not None:
+            for path, prepared_entity in markdown_upserts.items():
+                existing_permalink_by_path[path] = prepared_entity.permalink
+
+        regular_upserts, regular_errors = await self._run_bounded(
+            regular_paths,
+            limit=max_concurrent,
+            worker=lambda path: self._upsert_regular_file(files[path]),
+        )
+        error_by_path.update(regular_errors)
+        prepared_entities.update(regular_upserts)
+
+        markdown_entity_ids = [
+            prepared_entities[path].entity_id
+            for path in markdown_paths
+            if path in prepared_entities
+        ]
+        if markdown_entity_ids:
+            resolved_count, unresolved_count = await self._resolve_batch_relations(
+                markdown_entity_ids,
+                max_concurrent=max_concurrent,
+            )
+
+        refreshed_entities = await self.entity_repository.find_by_ids(
+            [prepared.entity_id for prepared in prepared_entities.values()]
+        )
+        entities_by_id = {entity.id: entity for entity in refreshed_entities}
+
+        refreshed, refresh_errors = await self._run_bounded(
+            [path for path in ordered_paths if path in prepared_entities],
+            limit=self.app_config.index_metadata_update_max_concurrent,
+            worker=lambda path: self._refresh_search_index(
+                prepared_entities[path],
+                entities_by_id[prepared_entities[path].entity_id],
+            ),
+        )
+        error_by_path.update(refresh_errors)
+
+        for path in ordered_paths:
+            indexed = refreshed.get(path)
+            if indexed is not None:
+                indexed_entities.append(indexed)
+
+        search_indexed = len(indexed_entities)
+
+        return IndexingBatchResult(
+            indexed=indexed_entities,
+            errors=[(path, error_by_path[path]) for path in ordered_paths if path in error_by_path],
+            relations_resolved=resolved_count,
+            relations_unresolved=unresolved_count,
+            search_indexed=search_indexed,
+        )
+
+    async def index_markdown_file(
+        self,
+        file: IndexInputFile,
+        *,
+        new: bool | None = None,
+        existing_permalink_by_path: dict[str, str | None] | None = None,
+        index_search: bool = True,
+        resolve_relations: bool = True,
+    ) -> IndexedEntity:
+        """Index one markdown file using the same normalization and upsert path as batches."""
+        if not self._is_markdown(file):
+            raise ValueError(f"index_markdown_file requires markdown input: {file.path}")
+
+        with logfire.span("index.markdown_file.prepare", path=file.path):
+            prepared = await self._prepare_markdown_file(file)
+        if existing_permalink_by_path is None:
+            with logfire.span("index.markdown_file.load_permalink_map", path=file.path):
+                existing_permalink_by_path = {
+                    path: permalink
+                    for path, permalink in (
+                        await self.entity_repository.get_file_path_to_permalink_map()
+                    ).items()
+                }
+
+        reserved_permalinks = {
+            permalink
+            for path, permalink in existing_permalink_by_path.items()
+            if path != file.path and permalink
+        }
+        with logfire.span("index.markdown_file.normalize", path=file.path):
+            prepared = await self._normalize_markdown_file(prepared, reserved_permalinks)
+        existing_permalink_by_path[file.path] = prepared.markdown.frontmatter.permalink
+
+        with logfire.span("index.markdown_file.persist", path=file.path, is_new=new):
+            persisted = await self._persist_markdown_file(
+                prepared,
+                is_new=new,
+                resolve_relations=resolve_relations,
+                reload_entity=False,
+            )
+        existing_permalink_by_path[file.path] = persisted.entity.permalink
+
+        with logfire.span(
+            "index.markdown_file.reload_entity",
+            path=file.path,
+            entity_id=persisted.entity.id,
+        ):
+            refreshed = await self.entity_repository.find_by_ids([persisted.entity.id])
+        if len(refreshed) != 1:  # pragma: no cover
+            raise ValueError(f"Failed to reload indexed entity for {file.path}")
+        entity = refreshed[0]
+        prepared_entity = self._build_prepared_entity(persisted.prepared, entity)
+
+        if index_search:
+            with logfire.span(
+                "index.markdown_file.refresh_search_index",
+                path=file.path,
+                entity_id=entity.id,
+            ):
+                return await self._refresh_search_index(prepared_entity, entity)
+
+        return IndexedEntity(
+            path=prepared_entity.path,
+            entity_id=entity.id,
+            permalink=entity.permalink,
+            checksum=prepared_entity.checksum,
+            content_type=prepared_entity.content_type,
+            markdown_content=prepared_entity.markdown_content,
+        )
+
+    # --- Preparation ---
+
+    async def _prepare_markdown_file(self, file: IndexInputFile) -> _PreparedMarkdownFile:
+        if file.content is None:
+            raise ValueError(f"Missing content for markdown file: {file.path}")
+
+        content = file.content.decode("utf-8")
+        file_contains_frontmatter = has_frontmatter(content)
+        final_checksum = await self._resolve_checksum(file)
+        entity_markdown = await self.entity_service.entity_parser.parse_markdown_content(
+            file_path=Path(file.path),
+            content=content,
+            mtime=file.last_modified.timestamp() if file.last_modified else None,
+            ctime=file.created_at.timestamp() if file.created_at else None,
+        )
+
+        return _PreparedMarkdownFile(
+            file=file,
+            content=content,
+            final_checksum=final_checksum,
+            markdown=entity_markdown,
+            file_contains_frontmatter=file_contains_frontmatter,
+        )
+
+    async def _normalize_markdown_batch(
+        self,
+        prepared_markdown: dict[str, _PreparedMarkdownFile],
+        *,
+        existing_permalink_by_path: dict[str, str | None] | None = None,
+    ) -> tuple[dict[str, _PreparedMarkdownFile], dict[str, str]]:
+        if not prepared_markdown:
+            return {}, {}
+
+        if existing_permalink_by_path is None:
+            existing_permalink_by_path = {
+                path: permalink
+                for path, permalink in (
+                    await self.entity_repository.get_file_path_to_permalink_map()
+                ).items()
+            }
+
+        batch_paths = set(prepared_markdown)
+        reserved_permalinks = {
+            permalink
+            for path, permalink in existing_permalink_by_path.items()
+            if path not in batch_paths and permalink
+        }
+
+        normalized: dict[str, _PreparedMarkdownFile] = {}
+        errors: dict[str, str] = {}
+
+        for path in sorted(prepared_markdown):
+            try:
+                normalized[path] = await self._normalize_markdown_file(
+                    prepared_markdown[path],
+                    reserved_permalinks,
+                )
+                existing_permalink_by_path[path] = normalized[path].markdown.frontmatter.permalink
+            except Exception as exc:
+                errors[path] = str(exc)
+                logger.warning("Batch markdown normalization failed", path=path, error=str(exc))
+
+        return normalized, errors
+
+    async def _normalize_markdown_file(
+        self,
+        prepared: _PreparedMarkdownFile,
+        reserved_permalinks: set[str],
+    ) -> _PreparedMarkdownFile:
+        final_checksum = prepared.final_checksum
+        final_content = prepared.content
+        final_permalink = await self._resolve_batch_permalink(prepared, reserved_permalinks)
+
+        # Trigger: markdown file has no frontmatter and sync enforcement is enabled.
+        # Why: downstream indexing relies on normalized metadata and stable permalinks.
+        # Outcome: write derived metadata back through the storage-agnostic writer.
+        if not prepared.file_contains_frontmatter and self.app_config.ensure_frontmatter_on_sync:
+            frontmatter_updates = {
+                "title": prepared.markdown.frontmatter.title,
+                "type": prepared.markdown.frontmatter.type,
+                "permalink": final_permalink,
+            }
+            write_result = await self.file_writer.write_frontmatter(
+                IndexFrontmatterUpdate(path=prepared.file.path, metadata=frontmatter_updates)
+            )
+            final_checksum = write_result.checksum
+            final_content = write_result.content
+            prepared.markdown.frontmatter.metadata.update(frontmatter_updates)
+
+        # Trigger: existing markdown frontmatter may lack the canonical permalink.
+        # Why: batch sync keeps permalinks stable without forcing a full rewrite when unchanged.
+        # Outcome: only the permalink field is updated when it actually differs.
+        elif (
+            prepared.file_contains_frontmatter
+            and not self.app_config.disable_permalinks
+            and final_permalink != prepared.markdown.frontmatter.permalink
+        ):
+            prepared.markdown.frontmatter.metadata["permalink"] = final_permalink
+            write_result = await self.file_writer.write_frontmatter(
+                IndexFrontmatterUpdate(
+                    path=prepared.file.path,
+                    metadata={"permalink": final_permalink},
+                )
+            )
+            final_checksum = write_result.checksum
+            final_content = write_result.content
+
+        return _PreparedMarkdownFile(
+            file=prepared.file,
+            content=final_content,
+            final_checksum=final_checksum,
+            markdown=prepared.markdown,
+            file_contains_frontmatter=prepared.file_contains_frontmatter,
+        )
+
+    async def _resolve_batch_permalink(
+        self,
+        prepared: _PreparedMarkdownFile,
+        reserved_permalinks: set[str],
+    ) -> str | None:
+        should_resolve_permalink = (
+            not prepared.file_contains_frontmatter and self.app_config.ensure_frontmatter_on_sync
+        ) or (prepared.file_contains_frontmatter and not self.app_config.disable_permalinks)
+        if not should_resolve_permalink:
+            permalink = prepared.markdown.frontmatter.permalink
+            if permalink:
+                reserved_permalinks.add(permalink)
+            return permalink
+
+        desired_permalink = await self.entity_service.resolve_permalink(
+            prepared.file.path,
+            markdown=prepared.markdown,
+            skip_conflict_check=True,
+        )
+        return self._reserve_batch_permalink(desired_permalink, reserved_permalinks)
+
+    def _reserve_batch_permalink(
+        self,
+        desired_permalink: str,
+        reserved_permalinks: set[str],
+    ) -> str:
+        permalink = desired_permalink
+        suffix = 1
+        while permalink in reserved_permalinks:
+            permalink = f"{desired_permalink}-{suffix}"
+            suffix += 1
+        reserved_permalinks.add(permalink)
+        return permalink
+
+    # --- Persistence ---
+
+    async def _upsert_markdown_file(self, prepared: _PreparedMarkdownFile) -> _PreparedEntity:
+        persisted = await self._persist_markdown_file(prepared)
+        return self._build_prepared_entity(persisted.prepared, persisted.entity)
+
+    async def _upsert_regular_file(self, file: IndexInputFile) -> _PreparedEntity:
+        checksum = await self._resolve_checksum(file)
+        existing = await self.entity_repository.get_by_file_path(file.path, load_relations=False)
+        is_new_entity = existing is None
+
+        if existing is None:
+            await self.entity_service.resolve_permalink(file.path, skip_conflict_check=True)
+            entity = Entity(
+                note_type="file",
+                file_path=file.path,
+                checksum=checksum,
+                title=Path(file.path).name,
+                created_at=file.created_at or datetime.now().astimezone(),
+                updated_at=file.last_modified or datetime.now().astimezone(),
+                content_type=file.content_type or "text/plain",
+                mtime=file.last_modified.timestamp() if file.last_modified else None,
+                size=file.size,
+            )
+
+            try:
+                created = await self.entity_repository.add(entity)
+                entity_id = created.id
+            except IntegrityError as exc:
+                message = str(exc)
+                if (
+                    "UNIQUE constraint failed: entity.file_path" in message
+                    or "uix_entity_file_path_project" in message
+                    or (
+                        "duplicate key value violates unique constraint" in message
+                        and "file_path" in message
+                    )
+                ):
+                    existing = await self.entity_repository.get_by_file_path(
+                        file.path,
+                        load_relations=False,
+                    )
+                    if existing is None:
+                        raise ValueError(
+                            f"Entity not found after file_path conflict: {file.path}"
+                        ) from exc
+                    entity_id = existing.id
+                else:
+                    raise
+        else:
+            entity_id = existing.id
+
+        updated = await self.entity_repository.update(
+            entity_id,
+            self._entity_metadata_updates(file, checksum, include_created_at=is_new_entity),
+        )
+        if updated is None:
+            raise ValueError(f"Failed to update file entity metadata for {file.path}")
+
+        return _PreparedEntity(
+            path=file.path,
+            entity_id=updated.id,
+            permalink=updated.permalink,
+            checksum=checksum,
+            content_type=file.content_type,
+            search_content=None,
+            markdown_content=None,
+        )
+
+    # --- Relations ---
+
+    async def _resolve_batch_relations(
+        self,
+        entity_ids: list[int],
+        *,
+        max_concurrent: int,
+    ) -> tuple[int, int]:
+        unresolved_relation_lists = await asyncio.gather(
+            *(
+                self.relation_repository.find_unresolved_relations_for_entity(entity_id)
+                for entity_id in entity_ids
+            )
+        )
+        unresolved_relations = [
+            relation for relation_list in unresolved_relation_lists for relation in relation_list
+        ]
+
+        if not unresolved_relations:
+            return 0, 0
+
+        semaphore = asyncio.Semaphore(max_concurrent)
+
+        async def resolve_relation(relation: Relation) -> int:
+            async with semaphore:
+                try:
+                    resolved_entity = await self.entity_service.link_resolver.resolve_link(
+                        relation.to_name
+                    )
+                    if resolved_entity is None or resolved_entity.id == relation.from_id:
+                        return 0
+
+                    try:
+                        await self.relation_repository.update(
+                            relation.id,
+                            {
+                                "to_id": resolved_entity.id,
+                                "to_name": resolved_entity.title,
+                            },
+                        )
+                    except IntegrityError:
+                        await self.relation_repository.delete(relation.id)
+                    return 1
+                except Exception as exc:  # pragma: no cover - defensive logging
+                    logger.warning(
+                        "Batch relation resolution failed",
+                        relation_id=relation.id,
+                        from_id=relation.from_id,
+                        to_name=relation.to_name,
+                        error=str(exc),
+                    )
+                    return 0
+
+        resolved_counts = await asyncio.gather(
+            *(resolve_relation(relation) for relation in unresolved_relations)
+        )
+
+        remaining_relation_lists = await asyncio.gather(
+            *(
+                self.relation_repository.find_unresolved_relations_for_entity(entity_id)
+                for entity_id in entity_ids
+            )
+        )
+        remaining_unresolved = sum(len(relations) for relations in remaining_relation_lists)
+
+        return sum(resolved_counts), remaining_unresolved
+
+    # --- Search refresh ---
+
+    async def _refresh_search_index(
+        self, prepared: _PreparedEntity, entity: Entity
+    ) -> IndexedEntity:
+        await self.search_service.index_entity_data(entity, content=prepared.search_content)
+        return IndexedEntity(
+            path=prepared.path,
+            entity_id=entity.id,
+            permalink=entity.permalink,
+            checksum=prepared.checksum,
+            content_type=prepared.content_type,
+            markdown_content=prepared.markdown_content,
+        )
+
+    # --- Helpers ---
+
+    async def _persist_markdown_file(
+        self,
+        prepared: _PreparedMarkdownFile,
+        *,
+        is_new: bool | None = None,
+        resolve_relations: bool = True,
+        reload_entity: bool = True,
+    ) -> _PersistedMarkdownFile:
+        existing = await self.entity_repository.get_by_file_path(
+            prepared.file.path,
+            load_relations=False,
+        )
+        if is_new is None:
+            is_new = existing is None
+        entity = await self.entity_service.upsert_entity_from_markdown(
+            Path(prepared.file.path),
+            prepared.markdown,
+            is_new=is_new,
+            existing_entity=existing,
+            resolve_relations=resolve_relations,
+            reload_entity=reload_entity,
+        )
+        prepared = await self._reconcile_persisted_permalink(prepared, entity)
+        metadata_updates = self._entity_metadata_updates(prepared.file, prepared.final_checksum)
+        updated = await self.entity_repository.update_fields(
+            entity.id,
+            metadata_updates,
+        )
+        if not updated:
+            raise ValueError(f"Failed to update markdown entity metadata for {prepared.file.path}")
+        self._apply_entity_metadata_updates(entity, metadata_updates)
+        return _PersistedMarkdownFile(prepared=prepared, entity=entity)
+
+    async def _reconcile_persisted_permalink(
+        self,
+        prepared: _PreparedMarkdownFile,
+        entity: Entity,
+    ) -> _PreparedMarkdownFile:
+        # Trigger: the source file started without frontmatter and sync is configured
+        #          to leave frontmatterless files alone.
+        # Why: upsert may still assign a DB permalink even when disk content should stay untouched.
+        # Outcome: skip reconciliation writes that would silently inject frontmatter.
+        if (
+            self.app_config.disable_permalinks
+            or (
+                not prepared.file_contains_frontmatter
+                and not self.app_config.ensure_frontmatter_on_sync
+            )
+            or entity.permalink is None
+            or entity.permalink == prepared.markdown.frontmatter.permalink
+        ):
+            return prepared
+
+        logger.debug(
+            "Updating permalink after upsert conflict resolution",
+            path=prepared.file.path,
+            old_permalink=prepared.markdown.frontmatter.permalink,
+            new_permalink=entity.permalink,
+        )
+        prepared.markdown.frontmatter.metadata["permalink"] = entity.permalink
+        write_result = await self.file_writer.write_frontmatter(
+            IndexFrontmatterUpdate(
+                path=prepared.file.path,
+                metadata={"permalink": entity.permalink},
+            )
+        )
+        return _PreparedMarkdownFile(
+            file=prepared.file,
+            content=write_result.content,
+            final_checksum=write_result.checksum,
+            markdown=prepared.markdown,
+            file_contains_frontmatter=prepared.file_contains_frontmatter,
+        )
+
+    def _build_prepared_entity(
+        self,
+        prepared: _PreparedMarkdownFile,
+        entity: Entity,
+    ) -> _PreparedEntity:
+        return _PreparedEntity(
+            path=prepared.file.path,
+            entity_id=entity.id,
+            permalink=entity.permalink,
+            checksum=prepared.final_checksum,
+            content_type=prepared.file.content_type,
+            search_content=(
+                prepared.markdown.content
+                if prepared.markdown.content is not None
+                else remove_frontmatter(prepared.content)
+            ),
+            markdown_content=prepared.content,
+        )
+
+    async def _resolve_checksum(self, file: IndexInputFile) -> str:
+        if file.checksum is not None:
+            return file.checksum
+        if file.content is None:
+            raise ValueError(f"Missing checksum and content for file: {file.path}")
+        return await compute_checksum(file.content)
+
+    def _entity_metadata_updates(
+        self,
+        file: IndexInputFile,
+        checksum: str,
+        *,
+        include_created_at: bool = True,
+    ) -> dict[str, object]:
+        updates: dict[str, object] = {
+            "file_path": file.path,
+            "checksum": checksum,
+            "size": file.size,
+        }
+        if include_created_at and file.created_at is not None:
+            updates["created_at"] = file.created_at
+        if file.last_modified is not None:
+            updates["updated_at"] = file.last_modified
+            updates["mtime"] = file.last_modified.timestamp()
+        if file.content_type is not None:
+            updates["content_type"] = file.content_type
+        return updates
+
+    def _apply_entity_metadata_updates(self, entity: Entity, updates: dict[str, object]) -> None:
+        """Keep the returned entity aligned with metadata written without reload."""
+        for key, value in updates.items():
+            setattr(entity, key, value)
+
+    def _is_markdown(self, file: IndexInputFile) -> bool:
+        if file.content_type is not None:
+            return file.content_type == "text/markdown"
+        return Path(file.path).suffix.lower() in {".md", ".markdown"}
+
+    async def _run_bounded(
+        self,
+        paths: list[str],
+        *,
+        limit: int,
+        worker: Callable[[str], Awaitable[T]],
+    ) -> tuple[dict[str, T], dict[str, str]]:
+        if not paths:
+            return {}, {}
+
+        semaphore = asyncio.Semaphore(limit)
+        results: dict[str, T] = {}
+        errors: dict[str, str] = {}
+
+        async def run(path: str) -> None:
+            async with semaphore:
+                try:
+                    results[path] = await worker(path)
+                except Exception as exc:
+                    if isinstance(exc, SyncFatalError) or isinstance(exc.__cause__, SyncFatalError):
+                        raise
+                    errors[path] = str(exc)
+                    logger.warning("Batch indexing failed", path=path, error=str(exc))
+
+        await asyncio.gather(*(run(path) for path in paths))
+        return results, errors

src/basic_memory/indexing/batching.py

@@ -0,0 +1,63 @@
+"""Deterministic helpers for planning bounded indexing batches."""
+
+from __future__ import annotations
+
+from collections.abc import Mapping, Sequence
+
+from basic_memory.indexing.models import IndexBatch, IndexFileMetadata
+
+
+def build_index_batches(
+    paths: Sequence[str],
+    metadata_by_path: Mapping[str, IndexFileMetadata],
+    *,
+    max_files: int,
+    max_bytes: int,
+) -> list[IndexBatch]:
+    """Build deterministic batches bounded by file count and total bytes."""
+    if max_files <= 0:
+        raise ValueError("max_files must be greater than zero")
+    if max_bytes <= 0:
+        raise ValueError("max_bytes must be greater than zero")
+
+    ordered_paths = sorted(paths)
+    batches: list[IndexBatch] = []
+    current_paths: list[str] = []
+    current_bytes = 0
+
+    for path in ordered_paths:
+        metadata = metadata_by_path.get(path)
+        if metadata is None:
+            raise KeyError(f"Missing metadata for path: {path}")
+
+        file_bytes = max(metadata.size, 0)
+
+        # Trigger: the next file would overflow the active batch.
+        # Why: keep batches memory-bounded and predictable for both local and remote callers.
+        # Outcome: flush the current batch before placing the next file.
+        if current_paths and (
+            len(current_paths) >= max_files or current_bytes + file_bytes > max_bytes
+        ):
+            batches.append(IndexBatch(paths=current_paths, total_bytes=current_bytes))
+            current_paths = []
+            current_bytes = 0
+
+        # Trigger: one file is larger than the configured byte budget.
+        # Why: we still need to index it, but splitting a single file is out of scope.
+        # Outcome: emit a dedicated single-file batch that may exceed max_bytes.
+        if file_bytes > max_bytes:
+            batches.append(IndexBatch(paths=[path], total_bytes=file_bytes))
+            continue
+
+        current_paths.append(path)
+        current_bytes += file_bytes
+
+        if len(current_paths) >= max_files or current_bytes == max_bytes:
+            batches.append(IndexBatch(paths=current_paths, total_bytes=current_bytes))
+            current_paths = []
+            current_bytes = 0
+
+    if current_paths:
+        batches.append(IndexBatch(paths=current_paths, total_bytes=current_bytes))
+
+    return batches

src/basic_memory/indexing/models.py

@@ -0,0 +1,110 @@
+"""Typed models for the reusable indexing execution path."""
+
+from __future__ import annotations
+
+from dataclasses import dataclass, field
+from datetime import datetime
+from typing import Any, Protocol, TYPE_CHECKING
+
+if TYPE_CHECKING:  # pragma: no cover
+    from basic_memory.models import Entity
+
+
+@dataclass(slots=True)
+class IndexFileMetadata:
+    """Storage-agnostic metadata for a file queued for indexing."""
+
+    path: str
+    size: int
+    checksum: str | None = None
+    content_type: str | None = None
+    last_modified: datetime | None = None
+    created_at: datetime | None = None
+
+
+@dataclass(slots=True)
+class IndexInputFile(IndexFileMetadata):
+    """Fully loaded file payload consumed by the batch executor."""
+
+    content: bytes | None = None
+
+
+@dataclass(slots=True)
+class IndexBatch:
+    """A deterministic batch of files bounded by count and total bytes."""
+
+    paths: list[str]
+    total_bytes: int
+
+
+@dataclass(slots=True)
+class IndexProgress:
+    """Batch indexing progress emitted to callers such as the CLI."""
+
+    files_total: int
+    files_processed: int
+    batches_total: int
+    batches_completed: int
+    current_batch_bytes: int = 0
+    files_per_minute: float = 0.0
+    eta_seconds: float | None = None
+
+
+@dataclass(slots=True)
+class IndexFrontmatterUpdate:
+    """A typed frontmatter write request for a single file."""
+
+    path: str
+    metadata: dict[str, Any]
+
+
+@dataclass(slots=True)
+class IndexFrontmatterWriteResult:
+    """Typed result for a frontmatter write performed during indexing."""
+
+    checksum: str
+    content: str
+
+
+@dataclass(slots=True)
+class IndexedEntity:
+    """Stable output describing one file that finished indexing successfully."""
+
+    path: str
+    entity_id: int
+    permalink: str | None
+    checksum: str
+    content_type: str | None = None
+    markdown_content: str | None = None
+
+
+@dataclass(slots=True)
+class SyncedMarkdownFile:
+    """Canonical result for syncing one markdown file end-to-end."""
+
+    entity: Entity
+    checksum: str
+    markdown_content: str
+    file_path: str
+    content_type: str
+    updated_at: datetime
+    size: int
+
+
+@dataclass(slots=True)
+class IndexingBatchResult:
+    """Outcome for one batch execution."""
+
+    indexed: list[IndexedEntity] = field(default_factory=list)
+    errors: list[tuple[str, str]] = field(default_factory=list)
+    relations_resolved: int = 0
+    relations_unresolved: int = 0
+    search_indexed: int = 0
+
+
+class IndexFileWriter(Protocol):
+    """Narrow protocol for frontmatter writes during indexing."""
+
+    async def write_frontmatter(
+        self, update: IndexFrontmatterUpdate
+    ) -> IndexFrontmatterWriteResult: ...

src/basic_memory/markdown/entity_parser.py

@@ -88,6 +88,22 @@ def normalize_frontmatter_value(value: Any) -> Any:
     return value
 
 
+def _coerce_to_string(value: Any) -> str:
+    """Coerce a frontmatter value to a string.
+
+    YAML can parse scalar-looking fields as lists when the author uses block
+    sequence syntax.  For fields like ``title`` and ``type`` that *must* be
+    strings, this helper converts lists to a comma-separated string and any
+    other non-string type via ``str()``.
+    """
+    if isinstance(value, str):
+        return value
+    if isinstance(value, list):
+        # Join list items, converting each to string first
+        return ", ".join(str(item) for item in value)
+    return str(value)
+
+
 def normalize_frontmatter_metadata(metadata: dict) -> dict:
     """Normalize all values in frontmatter metadata dict.
 
@@ -233,9 +249,19 @@ class EntityParser:
 
         content = strip_bom(content)
 
-        # Parse frontmatter with proper error handling for malformed YAML
+        # PostgreSQL rejects null bytes (0x00) in text columns.
+        # Some markdown files (e.g. Claude agent definitions) contain embedded nulls.
+        content = content.replace("\x00", "")
+
+        # Parse frontmatter with proper error handling for malformed YAML.
+        # We use frontmatter.parse() instead of frontmatter.loads() because
+        # loads() does Post(content, handler, **metadata), which crashes when
+        # the YAML contains reserved keys like 'content' or 'handler'.
+        # See basic-memory-cloud#375.
         try:
-            post = frontmatter.loads(content)
+            fm_metadata, fm_content = frontmatter.parse(content)
+            post = frontmatter.Post(fm_content)
+            post.metadata.update(fm_metadata)
         except yaml.YAMLError as e:
             logger.warning(
                 f"Failed to parse YAML frontmatter in {file_path}: {e}. "
@@ -248,15 +274,22 @@ class EntityParser:
         # Normalize frontmatter values
         metadata = normalize_frontmatter_metadata(post.metadata)
 
-        # Ensure required fields have defaults
+        # Ensure required string fields are always strings.
+        # YAML can parse these as lists when authors use block sequence syntax
+        # (e.g. "title:\n  - My Title"), causing 'list' has no attribute 'strip'
+        # downstream.  See basic-memory-cloud#376.
         title = metadata.get("title")
+        if title is not None:
+            title = _coerce_to_string(title)
         if not title or title == "None":
             metadata["title"] = file_path.stem
         else:
             metadata["title"] = title
 
-        entity_type = metadata.get("type")
-        metadata["type"] = entity_type if entity_type is not None else "note"
+        note_type = metadata.get("type")
+        if note_type is not None:
+            note_type = _coerce_to_string(note_type)
+        metadata["type"] = note_type if note_type is not None else "note"
 
         tags = parse_tags(metadata.get("tags", []))  # pyright: ignore
         if tags:

src/basic_memory/markdown/plugins.py

@@ -180,6 +180,9 @@ def observation_plugin(md: MarkdownIt) -> None:
     def observation_rule(state: Any) -> None:
         """Process observations in token stream."""
         tokens = state.tokens
+        # Track blockquote nesting so Obsidian callouts (`> [!info] Title`)
+        # don't get parsed as observations with category `!info`.
+        blockquote_depth = 0
 
         for idx in range(len(tokens)):
             token = tokens[idx]
@@ -187,6 +190,18 @@ def observation_plugin(md: MarkdownIt) -> None:
             # Initialize meta for all tokens
             token.meta = token.meta or {}
 
+            if token.type == "blockquote_open":
+                blockquote_depth += 1
+                continue
+            if token.type == "blockquote_close":
+                blockquote_depth -= 1
+                continue
+
+            # Skip parsing inside blockquotes — that's Obsidian callout
+            # territory, not Basic Memory observation syntax.
+            if blockquote_depth > 0:
+                continue
+
             # Parse observations in list items
             if token.type == "inline" and is_observation(token):
                 obs = parse_observation(token)

src/basic_memory/markdown/schemas.py

@@ -1,9 +1,9 @@
 """Schema models for entity markdown files."""
 
 from datetime import datetime
-from typing import List, Optional
+from typing import TYPE_CHECKING, Any, List, Optional
 
-from pydantic import BaseModel
+from pydantic import BaseModel, Field, model_validator
 
 
 class Observation(BaseModel):
@@ -38,23 +38,47 @@ class Relation(BaseModel):
 class EntityFrontmatter(BaseModel):
     """Required frontmatter fields for an entity."""
 
-    metadata: dict = {}
+    if TYPE_CHECKING:
+        # Frontmatter may be built from raw YAML keys. The validator below
+        # gathers those keys into the metadata mapping used at runtime.
+        def __init__(self, **data: Any) -> None: ...
+
+    metadata: dict[str, Any] = Field(default_factory=dict)
+
+    @model_validator(mode="before")
+    @classmethod
+    def collect_metadata(cls, data: Any) -> Any:
+        if not isinstance(data, dict):
+            return data
+
+        if "metadata" not in data:
+            return {"metadata": data}
+
+        metadata = data.get("metadata") or {}
+        extras = {key: value for key, value in data.items() if key != "metadata"}
+        if extras:
+            return {"metadata": {**extras, **metadata}}
+        return data
 
     @property
     def tags(self) -> List[str]:
-        return self.metadata.get("tags") if self.metadata else None  # pyright: ignore
+        tags = self.metadata.get("tags")
+        return [str(tag) for tag in tags] if isinstance(tags, list) else []
 
     @property
     def title(self) -> str:
-        return self.metadata.get("title") if self.metadata else None  # pyright: ignore
+        title = self.metadata.get("title")
+        return title if isinstance(title, str) else ""
 
     @property
     def type(self) -> str:
-        return self.metadata.get("type", "note") if self.metadata else "note"  # pyright: ignore
+        note_type = self.metadata.get("type", "note")
+        return note_type if isinstance(note_type, str) else "note"
 
     @property
-    def permalink(self) -> str:
-        return self.metadata.get("permalink") if self.metadata else None  # pyright: ignore
+    def permalink(self) -> Optional[str]:
+        permalink = self.metadata.get("permalink")
+        return permalink if isinstance(permalink, str) else None
 
 
 class EntityMarkdown(BaseModel):

src/basic_memory/markdown/utils.py

@@ -50,7 +50,7 @@ def entity_model_from_markdown(
 
     # Update basic fields
     model.title = markdown.frontmatter.title
-    model.entity_type = markdown.frontmatter.type
+    model.note_type = markdown.frontmatter.type
     # Only update permalink if it exists in frontmatter, otherwise preserve existing
     if markdown.frontmatter.permalink is not None:
         model.permalink = markdown.frontmatter.permalink
@@ -86,7 +86,7 @@ async def schema_to_markdown(schema: Any) -> Post:
     Convert schema to markdown Post object.
 
     Args:
-        schema: Schema to convert (must have title, entity_type, and permalink attributes)
+        schema: Schema to convert (must have title, note_type, and permalink attributes)
 
     Returns:
         Post object with frontmatter metadata
@@ -113,7 +113,7 @@ async def schema_to_markdown(schema: Any) -> Post:
     post = Post(
         content,
         title=schema.title,
-        type=schema.entity_type,
+        type=schema.note_type,
     )
     # set the permalink if passed in
     if schema.permalink:

src/basic_memory/mcp/async_client.py

@@ -5,6 +5,7 @@ from typing import AsyncIterator, Callable, Optional
 from httpx import ASGITransport, AsyncClient, Timeout
 from loguru import logger
 
+import logfire
 from basic_memory.api.app import app as fastapi_app
 from basic_memory.config import ConfigManager, ProjectMode
 
@@ -43,21 +44,47 @@ def _asgi_client(timeout: Timeout) -> AsyncClient:
 
 async def _resolve_cloud_token(config) -> str:
     """Resolve cloud token with API key preferred, OAuth fallback."""
-    token = config.cloud_api_key
-    if token:
-        return token
+    with logfire.span(
+        "routing.resolve_cloud_credentials",
+        has_api_key=bool(config.cloud_api_key),
+    ):
+        token = config.cloud_api_key
+        if token:
+            return token
 
-    from basic_memory.cli.auth import CLIAuth
+        from basic_memory.cli.auth import CLIAuth
 
-    auth = CLIAuth(client_id=config.cloud_client_id, authkit_domain=config.cloud_domain)
-    token = await auth.get_valid_token()
-    if token:
-        return token
+        auth = CLIAuth(client_id=config.cloud_client_id, authkit_domain=config.cloud_domain)
+        token = await auth.get_valid_token()
+        if token:
+            return token
 
-    raise RuntimeError(
-        "Cloud routing requested but no credentials found. "
-        "Run 'bm cloud set-key <key>' or 'bm cloud login' first."
-    )
+        logger.error("Cloud routing requested but no credentials were available")
+        raise RuntimeError(
+            "Cloud routing requested but no credentials found. "
+            "Run 'bm cloud api-key save <key>' or 'bm cloud login' first."
+        )
+
+
+def resolve_configured_workspace(
+    *,
+    config=None,
+    project_name: Optional[str] = None,
+    workspace: Optional[str] = None,
+) -> Optional[str]:
+    """Resolve workspace from explicit input, per-project config, then global default."""
+    if workspace is not None:
+        return workspace
+
+    if config is None:
+        config = ConfigManager().config
+
+    if project_name is not None:
+        project_entry = config.projects.get(project_name)
+        if project_entry and project_entry.workspace_id:
+            return project_entry.workspace_id
+
+    return config.default_workspace
 
 
 @asynccontextmanager
@@ -67,9 +94,12 @@ async def _cloud_client(
     workspace: Optional[str] = None,
 ) -> AsyncIterator[AsyncClient]:
     """Create a cloud proxy client with resolved credentials."""
+    from basic_memory.workspace_context import workspace_permalink_headers
+
     token = await _resolve_cloud_token(config)
     proxy_base_url = f"{config.cloud_host}/proxy"
     headers = {"Authorization": f"Bearer {token}"}
+    headers.update(workspace_permalink_headers())
     if workspace:
         headers["X-Workspace-ID"] = workspace
     logger.info(f"Creating HTTP client for cloud proxy at: {proxy_base_url}")
@@ -82,30 +112,59 @@ async def _cloud_client(
 
 
 @asynccontextmanager
-async def get_cloud_control_plane_client() -> AsyncIterator[AsyncClient]:
+async def get_cloud_control_plane_client(
+    workspace: Optional[str] = None,
+) -> AsyncIterator[AsyncClient]:
     """Create a control-plane cloud client for endpoints outside /proxy."""
     config = ConfigManager().config
     timeout = _build_timeout()
     token = await _resolve_cloud_token(config)
+    headers = {"Authorization": f"Bearer {token}"}
+    if workspace:
+        headers["X-Workspace-ID"] = workspace
     logger.info(f"Creating HTTP client for cloud control plane at: {config.cloud_host}")
     async with AsyncClient(
         base_url=config.cloud_host,
-        headers={"Authorization": f"Bearer {token}"},
+        headers=headers,
         timeout=timeout,
     ) as client:
         yield client
 
 
-# Optional factory override for dependency injection
-_client_factory: Optional[Callable[[], AbstractAsyncContextManager[AsyncClient]]] = None
+# Optional factory override for dependency injection.
+# The factory accepts an optional workspace keyword argument so that MCP tools
+# can route individual requests to a different workspace than the one set at
+# connection time.  See basic-memory-cloud main.py tenant_asgi_client_factory.
+_client_factory: Optional[Callable[..., AbstractAsyncContextManager[AsyncClient]]] = None
 
 
-def set_client_factory(factory: Callable[[], AbstractAsyncContextManager[AsyncClient]]) -> None:
+def set_client_factory(factory: Callable[..., AbstractAsyncContextManager[AsyncClient]]) -> None:
     """Override the default client factory (for cloud app, testing, etc)."""
     global _client_factory
     _client_factory = factory
 
 
+def is_factory_mode() -> bool:
+    """Return True when a client factory override is active (e.g., cloud app)."""
+    return _client_factory is not None
+
+
+@asynccontextmanager
+async def get_cloud_proxy_client(
+    workspace: Optional[str] = None,
+) -> AsyncIterator[AsyncClient]:
+    """Create a cloud proxy client for project-level operations.
+
+    Used by MCP tools to fetch cloud project lists independently of the
+    default get_client() routing, which always goes through the local ASGI
+    transport in stdio mode.
+    """
+    config = ConfigManager().config
+    timeout = _build_timeout()
+    async with _cloud_client(config, timeout, workspace=workspace) as client:
+        yield client
+
+
 @asynccontextmanager
 async def get_client(
     project_name: Optional[str] = None,
@@ -120,7 +179,7 @@ async def get_client(
     4. Local ASGI transport by default.
     """
     if _client_factory:
-        async with _client_factory() as client:
+        async with _client_factory(workspace=workspace) as client:
             yield client
         return
 
@@ -133,14 +192,19 @@ async def get_client(
     # Outcome: route strictly based on explicit flag.
     if _explicit_routing():
         if _force_local_mode():
-            logger.info("Explicit local routing enabled - using ASGI client")
+            logger.debug("Explicit local routing enabled - using ASGI client")
             async with _asgi_client(timeout) as client:
                 yield client
             return
 
         if _force_cloud_mode():
-            logger.info("Explicit cloud routing enabled - using cloud proxy client")
-            async with _cloud_client(config, timeout, workspace=workspace) as client:
+            logger.debug("Explicit cloud routing enabled - using cloud proxy client")
+            effective_workspace = resolve_configured_workspace(
+                config=config,
+                project_name=project_name,
+                workspace=workspace,
+            )
+            async with _cloud_client(config, timeout, workspace=effective_workspace) as client:
                 yield client
             return
 
@@ -151,24 +215,29 @@ async def get_client(
     if project_name is not None and not _explicit_routing():
         project_mode = config.get_project_mode(project_name)
         if project_mode == ProjectMode.CLOUD:
-            logger.info(f"Project '{project_name}' is cloud mode - using cloud proxy client")
+            logger.debug(f"Project '{project_name}' is cloud mode - using cloud proxy client")
+            effective_workspace = resolve_configured_workspace(
+                config=config,
+                project_name=project_name,
+                workspace=workspace,
+            )
             try:
-                async with _cloud_client(config, timeout, workspace=workspace) as client:
+                async with _cloud_client(config, timeout, workspace=effective_workspace) as client:
                     yield client
             except RuntimeError as exc:
                 raise RuntimeError(
                     f"Project '{project_name}' is set to cloud mode but no credentials found. "
-                    "Run 'bm cloud set-key <key>' or 'bm cloud login' first."
+                    "Run 'bm cloud api-key save <key>' or 'bm cloud login' first."
                 ) from exc
             return
 
-        logger.info(f"Project '{project_name}' is local mode - using ASGI client")
+        logger.debug(f"Project '{project_name}' is local mode - using ASGI client")
         async with _asgi_client(timeout) as client:
             yield client
         return
 
     # --- Default fallback ---
-    logger.info("Default routing - using ASGI client for local Basic Memory API")
+    logger.debug("Default routing - using ASGI client for local Basic Memory API")
     async with _asgi_client(timeout) as client:
         yield client
 

src/basic_memory/mcp/clients/knowledge.py

@@ -7,6 +7,7 @@ from typing import Any
 
 from httpx import AsyncClient
 
+import logfire
 from basic_memory.mcp.tools.utils import call_get, call_post, call_put, call_patch, call_delete
 from basic_memory.schemas.response import (
     EntityResponse,
@@ -43,9 +44,7 @@ class KnowledgeClient:
 
     # --- Entity CRUD Operations ---
 
-    async def create_entity(
-        self, entity_data: dict[str, Any], *, fast: bool | None = None
-    ) -> EntityResponse:
+    async def create_entity(self, entity_data: dict[str, Any]) -> EntityResponse:
         """Create a new entity.
 
         Args:
@@ -57,21 +56,25 @@ class KnowledgeClient:
         Raises:
             ToolError: If the request fails
         """
-        params = {"fast": fast} if fast is not None else None
-        response = await call_post(
-            self.http_client,
-            f"{self._base_path}/entities",
-            json=entity_data,
-            params=params,
-        )
+        with logfire.span(
+            "mcp.client.knowledge.create_entity",
+            client_name="knowledge",
+            operation="create_entity",
+        ):
+            response = await call_post(
+                self.http_client,
+                f"{self._base_path}/entities",
+                json=entity_data,
+                client_name="knowledge",
+                operation="create_entity",
+                path_template="/v2/projects/{project_id}/knowledge/entities",
+            )
         return EntityResponse.model_validate(response.json())
 
     async def update_entity(
         self,
         entity_id: str,
         entity_data: dict[str, Any],
-        *,
-        fast: bool | None = None,
     ) -> EntityResponse:
         """Update an existing entity (full replacement).
 
@@ -85,13 +88,19 @@ class KnowledgeClient:
         Raises:
             ToolError: If the request fails
         """
-        params = {"fast": fast} if fast is not None else None
-        response = await call_put(
-            self.http_client,
-            f"{self._base_path}/entities/{entity_id}",
-            json=entity_data,
-            params=params,
-        )
+        with logfire.span(
+            "mcp.client.knowledge.update_entity",
+            client_name="knowledge",
+            operation="update_entity",
+        ):
+            response = await call_put(
+                self.http_client,
+                f"{self._base_path}/entities/{entity_id}",
+                json=entity_data,
+                client_name="knowledge",
+                operation="update_entity",
+                path_template="/v2/projects/{project_id}/knowledge/entities/{entity_id}",
+            )
         return EntityResponse.model_validate(response.json())
 
     async def get_entity(self, entity_id: str) -> EntityResponse:
@@ -106,18 +115,24 @@ class KnowledgeClient:
         Raises:
             ToolError: If the entity is not found or request fails
         """
-        response = await call_get(
-            self.http_client,
-            f"{self._base_path}/entities/{entity_id}",
-        )
+        with logfire.span(
+            "mcp.client.knowledge.get_entity",
+            client_name="knowledge",
+            operation="get_entity",
+        ):
+            response = await call_get(
+                self.http_client,
+                f"{self._base_path}/entities/{entity_id}",
+                client_name="knowledge",
+                operation="get_entity",
+                path_template="/v2/projects/{project_id}/knowledge/entities/{entity_id}",
+            )
         return EntityResponse.model_validate(response.json())
 
     async def patch_entity(
         self,
         entity_id: str,
         patch_data: dict[str, Any],
-        *,
-        fast: bool | None = None,
     ) -> EntityResponse:
         """Partially update an entity.
 
@@ -131,13 +146,19 @@ class KnowledgeClient:
         Raises:
             ToolError: If the request fails
         """
-        params = {"fast": fast} if fast is not None else None
-        response = await call_patch(
-            self.http_client,
-            f"{self._base_path}/entities/{entity_id}",
-            json=patch_data,
-            params=params,
-        )
+        with logfire.span(
+            "mcp.client.knowledge.patch_entity",
+            client_name="knowledge",
+            operation="patch_entity",
+        ):
+            response = await call_patch(
+                self.http_client,
+                f"{self._base_path}/entities/{entity_id}",
+                json=patch_data,
+                client_name="knowledge",
+                operation="patch_entity",
+                path_template="/v2/projects/{project_id}/knowledge/entities/{entity_id}",
+            )
         return EntityResponse.model_validate(response.json())
 
     async def delete_entity(self, entity_id: str) -> DeleteEntitiesResponse:
@@ -152,10 +173,18 @@ class KnowledgeClient:
         Raises:
             ToolError: If the entity is not found or request fails
         """
-        response = await call_delete(
-            self.http_client,
-            f"{self._base_path}/entities/{entity_id}",
-        )
+        with logfire.span(
+            "mcp.client.knowledge.delete_entity",
+            client_name="knowledge",
+            operation="delete_entity",
+        ):
+            response = await call_delete(
+                self.http_client,
+                f"{self._base_path}/entities/{entity_id}",
+                client_name="knowledge",
+                operation="delete_entity",
+                path_template="/v2/projects/{project_id}/knowledge/entities/{entity_id}",
+            )
         return DeleteEntitiesResponse.model_validate(response.json())
 
     async def move_entity(self, entity_id: str, destination_path: str) -> EntityResponse:
@@ -171,11 +200,19 @@ class KnowledgeClient:
         Raises:
             ToolError: If the request fails
         """
-        response = await call_put(
-            self.http_client,
-            f"{self._base_path}/entities/{entity_id}/move",
-            json={"destination_path": destination_path},
-        )
+        with logfire.span(
+            "mcp.client.knowledge.move_entity",
+            client_name="knowledge",
+            operation="move_entity",
+        ):
+            response = await call_put(
+                self.http_client,
+                f"{self._base_path}/entities/{entity_id}/move",
+                json={"destination_path": destination_path},
+                client_name="knowledge",
+                operation="move_entity",
+                path_template="/v2/projects/{project_id}/knowledge/entities/{entity_id}/move",
+            )
         return EntityResponse.model_validate(response.json())
 
     async def move_directory(
@@ -193,14 +230,22 @@ class KnowledgeClient:
         Raises:
             ToolError: If the request fails
         """
-        response = await call_post(
-            self.http_client,
-            f"{self._base_path}/move-directory",
-            json={
-                "source_directory": source_directory,
-                "destination_directory": destination_directory,
-            },
-        )
+        with logfire.span(
+            "mcp.client.knowledge.move_directory",
+            client_name="knowledge",
+            operation="move_directory",
+        ):
+            response = await call_post(
+                self.http_client,
+                f"{self._base_path}/move-directory",
+                json={
+                    "source_directory": source_directory,
+                    "destination_directory": destination_directory,
+                },
+                client_name="knowledge",
+                operation="move_directory",
+                path_template="/v2/projects/{project_id}/knowledge/move-directory",
+            )
         return DirectoryMoveResult.model_validate(response.json())
 
     async def delete_directory(self, directory: str) -> DirectoryDeleteResult:
@@ -215,11 +260,19 @@ class KnowledgeClient:
         Raises:
             ToolError: If the request fails
         """
-        response = await call_post(
-            self.http_client,
-            f"{self._base_path}/delete-directory",
-            json={"directory": directory},
-        )
+        with logfire.span(
+            "mcp.client.knowledge.delete_directory",
+            client_name="knowledge",
+            operation="delete_directory",
+        ):
+            response = await call_post(
+                self.http_client,
+                f"{self._base_path}/delete-directory",
+                json={"directory": directory},
+                client_name="knowledge",
+                operation="delete_directory",
+                path_template="/v2/projects/{project_id}/knowledge/delete-directory",
+            )
         return DirectoryDeleteResult.model_validate(response.json())
 
     # --- Resolution ---
@@ -237,10 +290,18 @@ class KnowledgeClient:
         Raises:
             ToolError: If the identifier cannot be resolved
         """
-        response = await call_post(
-            self.http_client,
-            f"{self._base_path}/resolve",
-            json={"identifier": identifier, "strict": strict},
-        )
+        with logfire.span(
+            "mcp.client.knowledge.resolve_entity",
+            client_name="knowledge",
+            operation="resolve_entity",
+        ):
+            response = await call_post(
+                self.http_client,
+                f"{self._base_path}/resolve",
+                json={"identifier": identifier, "strict": strict},
+                client_name="knowledge",
+                operation="resolve_entity",
+                path_template="/v2/projects/{project_id}/knowledge/resolve",
+            )
         data = response.json()
         return data["external_id"]

src/basic_memory/mcp/clients/memory.py

@@ -7,6 +7,7 @@ from typing import Optional
 
 from httpx import AsyncClient
 
+import logfire
 from basic_memory.mcp.tools.utils import call_get
 from basic_memory.schemas.memory import GraphContext
 
@@ -71,11 +72,21 @@ class MemoryClient:
         if timeframe:
             params["timeframe"] = timeframe
 
-        response = await call_get(
-            self.http_client,
-            f"{self._base_path}/{path}",
-            params=params,
-        )
+        with logfire.span(
+            "mcp.client.memory.build_context",
+            client_name="memory",
+            operation="build_context",
+            page=page,
+            page_size=page_size,
+        ):
+            response = await call_get(
+                self.http_client,
+                f"{self._base_path}/{path}",
+                params=params,
+                client_name="memory",
+                operation="build_context",
+                path_template="/v2/projects/{project_id}/memory/{path}",
+            )
         return GraphContext.model_validate(response.json())
 
     async def recent(
@@ -112,9 +123,19 @@ class MemoryClient:
             # Join types as comma-separated string if provided
             params["type"] = ",".join(types) if isinstance(types, list) else types
 
-        response = await call_get(
-            self.http_client,
-            f"{self._base_path}/recent",
-            params=params,
-        )
+        with logfire.span(
+            "mcp.client.memory.recent_activity",
+            client_name="memory",
+            operation="recent_activity",
+            page=page,
+            page_size=page_size,
+        ):
+            response = await call_get(
+                self.http_client,
+                f"{self._base_path}/recent",
+                params=params,
+                client_name="memory",
+                operation="recent_activity",
+                path_template="/v2/projects/{project_id}/memory/recent",
+            )
         return GraphContext.model_validate(response.json())

src/basic_memory/mcp/clients/project.py

@@ -7,8 +7,16 @@ from typing import Any
 
 from httpx import AsyncClient
 
-from basic_memory.mcp.tools.utils import call_get, call_post, call_delete
+from basic_memory.mcp.tools.utils import (
+    call_delete,
+    call_get,
+    call_patch,
+    call_post,
+    call_put,
+)
+from basic_memory.schemas import ProjectInfoResponse, SyncReportResponse
 from basic_memory.schemas.project_info import ProjectList, ProjectStatusResponse
+from basic_memory.schemas.v2 import ProjectResolveResponse
 
 
 class ProjectClient:
@@ -70,11 +78,14 @@ class ProjectClient:
         )
         return ProjectStatusResponse.model_validate(response.json())
 
-    async def delete_project(self, project_external_id: str) -> ProjectStatusResponse:
+    async def delete_project(
+        self, project_external_id: str, delete_notes: bool = False
+    ) -> ProjectStatusResponse:
         """Delete a project by its external ID.
 
         Args:
             project_external_id: Project external ID (UUID)
+            delete_notes: If True, also delete project files from disk
 
         Returns:
             ProjectStatusResponse with deletion result
@@ -82,8 +93,137 @@ class ProjectClient:
         Raises:
             ToolError: If the request fails
         """
+        url = f"/v2/projects/{project_external_id}"
+        if delete_notes:
+            url += "?delete_notes=true"
         response = await call_delete(
             self.http_client,
-            f"/v2/projects/{project_external_id}",
+            url,
         )
         return ProjectStatusResponse.model_validate(response.json())
+
+    async def resolve_project(self, identifier: str) -> ProjectResolveResponse:
+        """Resolve a project name/permalink to its full project record.
+
+        Args:
+            identifier: Project name or permalink
+
+        Returns:
+            ProjectResolveResponse with project metadata
+
+        Raises:
+            ToolError: If the request fails
+        """
+        response = await call_post(
+            self.http_client,
+            "/v2/projects/resolve",
+            json={"identifier": identifier},
+        )
+        return ProjectResolveResponse.model_validate(response.json())
+
+    async def set_default(self, project_external_id: str) -> ProjectStatusResponse:
+        """Set a project as the default.
+
+        Args:
+            project_external_id: Project external ID (UUID)
+
+        Returns:
+            ProjectStatusResponse with result
+
+        Raises:
+            ToolError: If the request fails
+        """
+        response = await call_put(
+            self.http_client,
+            f"/v2/projects/{project_external_id}/default",
+        )
+        return ProjectStatusResponse.model_validate(response.json())
+
+    async def update_project(
+        self, project_external_id: str, data: dict[str, Any]
+    ) -> ProjectStatusResponse:
+        """Update a project's configuration (e.g. path).
+
+        Args:
+            project_external_id: Project external ID (UUID)
+            data: Fields to update
+
+        Returns:
+            ProjectStatusResponse with update result
+
+        Raises:
+            ToolError: If the request fails
+        """
+        response = await call_patch(
+            self.http_client,
+            f"/v2/projects/{project_external_id}",
+            json=data,
+        )
+        return ProjectStatusResponse.model_validate(response.json())
+
+    async def sync(
+        self,
+        project_external_id: str,
+        force_full: bool = False,
+        run_in_background: bool = True,
+    ) -> dict[str, Any]:
+        """Trigger a sync operation for a project.
+
+        Args:
+            project_external_id: Project external ID (UUID)
+            force_full: If True, force a full scan bypassing watermark optimization
+            run_in_background: If True, return immediately; if False, wait for completion
+
+        Returns:
+            Raw response dict — background mode returns {"message": ...},
+            foreground mode returns a SyncReportResponse-shaped dict.
+
+        Raises:
+            ToolError: If the request fails
+        """
+        url = f"/v2/projects/{project_external_id}/sync"
+        params = []
+        if force_full:
+            params.append("force_full=true")
+        if not run_in_background:
+            params.append("run_in_background=false")
+        if params:
+            url += "?" + "&".join(params)
+        response = await call_post(self.http_client, url)
+        return response.json()
+
+    async def get_status(self, project_external_id: str) -> SyncReportResponse:
+        """Get the sync status for a project.
+
+        Args:
+            project_external_id: Project external ID (UUID)
+
+        Returns:
+            SyncReportResponse describing pending changes
+
+        Raises:
+            ToolError: If the request fails
+        """
+        response = await call_post(
+            self.http_client,
+            f"/v2/projects/{project_external_id}/status",
+        )
+        return SyncReportResponse.model_validate(response.json())
+
+    async def get_info(self, project_external_id: str) -> ProjectInfoResponse:
+        """Get detailed project information and statistics.
+
+        Args:
+            project_external_id: Project external ID (UUID)
+
+        Returns:
+            ProjectInfoResponse with project details
+
+        Raises:
+            ToolError: If the request fails
+        """
+        response = await call_get(
+            self.http_client,
+            f"/v2/projects/{project_external_id}/info",
+        )
+        return ProjectInfoResponse.model_validate(response.json())

src/basic_memory/mcp/clients/resource.py

@@ -3,10 +3,9 @@
 Encapsulates all /v2/projects/{project_id}/resource/* endpoints.
 """
 
-from typing import Optional
-
 from httpx import AsyncClient, Response
 
+import logfire
 from basic_memory.mcp.tools.utils import call_get
 
 
@@ -38,19 +37,11 @@ class ResourceClient:
         self.project_id = project_id
         self._base_path = f"/v2/projects/{project_id}/resource"
 
-    async def read(
-        self,
-        entity_id: str,
-        *,
-        page: Optional[int] = None,
-        page_size: Optional[int] = None,
-    ) -> Response:
+    async def read(self, entity_id: str) -> Response:
         """Read a resource by entity ID.
 
         Args:
             entity_id: Entity external_id (UUID)
-            page: Optional page number for paginated content
-            page_size: Optional page size for paginated content
 
         Returns:
             Raw HTTP Response (caller handles text/binary content)
@@ -58,14 +49,15 @@ class ResourceClient:
         Raises:
             ToolError: If the resource is not found or request fails
         """
-        params: dict = {}
-        if page is not None:
-            params["page"] = page
-        if page_size is not None:
-            params["page_size"] = page_size
-
-        return await call_get(
-            self.http_client,
-            f"{self._base_path}/{entity_id}",
-            params=params if params else None,
-        )
+        with logfire.span(
+            "mcp.client.resource.read",
+            client_name="resource",
+            operation="read",
+        ):
+            return await call_get(
+                self.http_client,
+                f"{self._base_path}/{entity_id}",
+                client_name="resource",
+                operation="read",
+                path_template="/v2/projects/{project_id}/resource/{entity_id}",
+            )

src/basic_memory/mcp/clients/schema.py

@@ -24,7 +24,7 @@ class SchemaClient:
     Usage:
         async with get_client() as http_client:
             client = SchemaClient(http_client, project_id)
-            report = await client.validate(entity_type="Person")
+            report = await client.validate(note_type="person")
     """
 
     def __init__(self, http_client: AsyncClient, project_id: str):
@@ -41,13 +41,13 @@ class SchemaClient:
     async def validate(
         self,
         *,
-        entity_type: str | None = None,
+        note_type: str | None = None,
         identifier: str | None = None,
     ) -> ValidationReport:
         """Validate notes against their resolved schemas.
 
         Args:
-            entity_type: Optional entity type to batch-validate
+            note_type: Optional note type to batch-validate
             identifier: Optional specific note to validate
 
         Returns:
@@ -57,8 +57,8 @@ class SchemaClient:
             ToolError: If the request fails
         """
         params: dict[str, str] = {}
-        if entity_type:
-            params["entity_type"] = entity_type
+        if note_type:
+            params["note_type"] = note_type
         if identifier:
             params["identifier"] = identifier
 
@@ -71,14 +71,14 @@ class SchemaClient:
 
     async def infer(
         self,
-        entity_type: str,
+        note_type: str,
         *,
         threshold: float = 0.25,
     ) -> InferenceReport:
         """Infer a schema from existing notes of a given type.
 
         Args:
-            entity_type: The entity type to analyze
+            note_type: The note type to analyze
             threshold: Minimum frequency for optional fields (0-1)
 
         Returns:
@@ -90,15 +90,15 @@ class SchemaClient:
         response = await call_post(
             self.http_client,
             f"{self._base_path}/infer",
-            params={"entity_type": entity_type, "threshold": threshold},
+            params={"note_type": note_type, "threshold": threshold},
         )
         return InferenceReport.model_validate(response.json())
 
-    async def diff(self, entity_type: str) -> DriftReport:
+    async def diff(self, note_type: str) -> DriftReport:
         """Show drift between schema definition and actual usage.
 
         Args:
-            entity_type: The entity type to check for drift
+            note_type: The note type to check for drift
 
         Returns:
             DriftReport with detected differences
@@ -108,6 +108,6 @@ class SchemaClient:
         """
         response = await call_get(
             self.http_client,
-            f"{self._base_path}/diff/{entity_type}",
+            f"{self._base_path}/diff/{note_type}",
         )
         return DriftReport.model_validate(response.json())

src/basic_memory/mcp/clients/search.py

@@ -7,6 +7,7 @@ from typing import Any
 
 from httpx import AsyncClient
 
+import logfire
 from basic_memory.mcp.tools.utils import call_post
 from basic_memory.schemas.search import SearchResponse
 
@@ -56,10 +57,20 @@ class SearchClient:
         Raises:
             ToolError: If the request fails
         """
-        response = await call_post(
-            self.http_client,
-            f"{self._base_path}/",
-            json=query,
-            params={"page": page, "page_size": page_size},
-        )
+        with logfire.span(
+            "mcp.client.search.search",
+            client_name="search",
+            operation="search",
+            page=page,
+            page_size=page_size,
+        ):
+            response = await call_post(
+                self.http_client,
+                f"{self._base_path}/",
+                json=query,
+                params={"page": page, "page_size": page_size},
+                client_name="search",
+                operation="search",
+                path_template="/v2/projects/{project_id}/search/",
+            )
         return SearchResponse.model_validate(response.json())

src/basic_memory/mcp/prompts/continue_conversation.py

@@ -4,17 +4,15 @@ These prompts help users continue conversations and work across sessions,
 providing context from previous interactions to maintain continuity.
 """
 
+from textwrap import dedent
 from typing import Annotated, Optional
 
 from loguru import logger
 from pydantic import Field
 
-from basic_memory.config import ConfigManager
-from basic_memory.mcp.async_client import get_client
-from basic_memory.mcp.project_context import get_active_project
 from basic_memory.mcp.server import mcp
-from basic_memory.mcp.tools.utils import call_post
-from basic_memory.schemas.prompt import ContinueConversationRequest
+from basic_memory.mcp.tools.recent_activity import recent_activity
+from basic_memory.mcp.tools.search import search_notes
 
 
 @mcp.prompt(
@@ -42,22 +40,92 @@ async def continue_conversation(
     """
     logger.info(f"Continuing session, topic: {topic}, timeframe: {timeframe}")
 
-    async with get_client() as client:
-        config = ConfigManager().config
-        active_project = await get_active_project(client, project=config.default_project)
+    if topic:
+        # Use json format to get structured data for result counting and branching
+        result = await search_notes(query=topic, after_date=timeframe, output_format="json")
 
-        # Create request model
-        request = ContinueConversationRequest(  # pyright: ignore [reportCallIssue]
-            topic=topic, timeframe=timeframe
-        )
+        if isinstance(result, dict):
+            results = result.get("results", [])
+            context_text = _format_continuation_results(results, topic)
+            result_count = len(results)
+        else:
+            # Error string
+            context_text = str(result)
+            result_count = 0
+    else:
+        # No topic — show recent activity
+        effective_timeframe = timeframe or "7d"
+        activity_text = await recent_activity(timeframe=effective_timeframe)
+        context_text = str(activity_text)
+        result_count = -1  # Signals we used recent_activity
 
-        # Call the prompt API endpoint
-        response = await call_post(
-            client,
-            f"/v2/projects/{active_project.external_id}/prompt/continue-conversation",
-            json=request.model_dump(exclude_none=True),
-        )
+    target = f"'{topic}'" if topic else "recent activity"
 
-        # Extract the rendered prompt from the response
-        result = response.json()
-        return result["prompt"]
+    prompt = dedent(f"""
+        # Continuing conversation on: {target}
+
+        This is a memory retrieval session.
+
+        Please use the available basic-memory tools to gather relevant context before responding.
+        Start by executing one of the suggested commands below to retrieve content.
+
+        {context_text}
+
+        ---
+
+        ## Next Steps
+    """)
+
+    if topic and result_count > 0:
+        prompt += dedent(f"""
+            Found {result_count} results related to '{topic}'.
+
+            1. **Read full content** - Use `read_note("permalink")` to dive into specific notes
+            2. **Build context** - Use `build_context("memory://path")` to see relationships
+            3. **Search deeper** - Use `search_notes("{topic}")` with different filters
+
+            > **Knowledge Capture:** As you continue this conversation, actively look for
+            > opportunities to record new information, decisions, or insights using `write_note()`.
+        """)
+    elif topic:
+        prompt += dedent(f"""
+            No previous context found for '{topic}'.
+
+            This is an opportunity to start documenting this topic:
+
+            1. **Create a new note** - Use `write_note(title="{topic}", content="...")` to start
+            2. **Search with variations** - Try `search_notes("{topic}")` with different terms
+            3. **Check recent activity** - Use `recent_activity(timeframe="7d")` to see what's new
+        """)
+    else:
+        prompt += dedent("""
+            1. **Explore specific items** - Use `read_note("permalink")` to dive deeper
+            2. **Search for topics** - Use `search_notes("topic")` to find specific content
+            3. **Build context** - Use `build_context("memory://path")` to see relationships
+        """)
+
+    return prompt
+
+
+def _format_continuation_results(results: list[dict], topic: str) -> str:
+    """Format search result dicts for conversation continuation context."""
+    if not results:
+        return f"No previous context found for '{topic}'."
+
+    lines = [f"## Previous Context for '{topic}'\n"]
+
+    for item in results:
+        title = item.get("title", "Untitled")
+        permalink = item.get("permalink", "")
+
+        lines.append(f"### {title}")
+        if permalink:
+            lines.append(f"permalink: {permalink}")
+            lines.append(f'Read with: `read_note("{permalink}")`')
+        content = item.get("content")
+        if content:
+            content = content[:300] + "..." if len(content) > 300 else content
+            lines.append(f"\n{content}")
+        lines.append("")
+
+    return "\n".join(lines)

src/basic_memory/mcp/prompts/recent_activity.py

@@ -46,7 +46,7 @@ async def recent_activity_prompt(
     logger.info(f"Getting recent activity, timeframe: {timeframe}, project: {project}")
 
     # Call the tool function - it returns a well-formatted string
-    activity_summary = await recent_activity.fn(project=project, timeframe=timeframe)
+    activity_summary = await recent_activity(project=project, timeframe=timeframe)
 
     # Build the prompt response
     # The tool already returns formatted markdown, so we use it directly

src/basic_memory/mcp/prompts/search.py

@@ -3,17 +3,14 @@
 These prompts help users search and explore their knowledge base.
 """
 
+from textwrap import dedent
 from typing import Annotated, Optional
 
 from loguru import logger
 from pydantic import Field
 
-from basic_memory.config import ConfigManager
-from basic_memory.mcp.async_client import get_client
-from basic_memory.mcp.project_context import get_active_project
 from basic_memory.mcp.server import mcp
-from basic_memory.mcp.tools.utils import call_post
-from basic_memory.schemas.prompt import SearchPromptRequest
+from basic_memory.mcp.tools.search import search_notes
 
 
 @mcp.prompt(
@@ -41,20 +38,60 @@ async def search_prompt(
     """
     logger.info(f"Searching knowledge base, query: {query}, timeframe: {timeframe}")
 
-    async with get_client() as client:
-        config = ConfigManager().config
-        active_project = await get_active_project(client, project=config.default_project)
+    # Use json format to get structured data for result counting and formatting
+    result = await search_notes(query=query, after_date=timeframe, output_format="json")
 
-        # Create request model
-        request = SearchPromptRequest(query=query, timeframe=timeframe)
+    # Format the tool output into a prompt with guidance
+    if isinstance(result, dict):
+        results = result.get("results", [])
+        result_count = len(results)
+        result_text = _format_search_results(results, query)
+    else:
+        # Error string from search tool
+        result_count = 0
+        result_text = str(result)
 
-        # Call the prompt API endpoint
-        response = await call_post(
-            client,
-            f"/v2/projects/{active_project.external_id}/prompt/search",
-            json=request.model_dump(exclude_none=True),
-        )
+    return dedent(f"""
+        # Search Results: "{query}"
 
-        # Extract the rendered prompt from the response
-        result = response.json()
-        return result["prompt"]
+        This is a memory retrieval session showing search results.
+
+        {result_text}
+
+        ---
+
+        ## Next Steps
+
+        Based on these {result_count} results, you can:
+
+        1. **Read a specific note** - Use `read_note("permalink")` to see full content
+        2. **Build context** - Use `build_context("memory://path")` to see relationships
+        3. **Refine search** - Use `search_notes("refined query")` to narrow results
+        4. **Check recent activity** - Use `recent_activity(timeframe="7d")` for recent changes
+    """)
+
+
+def _format_search_results(results: list[dict], query: str) -> str:
+    """Format search result dicts into readable markdown."""
+    if not results:
+        return f"No results found for '{query}'."
+
+    lines = [f"Found {len(results)} results:\n"]
+
+    for item in results:
+        title = item.get("title", "Untitled")
+        permalink = item.get("permalink", "")
+        score = item.get("score")
+        score_text = f" (score: {score:.2f})" if score else ""
+
+        lines.append(f"- **{title}**{score_text}")
+        if permalink:
+            lines.append(f"  permalink: {permalink}")
+        content = item.get("content")
+        if content:
+            # Truncate content snippet
+            content = content[:200] + "..." if len(content) > 200 else content
+            lines.append(f"  {content}")
+        lines.append("")
+
+    return "\n".join(lines)

src/basic_memory/mcp/prompts/utils.py

@@ -95,8 +95,8 @@ def format_prompt_context(context: PromptContext) -> str:
     sections = []
 
     # Process each context
-    for context in context.results:  # pyright: ignore
-        for primary in context.primary_results:  # pyright: ignore
+    for context_item in context.results:
+        for primary in context_item.primary_results:
             if primary.permalink not in added_permalinks:
                 primary_permalink = primary.permalink
 
@@ -121,8 +121,8 @@ def format_prompt_context(context: PromptContext) -> str:
                 section += f"- **Created**: {primary.created_at.strftime('%Y-%m-%d %H:%M')}\n"
 
                 # Add content snippet
-                if hasattr(primary, "content") and primary.content:  # pyright: ignore
-                    content = primary.content or ""  # pyright: ignore  # pragma: no cover
+                if hasattr(primary, "content") and primary.content:
+                    content = primary.content or ""  # pragma: no cover
                     if content:  # pragma: no cover
                         section += f"\n**Excerpt**:\n{content}\n"  # pragma: no cover
 
@@ -132,14 +132,14 @@ def format_prompt_context(context: PromptContext) -> str:
                     """)
                 sections.append(section)
 
-        if context.related_results:  # pyright: ignore
-            section += dedent(  # pyright: ignore
+        if context_item.related_results:
+            section += dedent(
                 """   
                 ## Related Context
                 """
             )
 
-            for related in context.related_results:  # pyright: ignore
+            for related in context_item.related_results:
                 section_content = dedent(f"""
                     - type: **{related.type}**
                     - title: {related.title}