chore: update version to 0.21.0 for v0.21.0 release

docs: add v0.21.0 changelog entry
Promotes the Unreleased breaking-change note and adds the full v0.21.0 section covering ~80 commits since v0.20.3: workspace-routing fixes across MCP/CLI/API, recent_activity ordering and search opt-in changes, sync hardening, sqlite-vec graceful degrade, perf wins on CLI startup and sync, and the project-delete cleanup landed in #832. Signed-off-by: phernandez <paul@basicmachines.co>
2026-06-21 13:47:35 +00:00 · 2026-05-16 17:15:53 -05:00 · 2026-05-16 17:15:43 -05:00 · 2026-05-16 16:47:24 -05:00 · 2026-05-15 17:59:58 -05:00 · 2026-05-15 17:48:49 -05:00
110 changed files with 9311 additions and 2387 deletions
@@ -10,6 +10,9 @@ on:
    #   - "src/**/*.js"
    #   - "src/**/*.jsx"

+env:
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: "true"
+
 jobs:
  claude-review:
    # Only run for organization members and collaborators
@@ -27,7 +30,7 @@ jobs:

    steps:
      - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
        with:
          fetch-depth: 1

@@ -4,6 +4,9 @@ on:
  issues:
    types: [opened]

+env:
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: "true"
+
 jobs:
  triage:
    runs-on: ubuntu-latest
@@ -12,7 +15,7 @@ jobs:
      id-token: write
    steps:
      - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
        with:
          fetch-depth: 1

@@ -68,4 +71,4 @@ jobs:

            Read the issue carefully and provide helpful triage with appropriate labels.

-          claude_args: '--allowed-tools "Bash(gh issue:*),Bash(gh search:*),Read"'
+          claude_args: '--allowed-tools "Bash(gh issue:*),Bash(gh search:*),Read"'
@@ -12,6 +12,9 @@ on:
  pull_request_target:
    types: [opened, synchronize]

+env:
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: "true"
+
 jobs:
  claude:
    if: |
@@ -41,7 +44,7 @@ jobs:
      actions: read # Required for Claude to read CI results on PRs
    steps:
      - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
        with:
          # For pull_request_target, checkout the PR head to review the actual changes
          ref: ${{ github.event_name == 'pull_request_target' && github.event.pull_request.head.sha || github.sha }}
@@ -65,4 +68,3 @@ jobs:
          # See https://github.com/anthropics/claude-code-action/blob/main/docs/usage.md
          # or https://docs.claude.com/en/docs/claude-code/sdk#command-line for available options
          # claude_args: '--model claude-opus-4-1-20250805 --allowed-tools Bash(gh pr:*)'
-
@@ -5,6 +5,9 @@ on:
    branches: [main]
  workflow_dispatch:  # Allow manual triggering

+env:
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: "true"
+
 jobs:
  dev-release:
    runs-on: ubuntu-latest
@@ -13,12 +16,12 @@ jobs:
      contents: write

    steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
        with:
          fetch-depth: 0

      - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
        with:
          python-version: "3.12"

@@ -50,4 +53,4 @@ jobs:
        uses: pypa/gh-action-pypi-publish@release/v1
        with:
          password: ${{ secrets.PYPI_TOKEN }}
-          skip-existing: true  # Don't fail if version already exists
+          skip-existing: true  # Don't fail if version already exists
@@ -9,6 +9,7 @@ on:
 env:
  REGISTRY: ghcr.io
  IMAGE_NAME: basicmachines-co/basic-memory
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: "true"

 jobs:
  docker:
@@ -19,17 +20,17 @@ jobs:

    steps:
      - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
        with:
          fetch-depth: 0

      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
+        uses: docker/setup-buildx-action@v4
        with:
          platforms: linux/amd64,linux/arm64

      - name: Log in to GitHub Container Registry
-        uses: docker/login-action@v3
+        uses: docker/login-action@v4
        with:
          registry: ${{ env.REGISTRY }}
          username: ${{ github.actor }}
@@ -37,7 +38,7 @@ jobs:

      - name: Extract metadata
        id: meta
-        uses: docker/metadata-action@v5
+        uses: docker/metadata-action@v6
        with:
          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
          tags: |
@@ -48,7 +49,7 @@ jobs:
            type=raw,value=latest,enable={{is_default_branch}}

      - name: Build and push Docker image
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v7
        with:
          context: .
          file: ./Dockerfile
@@ -58,4 +59,3 @@ jobs:
          labels: ${{ steps.meta.outputs.labels }}
          cache-from: type=gha
          cache-to: type=gha,mode=max
-
@@ -7,11 +7,14 @@ on:
      - edited
      - synchronize

+env:
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: "true"
+
 jobs:
  main:
    runs-on: ubuntu-latest
    steps:
-      - uses: amannn/action-semantic-pull-request@v5
+      - uses: amannn/action-semantic-pull-request@v6
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        with:
@@ -38,4 +41,4 @@ jobs:
            deps
            installer
          # Allow breaking changes (needs "!" after type/scope)
-          requireScopeForBreakingChange: true
+          requireScopeForBreakingChange: true
@@ -5,6 +5,9 @@ on:
    tags:
      - 'v*'  # Trigger on version tags like v1.0.0, v0.13.0, etc.

+env:
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: "true"
+
 jobs:
  release:
    runs-on: ubuntu-latest
@@ -13,12 +16,12 @@ jobs:
      contents: write

    steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
        with:
          fetch-depth: 0

      - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
        with:
          python-version: "3.12"

@@ -39,7 +42,7 @@ jobs:
          echo "Build completed successfully"

      - name: Create GitHub Release
-        uses: softprops/action-gh-release@v2
+        uses: softprops/action-gh-release@v3
        with:
          files: |
            dist/*.whl
@@ -64,7 +67,7 @@ jobs:
      actions: read
    steps:
      - name: Update Homebrew formula
-        uses: mislav/bump-homebrew-formula-action@v3
+        uses: mislav/bump-homebrew-formula-action@v4.1
        with:
          # Formula name in homebrew-basic-memory repo
          formula-name: basic-memory
@@ -82,4 +85,3 @@ jobs:
        env:
          # Personal Access Token with repo scope for homebrew-basic-memory repo
          COMMITTER_TOKEN: ${{ secrets.HOMEBREW_TOKEN }}
-
@@ -11,6 +11,9 @@ on:
  # Outcome: each branch push runs the test suite once, including PR updates.
  push:

+env:
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: "true"
+
 jobs:
  static-checks:
    name: Static Checks (Python 3.12)
@@ -18,12 +21,12 @@ jobs:
    runs-on: ubuntu-latest

    steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
        with:
          submodules: true

      - name: Set up Python 3.12
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v6
        with:
          python-version: "3.12"
          cache: "pip"
@@ -32,7 +35,7 @@ jobs:
        run: |
          pip install uv

-      - uses: extractions/setup-just@v3
+      - uses: extractions/setup-just@v4

      - name: Create virtual env
        run: |
@@ -52,7 +55,7 @@ jobs:

  test-sqlite-unit:
    name: Test SQLite Unit (${{ matrix.os }}, Python ${{ matrix.python-version }})
-    timeout-minutes: 30
+    timeout-minutes: 45
    strategy:
      fail-fast: false
      matrix:
@@ -68,12 +71,12 @@ jobs:
    runs-on: ${{ matrix.os }}

    steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
        with:
          submodules: true

      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v6
        with:
          python-version: ${{ matrix.python-version }}
          cache: 'pip'
@@ -82,7 +85,7 @@ jobs:
        run: |
          pip install uv

-      - uses: extractions/setup-just@v3
+      - uses: extractions/setup-just@v4

      - name: Create virtual env
        run: |
@@ -114,12 +117,12 @@ jobs:
    runs-on: ${{ matrix.os }}

    steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
        with:
          submodules: true

      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v6
        with:
          python-version: ${{ matrix.python-version }}
          cache: 'pip'
@@ -128,7 +131,7 @@ jobs:
        run: |
          pip install uv

-      - uses: extractions/setup-just@v3
+      - uses: extractions/setup-just@v4

      - name: Create virtual env
        run: |
@@ -144,7 +147,7 @@ jobs:

  test-postgres-unit:
    name: Test Postgres Unit (Python ${{ matrix.python-version }})
-    timeout-minutes: 30
+    timeout-minutes: 60
    strategy:
      fail-fast: false
      matrix:
@@ -171,12 +174,12 @@ jobs:
      BASIC_MEMORY_TEST_POSTGRES_URL: postgresql://basic_memory_user:dev_password@127.0.0.1:5432/basic_memory_test

    steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
        with:
          submodules: true

      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v6
        with:
          python-version: ${{ matrix.python-version }}
          cache: 'pip'
@@ -185,7 +188,7 @@ jobs:
        run: |
          pip install uv

-      - uses: extractions/setup-just@v3
+      - uses: extractions/setup-just@v4

      - name: Create virtual env
        run: |
@@ -228,12 +231,12 @@ jobs:
      BASIC_MEMORY_TEST_POSTGRES_URL: postgresql://basic_memory_user:dev_password@127.0.0.1:5432/basic_memory_test

    steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
        with:
          submodules: true

      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v6
        with:
          python-version: ${{ matrix.python-version }}
          cache: 'pip'
@@ -242,7 +245,7 @@ jobs:
        run: |
          pip install uv

-      - uses: extractions/setup-just@v3
+      - uses: extractions/setup-just@v4

      - name: Create virtual env
        run: |
@@ -262,12 +265,12 @@ jobs:
    runs-on: ubuntu-latest

    steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
        with:
          submodules: true

      - name: Set up Python 3.12
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v6
        with:
          python-version: "3.12"
          cache: "pip"
@@ -276,7 +279,7 @@ jobs:
        run: |
          pip install uv

-      - uses: extractions/setup-just@v3
+      - uses: extractions/setup-just@v4

      - name: Create virtual env
        run: |
@@ -1,6 +1,123 @@
 # CHANGELOG

-## Unreleased
+## v0.21.0 (2026-05-16)
+
+Workspace-aware everywhere: every MCP tool and CLI command now routes through the
+same workspace/project model, the search and sync paths are noticeably faster,
+and a handful of long-standing parsing and routing footguns are gone.
+
+### Breaking Changes
+
+- Relation parsing no longer treats unquoted multi-word text before a wikilink as a
+  custom relation type. Use single-token relation types like `relates_to [[Target]]`,
+  or quote multi-word relation types like `"relates to" [[Target]]` or
+  `'relates to' [[Target]]`.
+  - Bare list wikilinks like `- [[Target]]` now index as `links_to`.
+  - Prose list items like `- some other thing [[Target]]` now index as `links_to`.
+  - To preserve existing multi-word relation types on re-sync, quote them before upgrading.
+  - See **#824**.
+
+### Features
+
+- **#816**: `bm orphan` CLI command surfaces entities whose underlying markdown
+  files are gone, with a flag to clean them out.
+- **#789**: Create projects directly by cloud workspace slug from MCP
+  (`create_memory_project(workspace=...)`).
+- **#757**: Discover projects across every accessible cloud workspace in MCP's
+  project list — no more per-workspace blind spots.
+- **#766**: MCP tools accept training-data-friendly parameter aliases
+  (`q`/`search`/`text` for `query`, etc.) so models reach for them naturally.
+- **#776**: `bm db reset` refuses to run while a `basic-memory mcp` process is
+  alive, so resets can no longer corrupt an open session.
+- **#791**: Search responses include result totals so pagers can stop guessing.
+- **#719**: Cloud `note_content` tenant schema primitive lands on the backend.
+- **#715**: `bm project add` accepts a `--visibility` flag for cloud projects.
+
+### Bug Fixes
+
+#### Search and recent activity
+- **#832**: SQLite project deletion now sweeps `search_index`,
+  `search_vector_chunks`, and `search_vector_embeddings`, so a project that
+  reuses a recycled auto-increment id can't inherit the previous tenant's content.
+- **#812**: `recent_activity` orders and filters by `updated_at`, so edits bubble
+  to the top instead of staying pinned to creation time.
+- **#807**: Multi-project `search_notes` is opt-in (`search_all_projects=True`);
+  default search stays scoped to the resolved project.
+- **#785**: `recent_activity` caps responses and emits an explicit truncation
+  footer instead of silently dropping rows.
+- **#713**: Eliminated an N+1 query in search result hydration.
+
+#### Workspace / project routing
+- **#822**: `bm project list` now includes projects from every workspace, not
+  just the current one.
+- **#813**, **#808**, **#806**, **#803**, **#801**, **#795**, **#790**, **#778**,
+  **#777**, **#722**, **#712**, **#704**: Workspace-qualified permalink routing
+  is centralized and applied consistently across `edit_note`, `delete_project`,
+  `build_context`, `memory://` URLs, factory-mode project listing, cloud uploads,
+  and the API client.
+
+#### Sync
+- **#827**: `rclone bisync` filters from `.bmignore` are preserved across syncs.
+- **#815**: Watch service ignores hidden paths relative to the watched project,
+  not just relative to `$HOME`.
+- **#814**: `scan` subprocesses no longer go through the shell, avoiding quoting
+  issues with paths that contain special characters.
+- **#759**: Watch service stays inside `--project` scope.
+- **#746**: Canonical markdown is preserved during single-file sync.
+
+#### Parsing
+- **#796**: Picoschema modifier descriptions (`field?(modifier, description)`)
+  parse correctly.
+- **#769**: Obsidian callout blocks are skipped by the observation parser
+  instead of being mis-extracted as observations.
+
+#### CLI
+- **#775**: `bm project set-cloud` / `set-local` cleans up local DB state for
+  the affected project.
+- **#773**: `bm cloud logout` clears `default_workspace`.
+- **#780**: `bm cloud setup` hint points at `bm cloud sync-setup`.
+- **#734**: `bm project info` shows cloud index freshness.
+- **#718**: Private cloud projects display under their `display_name` instead of
+  raw UUID.
+- **#768**: `read_note` / `view_note` drop no-op pagination params from their
+  signatures.
+
+#### Stability
+- **#774**: `sqlite-vec` failures during init degrade gracefully to keyword-only
+  search instead of crashing startup.
+- **#733**: Delete-vector and cloud-sync cleanup is now consistent.
+- **#702**: Race conditions in concurrent `delete_entity` are resolved.
+- **#724**: `external_id` is preserved when entities are re-upserted during a
+  re-index.
+- **#728**: Vector init no longer issues runtime `ALTER TABLE`.
+- **#744**: `BASIC_MEMORY_CONFIG_DIR` is honored across remaining call sites.
+- **#743**: FastEmbed cache lives under the data dir instead of `/tmp`.
+- **#752**: Cloud projects report `source=cloud` in factory mode.
+- Stripped null bytes from markdown content before DB insert.
+- Allowed long `relation_type` values in API responses.
+
+#### Installer
+- **#772**: Docker-compose config volume mounts under the `appuser` home.
+- **#695**: Bumped `brew outdated` timeout from 15s to 60s.
+
+### Performance
+
+- **#828**: CLI startup no longer pulls in the local ASGI FastAPI app when it
+  isn't needed.
+- **#751**, **#726**, **#717**, **#714**, single-file/batch indexing: marked
+  speedups on the sync hot path; unchanged markdown is skipped entirely.
+- **#731**, **#723**: Vector sync is faster on both backends, with tuned
+  fastembed defaults.
+
+### Maintenance
+
+- **#825**: Dependency refresh + security hardening.
+- Updated to `fastmcp` 3.3.1.
+- **#754**: Removed in-house telemetry wrappers in favor of direct `logfire`
+  usage.
+- **#736**: `ty` is now the default typechecker.
+- **#771**, **#770**, **#716**: New regression guards for vector-row cleanup,
+  long relation types, and recent activity hydration.

 ## v0.20.3 (2026-03-26)

@@ -8,6 +8,71 @@

 ## Reporting a Vulnerability

-Use this section to tell people how to report a vulnerability.
+If you find a vulnerability, please contact hello@basicmachines.co.

-If you find a vulnerability, please contact hello@basicmachines.co
+Please do not open a public GitHub issue for security vulnerabilities. We aim
+to respond within 72 hours and will coordinate a fix and disclosure timeline
+with you.
+
+## Threat Model
+
+Basic Memory is a local-first MCP server that reads and writes markdown files
+inside configured project directories. It runs on your machine with your user
+permissions, so local configuration deserves the same care as any other
+developer tool that can access your files.
+
+### What Basic Memory Controls
+
+- Filesystem-touching tools validate paths against the configured project root
+  with `validate_project_path()`, resolved paths, and `Path.is_relative_to()`.
+  Path traversal attempts such as `../../etc/passwd` are blocked at this layer.
+- Scan optimizations in `sync_service.py` call `find` through
+  `asyncio.create_subprocess_exec()` with explicit argument lists. Project paths
+  are passed as data, not interpolated into shell strings.
+- Auto-update code uses hardcoded commands, list-form arguments, and
+  `stdin=DEVNULL`. User-controlled strings do not reach a shell there.
+
+### MCP Client-Side Risk
+
+Recent MCP ecosystem research has highlighted a client-side pattern where an
+MCP host can be configured to run arbitrary commands as "servers." That risk is
+in the host configuration, not in notes or Basic Memory tool input.
+
+The recommended Basic Memory MCP configuration uses a known command with
+explicit arguments:
+
+```json
+{
+  "mcpServers": {
+    "basic-memory": {
+      "command": "uvx",
+      "args": ["basic-memory", "mcp"]
+    }
+  }
+}
+```
+
+Only add MCP server entries from sources you trust. Avoid inline shell scripts
+or command strings copied from untrusted sources. Treat third-party MCP server
+configuration with the same scrutiny as any locally executed program.
+
+Related ecosystem context:
+
+- OX Security: The Mother of All AI Supply Chains
+- CSO Online: RCE by design: MCP architectural choice haunts AI agent ecosystem
+
+### Out Of Scope
+
+- Basic Memory does not execute note content as code. Notes are returned as
+  data to the LLM.
+- Basic Memory does not open network ports by default. The MCP server uses
+  stdio; the optional REST API is intended for localhost use.
+- Basic Memory is designed for single-user local knowledge bases and does not
+  implement access controls between operating-system users.
+
+## Secure Configuration Checklist
+
+- MCP config `command` points to `uvx` or a trusted binary, not a shell string.
+- Project paths in Basic Memory config come from trusted local configuration.
+- If exposing the REST API, bind it only to localhost.
+- Review any third-party MCP servers before adding them to your host config.
@@ -106,7 +106,7 @@ The parser excludes these list item patterns:
 |---------|---------|--------|
 | Checkboxes | `- [ ] Todo item`, `- [x] Done`, `- [-] Cancelled` | Task list syntax |
 | Markdown links | `- [text](url)` | URL link syntax |
-| Bare wiki links | `- [[Target]]` | Treated as a relation instead |
+| Bare wiki links | `- [[Target]]` | Treated as a `links_to` relation instead |

 A list item with `#tags` but no `[category]` is still parsed — the tags are extracted and the category defaults to `Note`.

@@ -116,47 +116,65 @@ Relations connect documents to form the knowledge graph. There are two kinds.

 ### Explicit Relations

-Written as list items with a relation type and a `[[wiki link]]` target.
+Written as list items with a relation type and a `[[wiki link]]` target. Unquoted
+relation types are single tokens. Quote relation types that contain spaces.

 **Syntax:**

 ```
 - relation_type [[Target Entity]] (context)
+- "multi word relation type" [[Target Entity]] (context)
+- 'multi word relation type' [[Target Entity]] (context)
 ```

 | Part | Required | Description |
 |------|----------|-------------|
-| `relation_type` | No | Text before `[[`. Defaults to `relates_to` if omitted. |
+| `relation_type` | Yes | Single unquoted token before `[[`, or quoted text for multi-word labels. |
 | `[[Target]]` | Yes | Wiki link to the target entity. Matched by title or permalink. |
 | `(context)` | No | Parenthesized text after `]]`. Supporting details. |

 ### Examples

+Explicit relations:
+
 ```markdown
 - implements [[Search Design]]
 - depends_on [[Database Schema]]
 - works_at [[Y Combinator]] (co-founder)
- [[Some Entity]]
+- "based on" [[Customer Interview]]
+- 'in response to' [[Incident Review]]
 ```

-The last example — a bare `[[wiki link]]` in a list item — gets relation type `relates_to`.
+Bare wiki links and prose list items create implicit `links_to` relations:
+
+```markdown
+- [[Some Entity]]
+- some other thing [[Some Entity]]
+```
+
+Both examples above create `links_to [[Some Entity]]`. Use quotes when the words before
+`[[` are meant to be a multi-word relation type.

 Common relation types:
 - `implements`, `depends_on`, `relates_to`, `inspired_by`
 - `extends`, `part_of`, `contains`, `pairs_with`
 - `works_at`, `authored`, `collaborated_with`

-Any text works as a relation type. These are conventions, not a fixed set.
+Any single-token text or quoted text works as a relation type. These are conventions,
+not a fixed set.

 ### Inline References

-Wiki links appearing in regular prose (not as list items) create implicit `links_to` relations.
+Wiki links appearing in regular prose create implicit `links_to` relations. This includes
+list items that do not match the explicit relation grammar above.

 ```markdown
 This builds on [[Core Design]] and uses [[Utility Functions]].
+- We should revisit [[Search Design]] after the API changes.
 ```

-This creates two relations: `links_to [[Core Design]]` and `links_to [[Utility Functions]]`.
+This creates three relations: `links_to [[Core Design]]`, `links_to [[Utility Functions]]`,
+and `links_to [[Search Design]]`.

 ### Forward References

@@ -94,13 +94,18 @@ bm cloud setup
 ```

 **What this does:**
-1. Installs rclone automatically (if needed)
+1. Installs rclone with a supported package manager (if needed)
 2. Fetches your tenant information from cloud
 3. Generates scoped S3 credentials for sync
 4. Configures single rclone remote: `basic-memory-cloud`

 **Result:** You're ready to sync projects. No sync directories created yet - those come with project setup.

+Rclone setup uses package managers such as Homebrew, MacPorts, apt, dnf, yum, pacman,
+zypper, snap, winget, Chocolatey, or Scoop when available. It does not run remote
+install scripts with `sudo`; if no supported package manager is found, the CLI prints
+manual install instructions.
+
 ### 3. Add Projects with Sync

 Create projects with optional local sync paths:
@@ -485,6 +490,9 @@ bm cloud create-key "my-laptop"    # Creates key and saves it locally
 ```

 The API key is account-level — it grants access to all your cloud projects. It's stored in `~/.basic-memory/config.json` as `cloud_api_key`.
+On POSIX systems, Basic Memory writes `~/.basic-memory/` as user-private (`0700`) and
+`config.json` as user-read/write only (`0600`). Treat this config file as a credential
+file when an API key is saved.

 ### Setting Project Modes

@@ -574,33 +582,62 @@ bm cloud logout
 **Default patterns:**

 ```gitignore
-# Version control
-.git/**
-
-# Python
-__pycache__/**
-*.pyc
-.venv/**
-venv/**
-
-# Node.js
-node_modules/**
+# Hidden files and directories
+.*

 # Basic Memory internals
-memory.db/**
-memory.db-shm/**
-memory.db-wal/**
-config.json/**
-watch-status.json/**
-.bmignore.rclone/**
+*.db
+*.db-shm
+*.db-wal
+config.json
+
+# Version control
+.git
+.svn
+
+# Python
+__pycache__
+*.pyc
+*.pyo
+*.pyd
+.pytest_cache
+.coverage
+*.egg-info
+.tox
+.mypy_cache
+.ruff_cache
+
+# Virtual environments
+.venv
+venv
+env
+.env
+
+# Node.js
+node_modules
+
+# Build artifacts
+build
+dist
+.cache
+
+# IDE
+.idea
+.vscode

 # OS files
-.DS_Store/**
-Thumbs.db/**
+.DS_Store
+Thumbs.db
+desktop.ini

-# Environment files
-.env/**
-.env.local/**
+# Obsidian
+.obsidian
+
+# Temporary files
+*.tmp
+*.swp
+*.swo
+*~
 ```

 **How it works:**
@@ -609,6 +646,11 @@ Thumbs.db/**
 3. Rclone uses filters during sync
 4. Same patterns used by all projects

+During conversion, file patterns exclude the direct match and recursive contents.
+For example, `config.json` becomes both `- config.json` and `- config.json/**`,
+while `.*` becomes both `- .*` and `- .*/**`. Directory-only patterns keep
+their trailing slash, so `cache/` becomes `- cache/` and `- cache/**`.
+
 **Customizing:**

 ```bash
@@ -616,7 +658,7 @@ Thumbs.db/**
 code ~/.basic-memory/.bmignore

 # Add custom patterns
-echo "*.tmp/**" >> ~/.basic-memory/.bmignore
+echo "*.tmp" >> ~/.basic-memory/.bmignore

 # Next sync uses updated patterns
 bm project bisync --name research
@@ -624,6 +666,33 @@ bm project bisync --name research

 ## Troubleshooting

+### Rclone Setup Cannot Install Automatically
+
+**Problem:** `bm cloud setup` cannot find a supported package manager, or package-manager
+installation fails.
+
+**Explanation:** The CLI avoids remote privileged install scripts. It only invokes known
+package managers and otherwise asks you to install rclone manually.
+
+**Solution:** Install rclone with your OS package manager, then rerun setup:
+
+```bash
+# macOS
+brew install rclone
+
+# Debian/Ubuntu
+sudo apt install rclone
+
+# Fedora
+sudo dnf install rclone
+
+# Arch
+sudo pacman -S rclone
+
+# After rclone is on PATH
+bm cloud setup
+```
+
 ### Authentication Issues

 **Problem:** "Authentication failed" or "Invalid token"
@@ -759,8 +828,10 @@ If instance is down, wait a few minutes and retry.

 - **Authentication**: OAuth 2.1 with PKCE flow
 - **Tokens**: Stored securely in `~/.basic-memory/basic-memory-cloud.json`
+- **API keys**: Stored in `~/.basic-memory/config.json`, which is written with private file permissions on POSIX systems
 - **Transport**: All data encrypted in transit (HTTPS)
 - **Credentials**: Scoped S3 credentials (read-write to your tenant only)
+- **Rclone setup**: Uses package managers or manual instructions; no remote privileged install-script fallback
 - **Isolation**: Your data isolated from other tenants
 - **Ignore patterns**: Sensitive files automatically excluded via `.bmignore`

@@ -785,7 +856,7 @@ bm cloud create-key <name>  # Create API key via cloud API (requires OAuth login
 ### Setup

 ```bash
-bm cloud setup              # Install rclone and configure credentials
+bm cloud setup              # Install rclone via package manager and configure credentials
 ```

 ### Project Management
@@ -25,11 +25,12 @@ dependencies = [
    "unidecode>=1.3.8",
    "dateparser>=1.2.0",
    "watchfiles>=1.0.4",
-    "fastapi[standard]>=0.115.8",
+    "fastapi[standard]>=0.136.1",
    "alembic>=1.14.1",
    "pillow>=11.1.0",
    "pybars3>=0.9.7",
-    "fastmcp>=3.0.1,<4",
+    # Keep FastMCP pinned until each minor upgrade passes the MCP transport matrix.
+    "fastmcp==3.3.1",
    "pyjwt>=2.10.1",
    "python-dotenv>=1.1.0",
    "pytest-aio>=1.9.0",
@@ -6,12 +6,12 @@
    "url": "https://github.com/basicmachines-co/basic-memory.git",
    "source": "github"
  },
-  "version": "0.20.3",
+  "version": "0.21.0",
  "packages": [
    {
      "registryType": "pypi",
      "identifier": "basic-memory",
-      "version": "0.20.3",
+      "version": "0.21.0",
      "runtimeHint": "uvx",
      "runtimeArguments": [
        {"type": "positional", "value": "basic-memory"},
@@ -1,7 +1,7 @@
 """basic-memory - Local-first knowledge management combining Zettelkasten with knowledge graphs"""

 # Package version - updated by release automation
-__version__ = "0.20.3"
+__version__ = "0.21.0"

 # API version for FastAPI - independent of package version
 __api_version__ = "v0"
@@ -0,0 +1,86 @@
+"""Remove orphaned search rows whose project was already deleted.
+
+Revision ID: n7i8j9k0l1m2
+Revises: m6h7i8j9k0l1
+Create Date: 2026-05-15 18:30:00.000000
+
+"""
+
+from typing import Sequence, Union
+
+from alembic import op
+from sqlalchemy import inspect
+
+
+revision: str = "n7i8j9k0l1m2"
+down_revision: Union[str, None] = "m6h7i8j9k0l1"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def _table_exists(connection, table_name: str) -> bool:
+    """Inspector-based table check, dialect agnostic.
+
+    Trigger: SQLite creates search_index as an FTS5 virtual table at runtime
+    via SearchRepository.init_search_index, not through Alembic, so fresh
+    installs hit this migration before the table exists.
+    Why: a blind DELETE against a missing table fails the whole upgrade.
+    Outcome: callers skip the sweep when the table isn't present yet — the
+    runtime-created table on a fresh DB has no orphans to clean.
+    """
+    return table_name in inspect(connection).get_table_names()
+
+
+def upgrade() -> None:
+    """Purge orphaned search rows left over from prior project deletions.
+
+    Trigger: project deletion on SQLite never removed the derived FTS rows,
+    because the FTS5 virtual table can't carry a foreign key. The leak shows
+    up in two shapes:
+    1. project_id no longer exists in `project` (deleted project, id never
+       reused).
+    2. project_id still exists but `entity_id` no longer exists in `entity`
+       — auto-increment handed the id to a brand-new project and the FTS
+       rows from the deleted predecessor masquerade as the new tenant's data.
+    Why: search_index.project_id is the only scope predicate the search
+    repository applies, so leftover rows surface under the wrong project on
+    every search.
+    Outcome: a one-time sweep deletes both shapes, from the FTS index and
+    from search_vector_chunks. Postgres already cascaded on FK delete, so
+    these statements are no-ops there.
+    """
+    connection = op.get_bind()
+
+    if _table_exists(connection, "search_index"):
+        op.execute(
+            """
+            DELETE FROM search_index
+            WHERE project_id NOT IN (SELECT id FROM project)
+            """
+        )
+        op.execute(
+            """
+            DELETE FROM search_index
+            WHERE entity_id IS NOT NULL
+              AND entity_id NOT IN (SELECT id FROM entity)
+            """
+        )
+
+    if _table_exists(connection, "search_vector_chunks"):
+        op.execute(
+            """
+            DELETE FROM search_vector_chunks
+            WHERE project_id NOT IN (SELECT id FROM project)
+            """
+        )
+        op.execute(
+            """
+            DELETE FROM search_vector_chunks
+            WHERE entity_id NOT IN (SELECT id FROM entity)
+            """
+        )
+
+
+def downgrade() -> None:
+    """No-op: orphan rows cannot be reconstructed."""
+    pass
@@ -10,6 +10,7 @@ import logging
 from fastapi import APIRouter, Form, HTTPException, UploadFile, status, Path

 from basic_memory.deps import (
+    AppConfigDep,
    ChatGPTImporterV2ExternalDep,
    ClaudeConversationsImporterV2ExternalDep,
    ClaudeProjectsImporterV2ExternalDep,
@@ -27,9 +28,21 @@ logger = logging.getLogger(__name__)
 router = APIRouter(prefix="/import", tags=["import-v2"])


+async def read_import_upload(file: UploadFile, max_bytes: int) -> bytes:
+    """Read an import upload with a hard cap before JSON parsing."""
+    content = await file.read(max_bytes + 1)
+    if len(content) > max_bytes:
+        raise HTTPException(
+            status_code=status.HTTP_413_CONTENT_TOO_LARGE,
+            detail=f"Import file exceeds maximum size of {max_bytes} bytes.",
+        )
+    return content
+
+
@router.post("/chatgpt", response_model=ChatImportResult)
 async def import_chatgpt(
    importer: ChatGPTImporterV2ExternalDep,
+    config: AppConfigDep,
    file: UploadFile,
    project_id: str = Path(..., description="Project external UUID"),
    directory: str = Form("conversations"),
@@ -49,12 +62,13 @@ async def import_chatgpt(
        HTTPException: If import fails.
    """
    logger.info(f"V2 Importing ChatGPT conversations for project {project_id}")
-    return await import_file(importer, file, directory)
+    return await import_file(importer, file, directory, config.import_upload_max_bytes)


@router.post("/claude/conversations", response_model=ChatImportResult)
 async def import_claude_conversations(
    importer: ClaudeConversationsImporterV2ExternalDep,
+    config: AppConfigDep,
    file: UploadFile,
    project_id: str = Path(..., description="Project external UUID"),
    directory: str = Form("conversations"),
@@ -74,12 +88,13 @@ async def import_claude_conversations(
        HTTPException: If import fails.
    """
    logger.info(f"V2 Importing Claude conversations for project {project_id}")
-    return await import_file(importer, file, directory)
+    return await import_file(importer, file, directory, config.import_upload_max_bytes)


@router.post("/claude/projects", response_model=ProjectImportResult)
 async def import_claude_projects(
    importer: ClaudeProjectsImporterV2ExternalDep,
+    config: AppConfigDep,
    file: UploadFile,
    project_id: str = Path(..., description="Project external UUID"),
    directory: str = Form("projects"),
@@ -99,12 +114,13 @@ async def import_claude_projects(
        HTTPException: If import fails.
    """
    logger.info(f"V2 Importing Claude projects for project {project_id}")
-    return await import_file(importer, file, directory)
+    return await import_file(importer, file, directory, config.import_upload_max_bytes)


@router.post("/memory-json", response_model=EntityImportResult)
 async def import_memory_json(
    importer: MemoryJsonImporterV2ExternalDep,
+    config: AppConfigDep,
    file: UploadFile,
    project_id: str = Path(..., description="Project external UUID"),
    directory: str = Form("conversations"),
@@ -126,7 +142,7 @@ async def import_memory_json(
    logger.info(f"V2 Importing memory.json for project {project_id}")
    try:
        file_data = []
-        file_bytes = await file.read()
+        file_bytes = await read_import_upload(file, config.import_upload_max_bytes)
        file_str = file_bytes.decode("utf-8")
        for line in file_str.splitlines():
            json_data = json.loads(line)
@@ -138,6 +154,8 @@ async def import_memory_json(
                status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
                detail=result.error_message or "Import failed",
            )
+    except HTTPException:
+        raise
    except Exception as e:
        logger.exception("V2 Import failed")
        raise HTTPException(
@@ -147,13 +165,16 @@ async def import_memory_json(
    return result


-async def import_file(importer: Importer, file: UploadFile, destination_directory: str):
+async def import_file(
+    importer: Importer, file: UploadFile, destination_directory: str, max_bytes: int
+):
    """Helper function to import a file using an importer instance.

    Args:
        importer: The importer instance to use
        file: The file to import
        destination_directory: Destination directory for imported content
+        max_bytes: Maximum upload size in bytes; raises HTTP 413 if exceeded

    Returns:
        Import result from the importer
@@ -163,7 +184,8 @@ async def import_file(importer: Importer, file: UploadFile, destination_director
    """
    try:
        # Process file
-        json_data = json.load(file.file)
+        upload_bytes = await read_import_upload(file, max_bytes)
+        json_data = json.loads(upload_bytes)
        result = await importer.import_data(json_data, destination_directory)
        if not result.success:  # pragma: no cover
            raise HTTPException(
@@ -173,6 +195,8 @@ async def import_file(importer: Importer, file: UploadFile, destination_director

        return result

+    except HTTPException:
+        raise
    except Exception as e:
        logger.exception("V2 Import failed")
        raise HTTPException(
@@ -38,6 +38,7 @@ from basic_memory.schemas.v2 import (
    MoveEntityRequestV2,
    MoveDirectoryRequestV2,
    DeleteDirectoryRequestV2,
+    OrphanEntitiesResponse,
 )
 from basic_memory.schemas.response import DirectoryMoveResult, DirectoryDeleteResult

@@ -110,6 +111,38 @@ async def get_graph(
        return GraphResponse(nodes=nodes, edges=edges)


+## Orphan entities endpoint
+
+
+@router.get("/orphans", response_model=OrphanEntitiesResponse)
+async def get_orphan_entities(
+    project_id: ProjectExternalIdPathDep,
+    entity_repository: EntityRepositoryV2ExternalDep,
+) -> OrphanEntitiesResponse:
+    """Return entities that have no incoming or outgoing relations."""
+    with logfire.span(
+        "api.request.knowledge.get_orphans",
+        entrypoint="api",
+        domain="knowledge",
+        action="get_orphans",
+    ):
+        logger.info("API v2 request: get_orphan_entities")
+
+        entities = await entity_repository.find_without_relations()
+        nodes = [
+            GraphNode(
+                external_id=entity.external_id,
+                title=entity.title,
+                note_type=entity.note_type,
+                file_path=entity.file_path,
+            )
+            for entity in entities
+        ]
+
+        logger.info(f"API v2 response: {len(nodes)} orphan entities")
+        return OrphanEntitiesResponse(entities=nodes, total=len(nodes))
+
+
 ## Resolution endpoint


@@ -11,7 +11,7 @@ Key improvements:
 """

 import os
-from typing import Optional
+from typing import Literal, Optional

 from fastapi import APIRouter, HTTPException, Body, Query, Path
 from loguru import logger
@@ -25,6 +25,8 @@ from basic_memory.deps import (
    ProjectExternalIdPathDep,
 )
 from basic_memory.schemas import SyncReportResponse
+from basic_memory.models import Project
+from basic_memory.repository.project_repository import ProjectRepository
 from basic_memory.schemas.project_info import (
    ProjectItem,
    ProjectList,
@@ -36,6 +38,71 @@ from basic_memory.schemas.v2 import ProjectResolveRequest, ProjectResolveRespons
 from basic_memory.utils import normalize_project_path, generate_permalink

 router = APIRouter(prefix="/projects", tags=["project_management-v2"])
+ProjectResolveMethod = Literal["external_id", "name", "permalink"]
+
+
+def _split_qualified_project_identifier(identifier: str) -> tuple[str | None, str]:
+    """Split ``<workspace>/<project>`` identifiers while preserving plain project names."""
+    cleaned = identifier.strip()
+    if "/" not in cleaned:
+        return None, cleaned
+
+    workspace_identifier, project_identifier = cleaned.split("/", 1)
+    if not workspace_identifier or not project_identifier:
+        return None, cleaned
+    return workspace_identifier, project_identifier
+
+
+async def _resolve_project_identifier_candidate(
+    project_repository: ProjectRepository,
+    identifier: str,
+) -> tuple[Project | None, ProjectResolveMethod]:
+    """Resolve one project identifier candidate and report the matching method."""
+    identifier_permalink = generate_permalink(identifier)
+
+    project = await project_repository.get_by_external_id(identifier)
+    if project:
+        return project, "external_id"
+
+    project = await project_repository.get_by_permalink(identifier_permalink)
+    if project:
+        return project, "permalink"
+
+    project = await project_repository.get_by_name_case_insensitive(identifier)
+    if project:
+        return project, "name"  # pragma: no cover
+
+    return None, "name"
+
+
+async def _resolve_project_identifier(
+    project_repository: ProjectRepository,
+    identifier: str,
+) -> tuple[Project | None, ProjectResolveMethod]:
+    """Resolve exact identifiers first, then accepted workspace-qualified forms."""
+    project, resolution_method = await _resolve_project_identifier_candidate(
+        project_repository,
+        identifier,
+    )
+    if project:
+        return project, resolution_method
+
+    workspace_identifier, project_identifier = _split_qualified_project_identifier(identifier)
+    if workspace_identifier is None:
+        return None, resolution_method
+
+    # Trigger: an MCP disambiguation error suggested ``workspace/project``.
+    # Why: request routing already selected the workspace/tenant; this endpoint
+    #   only needs the project segment to validate the active project.
+    # Outcome: models can follow the hint verbatim instead of looping on a 404.
+    project, resolution_method = await _resolve_project_identifier_candidate(
+        project_repository,
+        project_identifier,
+    )
+    if project:
+        return project, resolution_method
+
+    return None, resolution_method


@router.get("/", response_model=ProjectList)
@@ -247,28 +314,10 @@ async def resolve_project_identifier(
    """
    logger.info(f"API v2 request: resolve_project_identifier for '{data.identifier}'")

-    # Generate permalink for comparison
-    identifier_permalink = generate_permalink(data.identifier)
-
-    resolution_method = "name"
-    project = None
-
-    # Try external_id first (UUID format)
-    project = await project_repository.get_by_external_id(data.identifier)
-    if project:
-        resolution_method = "external_id"
-
-    # If not found by external_id, try by permalink (exact match)
-    if not project:
-        project = await project_repository.get_by_permalink(identifier_permalink)
-        if project:
-            resolution_method = "permalink"
-
-    # If not found by permalink, try case-insensitive name search
-    if not project:
-        project = await project_repository.get_by_name_case_insensitive(data.identifier)
-        if project:
-            resolution_method = "name"  # pragma: no cover
+    project, resolution_method = await _resolve_project_identifier(
+        project_repository,
+        data.identifier,
+    )

    if not project:
        raise HTTPException(status_code=404, detail=f"Project not found: '{data.identifier}'")
@@ -4,6 +4,8 @@ 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
@@ -12,7 +14,7 @@ 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,
@@ -65,7 +67,7 @@ async def search(
        has_filters=bool(query.note_types or query.entity_types or query.metadata_filters),
    ):
        offset = (page - 1) * page_size
-        fetch_limit = page_size + 1
+        exact_count_available = query.retrieval_mode == SearchRetrievalMode.FTS
        try:
            with logfire.span(
                "api.search.search.execute_query",
@@ -75,7 +77,14 @@ async def search(
                page=page,
                page_size=page_size,
            ):
-                results = await search_service.search(query, limit=fetch_limit, offset=offset)
+                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:
@@ -90,9 +99,15 @@ async def search(
            phase="paginate_results",
            result_count=len(results),
        ):
-            has_more = len(results) > page_size
-            if has_more:
-                results = results[:page_size]
+            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",
@@ -113,6 +128,7 @@ async def search(
                results=search_results,
                current_page=page,
                page_size=page_size,
+                total=total,
                has_more=has_more,
            )

@@ -18,7 +18,7 @@ from basic_memory.services.context_service import (


 class EntityBatchLookup(Protocol):
-    async def find_by_ids(self, ids: List[int]) -> Sequence[Any]: ...
+    async def find_by_ids_for_hydration(self, ids: List[int]) -> Sequence[Any]: ...


 class EntityServiceBatchLookup(Protocol):
@@ -76,7 +76,7 @@ async def to_graph_context(
                    if item.to_id:
                        entity_ids_needed.add(item.to_id)

-        # Batch fetch all entities at once - get both title and external_id
+        # Batch fetch just the entity fields needed to shape the response.
        entity_title_lookup: dict[int, str] = {}
        entity_external_id_lookup: dict[int, str] = {}
        if entity_ids_needed:
@@ -87,7 +87,9 @@ async def to_graph_context(
                phase="lookup_entities",
                result_count=len(entity_ids_needed),
            ):
-                entities = await entity_repository.find_by_ids(list(entity_ids_needed))
+                entities = await entity_repository.find_by_ids_for_hydration(
+                    list(entity_ids_needed)
+                )
            for e in entities:
                entity_title_lookup[e.id] = e.title
                entity_external_id_lookup[e.id] = e.external_id
@@ -1,6 +1,6 @@
 """CLI commands for basic-memory."""

-from . import status, db, doctor, import_memory_json, mcp, import_claude_conversations
+from . import status, db, doctor, import_memory_json, mcp, import_claude_conversations, orphans
 from . import (
    import_claude_projects,
    import_chatgpt,
@@ -18,6 +18,7 @@ __all__ = [
    "import_memory_json",
    "mcp",
    "import_claude_conversations",
+    "orphans",
    "import_claude_projects",
    "import_chatgpt",
    "tool",
@@ -14,6 +14,24 @@ class BisyncError(Exception):
    pass


+def _rclone_exclude_filters(pattern: str) -> list[str]:
+    """Return rclone exclude filters for a gitignore-style pattern."""
+    if pattern.endswith("/"):
+        # Trigger: gitignore-style patterns ending in / are directory-only rules.
+        # Why: stripping the slash would also exclude a same-named file.
+        # Outcome: rclone keeps the directory rule and excludes recursive contents.
+        return [f"- {pattern}", f"- {pattern}**"]
+
+    path_pattern = pattern.removesuffix("/**")
+
+    # Trigger: rclone treats a directory contents filter separately from the
+    # directory/file path itself.
+    # Why: files like config.json and directory markers like .obsidian must both
+    # be excluded, along with anything below matching directories.
+    # Outcome: every ignore pattern excludes the direct match and recursive children.
+    return [f"- {path_pattern}", f"- {path_pattern}/**"]
+
+
 async def get_mount_info() -> TenantMountInfo:
    """Get current tenant information from cloud API."""
    try:
@@ -78,19 +96,11 @@ def convert_bmignore_to_rclone_filters() -> Path:
                    patterns.append(line)
                    continue

-                # Convert gitignore pattern to rclone filter syntax
-                # gitignore: node_modules  → rclone: - node_modules/**
-                # gitignore: *.pyc        → rclone: - *.pyc
-                if "*" in line:
-                    # Pattern already has wildcard, just add exclude prefix
-                    patterns.append(f"- {line}")
-                else:
-                    # Directory pattern - add /** for recursive exclude
-                    patterns.append(f"- {line}/**")
+                patterns.extend(_rclone_exclude_filters(line))

    except Exception:
        # If we can't read the file, create a minimal filter
-        patterns = ["# Error reading .bmignore, using minimal filters", "- .git/**"]
+        patterns = ["# Error reading .bmignore, using minimal filters", "- .git", "- .git/**"]

    # Write rclone filter file
    rclone_filter_path.write_text("\n".join(patterns) + "\n")
@@ -4,7 +4,7 @@ import os
 import platform
 import shutil
 import subprocess
-from typing import Optional
+from typing import Any, Optional, cast

 from rich.console import Console

@@ -53,7 +53,9 @@ def run_command(command: list[str], check: bool = True) -> subprocess.CompletedP


 def install_rclone_macos() -> None:
-    """Install rclone on macOS using Homebrew or official script."""
+    """Install rclone on macOS using package managers."""
+    install_errors: list[str] = []
+
    # Try Homebrew first
    if shutil.which("brew"):
        try:
@@ -61,35 +63,37 @@ def install_rclone_macos() -> None:
            run_command(["brew", "install", "rclone"])
            console.print("[green]rclone installed via Homebrew[/green]")
            return
-        except RcloneInstallError:
-            console.print(
-                "[yellow]Homebrew installation failed, trying official script...[/yellow]"
-            )
+        except RcloneInstallError as exc:
+            install_errors.append(f"Homebrew failed: {exc}")
+            console.print("[yellow]Homebrew installation failed, trying MacPorts...[/yellow]")

-    # Fallback to official script
-    console.print("[blue]Installing rclone via official script...[/blue]")
-    try:
-        run_command(["sh", "-c", "curl https://rclone.org/install.sh | sudo bash"])
-        console.print("[green]rclone installed via official script[/green]")
-    except RcloneInstallError:
-        raise RcloneInstallError(
-            "Failed to install rclone. Please install manually: brew install rclone"
-        )
+    if shutil.which("port"):
+        try:
+            console.print("[blue]Installing rclone via MacPorts...[/blue]")
+            run_command(["sudo", "port", "install", "rclone"])
+            console.print("[green]rclone installed via MacPorts[/green]")
+            return
+        except RcloneInstallError as exc:
+            install_errors.append(f"MacPorts failed: {exc}")
+            console.print("[yellow]MacPorts installation failed[/yellow]")
+
+    details = "\n".join(f"- {error}" for error in install_errors)
+    if details:
+        details = f"\n\nAttempts:\n{details}"
+    raise RcloneInstallError(
+        "Could not install rclone automatically with an available package manager.\n\n"
+        "Install rclone manually with one of:\n"
+        "  brew install rclone\n"
+        "  sudo port install rclone\n"
+        "  Download from https://rclone.org/downloads/ and add rclone to PATH"
+        f"{details}"
+    )


 def install_rclone_linux() -> None:
-    """Install rclone on Linux using package managers or official script."""
-    # Try snap first (most universal)
-    if shutil.which("snap"):
-        try:
-            console.print("[blue]Installing rclone via snap...[/blue]")
-            run_command(["sudo", "snap", "install", "rclone"])
-            console.print("[green]rclone installed via snap[/green]")
-            return
-        except RcloneInstallError:
-            console.print("[yellow]Snap installation failed, trying apt...[/yellow]")
+    """Install rclone on Linux using package managers."""
+    install_errors: list[str] = []

-    # Try apt (Debian/Ubuntu)
    if shutil.which("apt"):
        try:
            console.print("[blue]Installing rclone via apt...[/blue]")
@@ -97,18 +101,75 @@ def install_rclone_linux() -> None:
            run_command(["sudo", "apt", "install", "-y", "rclone"])
            console.print("[green]rclone installed via apt[/green]")
            return
-        except RcloneInstallError:
-            console.print("[yellow]apt installation failed, trying official script...[/yellow]")
+        except RcloneInstallError as exc:
+            install_errors.append(f"apt failed: {exc}")
+            console.print("[yellow]apt installation failed, trying dnf...[/yellow]")

-    # Fallback to official script
-    console.print("[blue]Installing rclone via official script...[/blue]")
-    try:
-        run_command(["sh", "-c", "curl https://rclone.org/install.sh | sudo bash"])
-        console.print("[green]rclone installed via official script[/green]")
-    except RcloneInstallError:
-        raise RcloneInstallError(
-            "Failed to install rclone. Please install manually: sudo snap install rclone"
-        )
+    if shutil.which("dnf"):
+        try:
+            console.print("[blue]Installing rclone via dnf...[/blue]")
+            run_command(["sudo", "dnf", "install", "-y", "rclone"])
+            console.print("[green]rclone installed via dnf[/green]")
+            return
+        except RcloneInstallError as exc:
+            install_errors.append(f"dnf failed: {exc}")
+            console.print("[yellow]dnf installation failed, trying yum...[/yellow]")
+
+    if shutil.which("yum"):
+        try:
+            console.print("[blue]Installing rclone via yum...[/blue]")
+            run_command(["sudo", "yum", "install", "-y", "rclone"])
+            console.print("[green]rclone installed via yum[/green]")
+            return
+        except RcloneInstallError as exc:
+            install_errors.append(f"yum failed: {exc}")
+            console.print("[yellow]yum installation failed, trying pacman...[/yellow]")
+
+    if shutil.which("pacman"):
+        try:
+            console.print("[blue]Installing rclone via pacman...[/blue]")
+            run_command(["sudo", "pacman", "-S", "--noconfirm", "rclone"])
+            console.print("[green]rclone installed via pacman[/green]")
+            return
+        except RcloneInstallError as exc:
+            install_errors.append(f"pacman failed: {exc}")
+            console.print("[yellow]pacman installation failed, trying zypper...[/yellow]")
+
+    if shutil.which("zypper"):
+        try:
+            console.print("[blue]Installing rclone via zypper...[/blue]")
+            run_command(["sudo", "zypper", "--non-interactive", "install", "rclone"])
+            console.print("[green]rclone installed via zypper[/green]")
+            return
+        except RcloneInstallError as exc:
+            install_errors.append(f"zypper failed: {exc}")
+            console.print("[yellow]zypper installation failed, trying snap...[/yellow]")
+
+    if shutil.which("snap"):
+        try:
+            console.print("[blue]Installing rclone via snap...[/blue]")
+            run_command(["sudo", "snap", "install", "rclone"])
+            console.print("[green]rclone installed via snap[/green]")
+            return
+        except RcloneInstallError as exc:
+            install_errors.append(f"snap failed: {exc}")
+            console.print("[yellow]snap installation failed[/yellow]")
+
+    details = "\n".join(f"- {error}" for error in install_errors)
+    if details:
+        details = f"\n\nAttempts:\n{details}"
+    raise RcloneInstallError(
+        "Could not install rclone automatically with an available package manager.\n\n"
+        "Install rclone manually with one of your OS package managers, for example:\n"
+        "  sudo apt install rclone\n"
+        "  sudo dnf install rclone\n"
+        "  sudo yum install rclone\n"
+        "  sudo pacman -S rclone\n"
+        "  sudo zypper install rclone\n"
+        "  sudo snap install rclone\n"
+        "Or download from https://rclone.org/downloads/ and add rclone to PATH"
+        f"{details}"
+    )


 def install_rclone_windows() -> None:
@@ -209,27 +270,38 @@ def refresh_windows_path() -> None:
    if platform.system().lower() != "windows":
        return

-    # Importing here after performing platform detection. Also note that we have to ignore pylance/pyright
-    # warnings about winreg attributes so that "errors" don't appear on non-Windows platforms.
+    # Importing here after performing platform detection. Non-Windows type checkers may still
+    # resolve a stub without registry members, so keep this platform-only module dynamic here.
    import winreg

+    winreg_module = cast(Any, winreg)
    user_key_path = r"Environment"
    system_key_path = r"System\CurrentControlSet\Control\Session Manager\Environment"
    new_path = ""

    # Read user PATH
    try:
-        reg_key = winreg.OpenKey(winreg.HKEY_CURRENT_USER, user_key_path, 0, winreg.KEY_READ)  # type: ignore[reportAttributeAccessIssue]
-        user_path, _ = winreg.QueryValueEx(reg_key, "PATH")  # type: ignore[reportAttributeAccessIssue]
-        winreg.CloseKey(reg_key)  # type: ignore[reportAttributeAccessIssue]
+        reg_key = winreg_module.OpenKey(
+            winreg_module.HKEY_CURRENT_USER,
+            user_key_path,
+            0,
+            winreg_module.KEY_READ,
+        )
+        user_path, _ = winreg_module.QueryValueEx(reg_key, "PATH")
+        winreg_module.CloseKey(reg_key)
    except Exception:
        user_path = ""

    # Read system PATH
    try:
-        reg_key = winreg.OpenKey(winreg.HKEY_LOCAL_MACHINE, system_key_path, 0, winreg.KEY_READ)  # type: ignore[reportAttributeAccessIssue]
-        system_path, _ = winreg.QueryValueEx(reg_key, "PATH")  # type: ignore[reportAttributeAccessIssue]
-        winreg.CloseKey(reg_key)  # type: ignore[reportAttributeAccessIssue]
+        reg_key = winreg_module.OpenKey(
+            winreg_module.HKEY_LOCAL_MACHINE,
+            system_key_path,
+            0,
+            winreg_module.KEY_READ,
+        )
+        system_path, _ = winreg_module.QueryValueEx(reg_key, "PATH")
+        winreg_module.CloseKey(reg_key)
    except Exception:
        system_path = ""

@@ -6,10 +6,11 @@ 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,
+from basic_memory.mcp.project_context import get_available_workspaces
+from basic_memory.schemas.cloud import (
+    format_workspace_choices,
+    format_workspace_selection_choices,
+    workspace_matches_identifier,
 )

 console = Console()
@@ -62,7 +63,10 @@ def list_workspaces() -> None:

@workspace_app.command("set-default")
 def set_default_workspace(
-    identifier: str = typer.Argument(..., help="Workspace name or tenant_id to set as default"),
+    identifier: str = typer.Argument(
+        ...,
+        help="Workspace name, slug, type, or tenant_id to set as default",
+    ),
 ) -> None:
    """Set the default cloud workspace.

@@ -71,6 +75,7 @@ def set_default_workspace(

    Examples:
      bm cloud workspace set-default Personal
+      bm cloud workspace set-default organization
      bm cloud workspace set-default 11111111-1111-1111-1111-111111111111
    """

@@ -87,19 +92,19 @@ def set_default_workspace(
        console.print("[yellow]No accessible workspaces found.[/yellow]")
        raise typer.Exit(1)

-    matches = [ws for ws in workspaces if _workspace_matches_identifier(ws, identifier)]
+    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]")
+        console.print(f"[dim]Available:\n{format_workspace_choices(workspaces)}[/dim]")
        raise typer.Exit(1)

    if len(matches) > 1:
+        console.print(f"[red]Error: Workspace '{identifier}' matches multiple workspaces.[/red]")
        console.print(
-            f"[red]Error: Workspace name '{identifier}' matches multiple workspaces. "
-            f"Use tenant_id instead.[/red]"
+            "[dim]Choose one of these matching workspaces by slug:\n"
+            f"{format_workspace_selection_choices(matches)}[/dim]"
        )
-        console.print(f"[dim]Available:\n{_workspace_choices(workspaces)}[/dim]")
        raise typer.Exit(1)

    selected = matches[0]
@@ -0,0 +1,93 @@
+"""Orphans command - show entities with no relations in the knowledge graph."""
+
+import json
+from typing import Annotated, Optional
+
+import typer
+from loguru import logger
+from mcp.server.fastmcp.exceptions import ToolError
+from rich.console import Console
+from rich.table import Table
+
+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.clients.knowledge import KnowledgeClient
+from basic_memory.mcp.project_context import get_active_project
+from basic_memory.schemas.v2.graph import GraphNode
+
+console = Console()
+
+
+async def run_orphans(project: Optional[str] = None) -> tuple[str, list[GraphNode]]:
+    """Fetch entities that have no relations in the knowledge graph."""
+    project = project or ConfigManager().default_project
+
+    async with get_client(project_name=project) as client:
+        project_item = await get_active_project(client, project, None)
+        entities = await KnowledgeClient(client, project_item.external_id).get_orphans()
+        return project_item.name, entities
+
+
+@app.command()
+def orphans(
+    project: Annotated[
+        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)"
+    ),
+    cloud: bool = typer.Option(False, "--cloud", help="Force cloud API routing"),
+):
+    """Show entities that have no relations in the knowledge graph.
+
+    Orphan entities have no incoming or outgoing connections. These may indicate
+    newly created notes not yet linked to other entities, or notes that have had
+    their relations removed.
+    """
+    from basic_memory.cli.commands.command_utils import run_with_cleanup
+
+    try:
+        validate_routing_flags(local, cloud)
+        with force_routing(local=local, cloud=cloud):
+            project_name, entities = run_with_cleanup(run_orphans(project))
+
+        if json_output:
+            print(json.dumps([entity.model_dump(mode="json") for entity in entities], indent=2))
+            return
+
+        if not entities:
+            console.print(f"[green]No orphan entities in project '{project_name}'[/green]")
+            return
+
+        table = Table(title=f"{project_name}: Entities Without Relations ({len(entities)} total)")
+        table.add_column("Title", style="cyan")
+        table.add_column("File Path", style="yellow")
+        table.add_column("Type", style="green")
+
+        for entity in entities:
+            table.add_row(
+                entity.title,
+                entity.file_path,
+                entity.note_type or "",
+            )
+
+        console.print(table)
+    except (ValueError, ToolError) as exc:
+        if json_output:
+            print(json.dumps({"error": str(exc)}, indent=2))
+        else:
+            console.print(f"[red]Error: {exc}[/red]")
+        raise typer.Exit(code=1)
+    except typer.Exit:
+        raise
+    except Exception as exc:
+        logger.error(f"Error fetching orphan entities: {exc}")
+        if json_output:
+            print(json.dumps({"error": str(exc)}, indent=2))
+        else:
+            console.print(f"[red]Error: {exc}[/red]")
+        raise typer.Exit(code=1)  # pragma: no cover
@@ -7,6 +7,7 @@ from pathlib import Path
 from typing import cast

 import typer
+from loguru import logger
 from rich.console import Console, Group
 from rich.panel import Panel
 from rich.table import Table
@@ -33,6 +34,10 @@ from basic_memory.schemas.cloud import (
    CloudProjectIndexStatus,
    CloudTenantIndexStatusResponse,
    ProjectVisibility,
+    WorkspaceInfo,
+    format_workspace_choices,
+    format_workspace_selection_choices,
+    workspace_matches_identifier,
 )
 from basic_memory.schemas.project_info import ProjectItem, ProjectList
 from basic_memory.utils import generate_permalink, normalize_project_path
@@ -281,27 +286,25 @@ def _normalize_project_visibility(visibility: str | None) -> ProjectVisibility:


 def _resolve_workspace_id(config, workspace: str | None) -> str | None:
-    """Resolve a workspace name or tenant_id to a tenant_id."""
+    """Resolve a workspace name, slug, type, or tenant_id to a tenant_id."""
    from basic_memory.mcp.project_context import (
-        _workspace_choices,
-        _workspace_matches_identifier,
        get_available_workspaces,
    )

    if workspace is not None:
        workspaces = run_with_cleanup(get_available_workspaces())
-        matches = [ws for ws in workspaces if _workspace_matches_identifier(ws, workspace)]
+        matches = [ws for ws in workspaces if workspace_matches_identifier(ws, workspace)]
        if not matches:
            console.print(f"[red]Error: Workspace '{workspace}' not found[/red]")
            if workspaces:
-                console.print(f"[dim]Available:\n{_workspace_choices(workspaces)}[/dim]")
+                console.print(f"[dim]Available:\n{format_workspace_choices(workspaces)}[/dim]")
            raise typer.Exit(1)
        if len(matches) > 1:
+            console.print(f"[red]Error: Workspace '{workspace}' matches multiple workspaces.[/red]")
            console.print(
-                f"[red]Error: Workspace name '{workspace}' matches multiple workspaces. "
-                f"Use tenant_id instead.[/red]"
+                "[dim]Choose one of these matching workspaces by slug:\n"
+                f"{format_workspace_selection_choices(matches)}[/dim]"
            )
-            console.print(f"[dim]Available:\n{_workspace_choices(workspaces)}[/dim]")
            raise typer.Exit(1)
        return matches[0].tenant_id

@@ -312,9 +315,9 @@ def _resolve_workspace_id(config, workspace: str | None) -> str | None:
        workspaces = run_with_cleanup(get_available_workspaces())
        if len(workspaces) == 1:
            return workspaces[0].tenant_id
-    except Exception:
+    except Exception as exc:
        # Workspace resolution is optional until a command needs a specific tenant.
-        pass
+        logger.debug("Workspace resolution failed: {}", exc)

    return None

@@ -323,7 +326,11 @@ def _resolve_workspace_id(config, workspace: str | None) -> str | None:
 def list_projects(
    local: bool = typer.Option(False, "--local", help="Force local routing for this command"),
    cloud: bool = typer.Option(False, "--cloud", help="Force cloud API routing"),
-    workspace: str = typer.Option(None, "--workspace", help="Cloud workspace name or tenant_id"),
+    workspace: str = typer.Option(
+        None,
+        "--workspace",
+        help="Cloud workspace name, slug, type, or tenant_id",
+    ),
    json_output: bool = typer.Option(False, "--json", help="Output in JSON format"),
 ) -> None:
    """List Basic Memory projects from local and (when available) cloud."""
@@ -339,17 +346,90 @@ def list_projects(

    try:
        config = ConfigManager().config
-        # Use explicit workspace, fall back to config default
-        effective_workspace = workspace or config.default_workspace
+        workspace_filter = workspace
+        workspace_filter_requested = workspace_filter is not None

        local_result: ProjectList | None = None
-        cloud_result: ProjectList | None = None
+        cloud_results: list[tuple[WorkspaceInfo | None, ProjectList]] = []
+        available_cloud_workspaces: list[WorkspaceInfo] = []
        cloud_error: Exception | None = None
+        cloud_workspace_error: Exception | None = None
+        failed_cloud_workspaces: list[tuple[WorkspaceInfo, Exception]] = []
+
+        def _fetch_cloud_workspace_results() -> tuple[
+            list[tuple[WorkspaceInfo | None, ProjectList]],
+            list[WorkspaceInfo],
+            Exception | None,
+            list[tuple[WorkspaceInfo, Exception]],
+        ]:
+            from basic_memory.mcp.project_context import (
+                get_available_workspaces,
+            )
+
+            try:
+                workspaces = run_with_cleanup(get_available_workspaces())
+            except Exception as exc:
+                fallback_workspace = workspace_filter or config.default_workspace
+                return (
+                    [(None, run_with_cleanup(_list_projects(fallback_workspace)))],
+                    [],
+                    exc,
+                    [],
+                )
+
+            selected_workspaces = workspaces
+            if workspace_filter is not None:
+                matches = [
+                    ws for ws in workspaces if workspace_matches_identifier(ws, workspace_filter)
+                ]
+                if not matches:
+                    console.print(f"[red]Error: Workspace '{workspace_filter}' not found[/red]")
+                    if workspaces:
+                        console.print(
+                            f"[dim]Available:\n{format_workspace_choices(workspaces)}[/dim]"
+                        )
+                    raise typer.Exit(1)
+                if len(matches) > 1:
+                    console.print(
+                        f"[red]Error: Workspace '{workspace_filter}' matches multiple workspaces.[/red]"
+                    )
+                    console.print(
+                        "[dim]Choose one of these matching workspaces by slug:\n"
+                        f"{format_workspace_selection_choices(matches)}[/dim]"
+                    )
+                    raise typer.Exit(1)
+                selected_workspaces = matches
+
+            if not selected_workspaces:
+                return [], workspaces, None, []
+
+            results: list[tuple[WorkspaceInfo | None, ProjectList]] = []
+            failed_workspaces: list[tuple[WorkspaceInfo, Exception]] = []
+            for cloud_workspace in selected_workspaces:
+                try:
+                    results.append(
+                        (
+                            cloud_workspace,
+                            run_with_cleanup(_list_projects(cloud_workspace.tenant_id)),
+                        )
+                    )
+                except Exception as exc:
+                    failed_workspaces.append((cloud_workspace, exc))
+
+            if not results and failed_workspaces:
+                raise failed_workspaces[0][1]
+
+            return results, workspaces, None, failed_workspaces

        if cloud:
            with console.status("[bold blue]Fetching cloud projects...", spinner="dots"):
                with force_routing(cloud=True):
-                    cloud_result = run_with_cleanup(_list_projects(effective_workspace))
+                    (
+                        cloud_results,
+                        available_cloud_workspaces,
+                        cloud_workspace_error,
+                        failed_cloud_workspaces,
+                    ) = _fetch_cloud_workspace_results()
        elif local:
            with force_routing(local=True):
                local_result = run_with_cleanup(_list_projects())
@@ -362,29 +442,17 @@ def list_projects(
                try:
                    with console.status("[bold blue]Fetching cloud projects...", spinner="dots"):
                        with force_routing(cloud=True):
-                            cloud_result = run_with_cleanup(_list_projects(effective_workspace))
+                            (
+                                cloud_results,
+                                available_cloud_workspaces,
+                                cloud_workspace_error,
+                                failed_cloud_workspaces,
+                            ) = _fetch_cloud_workspace_results()
+                except typer.Exit:
+                    raise
                except Exception as exc:  # pragma: no cover
                    cloud_error = exc

-        # Resolve workspace name for cloud projects (best-effort)
-        cloud_ws_name: str | None = None
-        cloud_ws_type: str | None = None
-        if cloud_result and effective_workspace:
-            try:
-                from basic_memory.mcp.project_context import get_available_workspaces
-
-                with console.status("[bold blue]Resolving workspace...", spinner="dots"):
-                    workspaces = run_with_cleanup(get_available_workspaces())
-                matched = next(
-                    (ws for ws in workspaces if ws.tenant_id == effective_workspace),
-                    None,
-                )
-                if matched:
-                    cloud_ws_name = matched.name
-                    cloud_ws_type = matched.workspace_type
-            except Exception:
-                pass
-
        table = Table(title="Basic Memory Projects")
        table.add_column("Name", style="cyan")
        table.add_column("Local Path", style="yellow", no_wrap=True, overflow="fold")
@@ -395,29 +463,126 @@ def list_projects(
        table.add_column("Sync", style="green")
        table.add_column("Default", style="magenta")

-        project_names_by_permalink: dict[str, str] = {}
+        row_names_by_key: dict[tuple[str | None, str], str] = {}
        local_projects_by_permalink: dict[str, ProjectItem] = {}
-        cloud_projects_by_permalink: dict[str, ProjectItem] = {}
+        cloud_projects_by_key: dict[tuple[str | None, str], ProjectItem] = {}
+        cloud_workspaces_by_key: dict[tuple[str | None, str], WorkspaceInfo | None] = {}

        if local_result:
            for project in local_result.projects:
                permalink = generate_permalink(project.name)
-                project_names_by_permalink[permalink] = project.name
                local_projects_by_permalink[permalink] = project

-        if cloud_result:
+        for cloud_workspace, cloud_result in cloud_results:
+            workspace_key = cloud_workspace.tenant_id if cloud_workspace else None
            for project in cloud_result.projects:
                permalink = generate_permalink(project.name)
-                project_names_by_permalink[permalink] = project.name
-                cloud_projects_by_permalink[permalink] = project
+                row_key = (workspace_key, permalink)
+                row_names_by_key[row_key] = project.name
+                cloud_projects_by_key[row_key] = project
+                cloud_workspaces_by_key[row_key] = cloud_workspace
+
+        cloud_permalinks = {permalink for _, permalink in cloud_projects_by_key}
+        for permalink, project in local_projects_by_permalink.items():
+            if permalink not in cloud_permalinks:
+                row_names_by_key[(None, permalink)] = project.name
+
+        cloud_keys_by_permalink: dict[str, list[tuple[str | None, str]]] = {}
+        for row_key in cloud_projects_by_key:
+            cloud_keys_by_permalink.setdefault(row_key[1], []).append(row_key)
+
+        configured_names_by_permalink = {
+            generate_permalink(project_name): project_name for project_name in config.projects
+        }
+
+        def _workspace_priority(row_key: tuple[str | None, str]) -> tuple[bool, int, str, str]:
+            """Prefer the user's default/personal workspace when a project is duplicated."""
+            workspace = cloud_workspaces_by_key.get(row_key)
+            if workspace is None:
+                return (True, 2, "", row_key[0] or "")
+            workspace_type_rank = 0 if workspace.workspace_type == "personal" else 1
+            return (
+                not workspace.is_default,
+                workspace_type_rank,
+                workspace.name.casefold(),
+                row_key[0] or "",
+            )
+
+        def _select_attached_row_key(
+            permalink: str, entry: ProjectEntry | None
+        ) -> tuple[str | None, str] | None:
+            """Choose the single row that owns local config/default/sync state."""
+            cloud_keys = cloud_keys_by_permalink.get(permalink, [])
+            if not cloud_keys:
+                return (None, permalink)
+
+            preferred_workspace_ids: list[str] = []
+            if entry and entry.workspace_id:
+                preferred_workspace_ids.append(entry.workspace_id)
+            if config.default_workspace and config.default_workspace not in preferred_workspace_ids:
+                preferred_workspace_ids.append(config.default_workspace)
+            default_cloud_workspace = next(
+                (item for item in available_cloud_workspaces if item.is_default),
+                None,
+            )
+            if (
+                default_cloud_workspace
+                and default_cloud_workspace.tenant_id not in preferred_workspace_ids
+            ):
+                preferred_workspace_ids.append(default_cloud_workspace.tenant_id)
+
+            for workspace_id in preferred_workspace_ids:
+                for row_key in cloud_keys:
+                    if row_key[0] == workspace_id:
+                        return row_key
+
+            if workspace_filter_requested and preferred_workspace_ids:
+                # A filtered list can exclude the workspace that owns local config state.
+                # In that case, do not attach local/default/sync state to another workspace row.
+                return None
+
+            default_workspace_keys = [
+                row_key
+                for row_key in cloud_keys
+                if (row_workspace := cloud_workspaces_by_key.get(row_key)) is not None
+                and row_workspace.is_default
+            ]
+            if len(default_workspace_keys) == 1:
+                return default_workspace_keys[0]
+
+            if len(cloud_keys) == 1:
+                return cloud_keys[0]
+
+            return sorted(cloud_keys, key=_workspace_priority)[0]
+
+        attached_row_by_permalink: dict[str, tuple[str | None, str] | None] = {}
+        for permalink in set(local_projects_by_permalink) | set(configured_names_by_permalink):
+            configured_name = configured_names_by_permalink.get(permalink)
+            local_project = local_projects_by_permalink.get(permalink)
+            entry_name = configured_name or (local_project.name if local_project else None)
+            entry = config.projects.get(entry_name) if entry_name else None
+            attached_row_by_permalink[permalink] = _select_attached_row_key(permalink, entry)

        # --- Build unified project list ---
        project_rows: list[dict] = []
-        for permalink in sorted(project_names_by_permalink):
-            project_name = project_names_by_permalink[permalink]
-            local_project = local_projects_by_permalink.get(permalink)
-            cloud_project = cloud_projects_by_permalink.get(permalink)
-            entry = config.projects.get(project_name)
+        sorted_row_keys = sorted(
+            row_names_by_key,
+            key=lambda key: (row_names_by_key[key], key[0] or ""),
+        )
+        for row_key in sorted_row_keys:
+            _, permalink = row_key
+            project_name = row_names_by_key[row_key]
+            is_attached_row = attached_row_by_permalink.get(permalink) == row_key
+            local_project = local_projects_by_permalink.get(permalink) if is_attached_row else None
+            cloud_project = cloud_projects_by_key.get(row_key)
+            cloud_workspace = cloud_workspaces_by_key.get(row_key)
+            configured_name = configured_names_by_permalink.get(permalink)
+            configured_entry = (
+                config.projects.get(configured_name)
+                if configured_name
+                else config.projects.get(project_name)
+            )
+            entry = configured_entry if is_attached_row else None

            local_path = ""
            if local_project is not None:
@@ -447,9 +612,13 @@ def list_projects(
            else:
                cli_route = ProjectMode.LOCAL.value

-            is_default = config.default_project == project_name
+            default_permalink = (
+                generate_permalink(config.default_project) if config.default_project else None
+            )
+            is_default = bool(is_attached_row and permalink == default_permalink)

-            has_sync = bool(entry and entry.local_sync_path)
+            sync_supported = cloud_workspace is None or cloud_workspace.workspace_type == "personal"
+            has_sync = bool(is_attached_row and entry and entry.local_sync_path and sync_supported)
            # Determine MCP transport based on project routing mode
            if entry and entry.mode == ProjectMode.CLOUD:
                mcp_transport = "https"
@@ -459,9 +628,8 @@ def list_projects(
                mcp_transport = "stdio"

            # Show workspace name (type) for cloud-sourced projects
-            ws_label = ""
-            if cloud_project is not None and cloud_ws_name:
-                ws_label = f"{cloud_ws_name} ({cloud_ws_type})" if cloud_ws_type else cloud_ws_name
+            cloud_ws_name = cloud_workspace.name if cloud_workspace else None
+            cloud_ws_type = cloud_workspace.workspace_type if cloud_workspace else None

            # display_name is a human label for private UUID-named projects (e.g., "My Project").
            # Keep "name" as the canonical identifier for scripting/JSON consumers;
@@ -481,8 +649,8 @@ def list_projects(
            }
            if display_name:
                row_data["display_name"] = display_name
-            if ws_label:
-                row_data["workspace"] = cloud_ws_name or ""
+            if cloud_project is not None and cloud_ws_name:
+                row_data["workspace"] = cloud_ws_name
                if cloud_ws_type:
                    row_data["workspace_type"] = cloud_ws_type

@@ -514,6 +682,20 @@ def list_projects(
                "[dim]Showing local projects only. "
                "Run 'bm cloud login' or 'bm cloud api-key save <key>' if this is a credentials issue.[/dim]"
            )
+        if cloud_workspace_error is not None:
+            console.print(
+                f"[yellow]Cloud workspace discovery failed: {cloud_workspace_error}[/yellow]"
+            )
+            console.print(
+                "[dim]Showing cloud projects from the configured/default workspace only.[/dim]"
+            )
+        for failed_workspace, error in failed_cloud_workspaces:
+            console.print(
+                f"[yellow]Cloud project discovery failed for workspace "
+                f"{failed_workspace.name}: {error}[/yellow]"
+            )
+    except typer.Exit:
+        raise
    except Exception as e:
        console.print(f"[red]Error listing projects: {str(e)}[/red]")
        raise typer.Exit(1)
@@ -531,7 +713,7 @@ def add_project(
    workspace: str = typer.Option(
        None,
        "--workspace",
-        help="Cloud workspace name or tenant_id (cloud mode only)",
+        help="Cloud workspace name, slug, type, or tenant_id (cloud mode only)",
    ),
    visibility: str = typer.Option(
        None,
@@ -914,7 +1096,7 @@ def set_cloud(
    workspace: str = typer.Option(
        None,
        "--workspace",
-        help="Cloud workspace name or tenant_id to associate with this project",
+        help="Cloud workspace name, slug, type, or tenant_id to associate with this project",
    ),
 ) -> None:
    """Set a project to cloud mode (route through cloud API).
@@ -24,6 +24,7 @@ if not _version_only_invocation(sys.argv[1:]):
        import_claude_projects,
        import_memory_json,
        mcp,
+        orphans,
        project,
        schema,
        status,
@@ -24,10 +24,24 @@ APP_DATABASE_NAME = "memory.db"  # Using the same name but in the app directory
 DATA_DIR_NAME = ".basic-memory"
 CONFIG_FILE_NAME = "config.json"
 WATCH_STATUS_JSON = "watch-status.json"
+CONFIG_DIR_MODE = 0o700
+CONFIG_FILE_MODE = 0o600

 Environment = Literal["test", "dev", "user"]


+def _secure_config_dir(path: Path) -> None:
+    """Restrict config directory permissions on platforms with POSIX modes."""
+    if os.name != "nt":
+        path.chmod(CONFIG_DIR_MODE)
+
+
+def _secure_config_file(path: Path) -> None:
+    """Restrict config file permissions because config can contain cloud credentials."""
+    if os.name != "nt":
+        path.chmod(CONFIG_FILE_MODE)
+
+
 class ProjectMode(str, Enum):
    """Per-project routing mode."""

@@ -168,13 +182,15 @@ class BasicMemoryConfig(BaseSettings):
    env: Environment = Field(default="dev", description="Environment name")

    projects: Dict[str, ProjectEntry] = Field(
-        default_factory=lambda: {
-            "main": ProjectEntry(
-                path=str(Path(os.getenv("BASIC_MEMORY_HOME", Path.home() / "basic-memory")))
-            )
-        }
-        if os.getenv("BASIC_MEMORY_HOME")
-        else {},
+        default_factory=lambda: (
+            {
+                "main": ProjectEntry(
+                    path=str(Path(os.getenv("BASIC_MEMORY_HOME", Path.home() / "basic-memory")))
+                )
+            }
+            if os.getenv("BASIC_MEMORY_HOME")
+            else {}
+        ),
        description="Mapping of project names to their ProjectEntry configuration",
    )
    default_project: Optional[str] = Field(
@@ -278,6 +294,11 @@ class BasicMemoryConfig(BaseSettings):
        description="Optional FastEmbed embed() parallelism override.",
        gt=0,
    )
+    import_upload_max_bytes: int = Field(
+        default=100 * 1024 * 1024,
+        description="Maximum uploaded JSON export size accepted by API import endpoints.",
+        gt=0,
+    )
    semantic_vector_k: int = Field(
        default=100,
        description="Vector candidate count for vector and hybrid retrieval.",
@@ -776,6 +797,7 @@ class ConfigManager:

        # Ensure config directory exists
        self.config_dir.mkdir(parents=True, exist_ok=True)
+        _secure_config_dir(self.config_dir)

    @property
    def config(self) -> BasicMemoryConfig:
@@ -888,6 +910,7 @@ class ConfigManager:
                    # 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)
+                    _secure_config_file(backup_path)
                    logger.info(f"Migrating config to current format (backup: {backup_path})")
                    save_basic_memory_config(self.config_file, _CONFIG_CACHE)

@@ -1043,9 +1066,12 @@ def has_cloud_credentials(config: BasicMemoryConfig) -> bool:
 def save_basic_memory_config(file_path: Path, config: BasicMemoryConfig) -> None:
    """Save configuration to file."""
    try:
+        file_path.parent.mkdir(parents=True, exist_ok=True)
+        _secure_config_dir(file_path.parent)
        # Use model_dump with mode='json' to serialize datetime objects properly
        config_dict = config.model_dump(mode="json")
        file_path.write_text(json.dumps(config_dict, indent=2))
+        _secure_config_file(file_path)
    except Exception as e:  # pragma: no cover
        logger.error(f"Failed to save config: {e}")

@@ -85,6 +85,28 @@ def parse_observation(token: Token) -> Dict[str, Any]:


 # Relation handling functions
+def parse_relation_type(content: str) -> str | None:
+    """Return the explicit relation label before the first wikilink, if any."""
+    before_link = content.partition("[[")[0].strip()
+    if not before_link:
+        return None
+
+    # Trigger: relation labels that need spaces must be quoted.
+    # Why: unquoted multi-word prefixes are indistinguishable from prose
+    # containing a wikilink.
+    # Outcome: `some_type [[Target]]`, `"some type" [[Target]]`, and
+    # `'some type' [[Target]]` are explicit; `some other thing [[Target]]`
+    # falls back to inline `links_to` handling.
+    quote = before_link[0]
+    if quote in {"'", '"'} and before_link.endswith(quote):
+        quoted_label = before_link[1:-1].strip()
+        return quoted_label or None
+
+    if any(char.isspace() for char in before_link):
+        return None
+    return before_link
+
+
 def is_explicit_relation(token: Token) -> bool:
    """Check if token looks like our relation format."""
    if token.type != "inline":  # pragma: no cover
@@ -92,7 +114,7 @@ def is_explicit_relation(token: Token) -> bool:

    # Use token.tag which contains the actual content for test tokens, fallback to content
    content = (token.tag or token.content).strip()
-    return "[[" in content and "]]" in content
+    return "[[" in content and "]]" in content and parse_relation_type(content) is not None


 def parse_relation(token: Token) -> Dict[str, Any] | None:
@@ -101,20 +123,18 @@ def parse_relation(token: Token) -> Dict[str, Any] | None:
    # Use token.tag which contains the actual content for test tokens, fallback to content
    content = (token.tag or token.content).strip()

+    rel_type = parse_relation_type(content)
+    if rel_type is None:
+        return None
+
    # Extract [[target]]
    target = None
-    rel_type = "relates_to"  # default
    context = None

    start = content.find("[[")
-    end = content.find("]]")
+    end = content.find("]]", start + 2)

    if start != -1 and end != -1:
-        # Get text before link as relation type
-        before = content[:start].strip()
-        if before:
-            rel_type = before
-
        # Get target
        target = normalize_project_reference(content[start + 2 : end].strip())

@@ -217,6 +237,8 @@ def relation_plugin(md: MarkdownIt) -> None:

    Explicit relations:
    - relation_type [[target]] (context)
+    - "multi word relation type" [[target]] (context)
+    - 'multi word relation type' [[target]] (context)

    Implicit relations (links in content):
    Some text with [[target]] reference
@@ -6,7 +6,6 @@ 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


@@ -37,8 +36,18 @@ def _build_timeout() -> Timeout:

 def _asgi_client(timeout: Timeout) -> AsyncClient:
    """Create a local ASGI client."""
+    # Import on first local-client use so CLI help/version paths can import
+    # routing helpers without constructing the full FastAPI router graph.
+    from basic_memory.api.app import app as fastapi_app
+    from basic_memory.workspace_context import workspace_permalink_headers
+
    return AsyncClient(
-        transport=ASGITransport(app=fastapi_app), base_url="http://test", timeout=timeout
+        transport=ASGITransport(app=fastapi_app),
+        base_url="http://test",
+        timeout=timeout,
+        # Local ASGI calls still cross the HTTP boundary, so request handlers need
+        # the same workspace permalink metadata that cloud proxy calls receive.
+        headers=workspace_permalink_headers(),
    )


@@ -15,6 +15,7 @@ from basic_memory.schemas.response import (
    DirectoryMoveResult,
    DirectoryDeleteResult,
 )
+from basic_memory.schemas.v2.graph import GraphNode, OrphanEntitiesResponse


 class KnowledgeClient:
@@ -275,6 +276,24 @@ class KnowledgeClient:
            )
        return DirectoryDeleteResult.model_validate(response.json())

+    # --- Orphan detection ---
+
+    async def get_orphans(self) -> list[GraphNode]:
+        """Get entities that have no incoming or outgoing relations."""
+        with logfire.span(
+            "mcp.client.knowledge.get_orphans",
+            client_name="knowledge",
+            operation="get_orphans",
+        ):
+            response = await call_get(
+                self.http_client,
+                f"{self._base_path}/orphans",
+                client_name="knowledge",
+                operation="get_orphans",
+                path_template="/v2/projects/{project_id}/knowledge/orphans",
+            )
+        return OrphanEntitiesResponse.model_validate(response.json()).entities
+
    # --- Resolution ---

    async def resolve_entity(self, identifier: str, *, strict: bool = False) -> str:
@@ -11,7 +11,7 @@ compatibility with existing MCP tools.
 import asyncio
 from contextlib import asynccontextmanager, nullcontext
 from dataclasses import dataclass, field
-from typing import AsyncIterator, Awaitable, Callable, Optional, List, Tuple, cast
+from typing import AsyncIterator, Awaitable, Callable, List, Optional, Sequence, Tuple, cast
 from uuid import UUID

 from httpx import AsyncClient
@@ -25,11 +25,22 @@ from mcp.server.fastmcp.exceptions import ToolError
 import logfire
 from basic_memory.config import BasicMemoryConfig, ConfigManager, ProjectMode, has_cloud_credentials
 from basic_memory.project_resolver import ProjectResolver
-from basic_memory.schemas.cloud import WorkspaceInfo, WorkspaceListResponse
+from basic_memory.schemas.cloud import (
+    WorkspaceInfo,
+    WorkspaceListResponse,
+    format_workspace_choices,
+    format_workspace_selection_choices,
+    workspace_matches_exact_identifier,
+    workspace_matches_identifier,
+)
 from basic_memory.schemas.project_info import ProjectItem, ProjectList
 from basic_memory.schemas.v2 import ProjectResolveResponse
 from basic_memory.schemas.memory import memory_url_path
-from basic_memory.utils import generate_permalink, normalize_project_reference
+from basic_memory.utils import (
+    build_qualified_permalink_reference,
+    generate_permalink,
+    normalize_project_reference,
+)
 from basic_memory.workspace_context import (
    current_workspace_permalink_context,
    workspace_permalink_context,
@@ -162,6 +173,17 @@ async def _set_cached_active_workspace(
    await context.set_state("active_workspace", active_workspace.model_dump())


+async def _clear_cached_active_workspace_for_local_route(context: Optional[Context]) -> None:
+    """Drop tenant workspace metadata before routing through a local project."""
+    if not context:
+        return
+
+    # Trigger: local routing follows a cloud route in the same MCP session
+    # Why: active_workspace is tenant metadata, not part of local project identity
+    # Outcome: memory:// resolution uses project-only local permalinks
+    await context.set_state("active_workspace", None)
+
+
 async def _get_cached_default_project(context: Optional[Context]) -> Optional[str]:
    """Return the cached default project name from context when available."""
    if not context:
@@ -284,29 +306,6 @@ async def get_project_names(client: AsyncClient, headers: HeaderTypes | None = N
    return [project.name for project in project_list.projects]


-def _workspace_matches_identifier(workspace: WorkspaceInfo, identifier: str) -> bool:
-    """Return True when identifier matches workspace tenant_id, slug, or name."""
-    if workspace.tenant_id == identifier:
-        return True
-    if workspace.slug.casefold() == identifier.casefold():
-        return True
-    return workspace.name.lower() == identifier.lower()
-
-
-def _workspace_choices(workspaces: list[WorkspaceInfo]) -> str:
-    """Format deterministic workspace choices for prompt-style errors."""
-    return "\n".join(
-        [
-            (
-                f"- {item.name} "
-                f"(slug={item.slug}, type={item.workspace_type}, "
-                f"role={item.role}, tenant_id={item.tenant_id})"
-            )
-            for item in workspaces
-        ]
-    )
-
-
 def _workspace_project_index_from_state(raw: object) -> WorkspaceProjectIndex | None:
    """Deserialize a cached workspace project index from MCP context state."""
    if not isinstance(raw, dict):
@@ -406,14 +405,20 @@ def _unqualified_project_identifier(identifier: str) -> str:
    return project_identifier


-def _split_workspace_memory_url_segments(identifier: str) -> tuple[str, str, str] | None:
-    """Split ``memory://<workspace>/<project>/<path>`` into route segments."""
-    if not identifier.strip().startswith("memory://"):
-        return None
+def _identifier_path(identifier: str) -> str:
+    """Return the routable path portion of a raw identifier or memory URL."""
+    stripped = identifier.strip()
+    return memory_url_path(stripped) if stripped.startswith("memory://") else stripped

-    normalized = normalize_project_reference(memory_url_path(identifier))
+
+def _split_workspace_identifier_segments(identifier: str) -> tuple[str, str, str] | None:
+    """Split ``<workspace>/<project>/<path>`` identifiers into route segments."""
+    normalized = normalize_project_reference(_identifier_path(identifier)).strip("/")
    parts = normalized.split("/", 2)
    if len(parts) != 3:
+        # Trigger: two-segment identifiers such as `workspace/project` or `project/path`.
+        # Why: without a remainder, the shape is ambiguous with existing project-prefix routing.
+        # Outcome: fall through so the normal project-prefix/default-project resolver decides.
        return None

    workspace_slug, project_identifier, remainder = parts
@@ -422,28 +427,81 @@ def _split_workspace_memory_url_segments(identifier: str) -> tuple[str, str, str
    return workspace_slug, project_identifier, remainder


+def _split_workspace_memory_url_segments(identifier: str) -> tuple[str, str, str] | None:
+    """Split ``memory://<workspace>/<project>/<path>`` into route segments."""
+    if not identifier.strip().startswith("memory://"):
+        return None
+
+    return _split_workspace_identifier_segments(identifier)
+
+
 def _canonical_memory_path_for_workspace(
    *,
    workspace_slug: str,
    workspace_type: str,
    project_permalink: str,
    remainder: str,
-    include_project: bool,
 ) -> str:
    """Return the stored canonical path for a workspace-qualified memory URL."""
    normalized_remainder = remainder.strip("/")
-    if workspace_type == "organization":
-        prefix = f"{generate_permalink(workspace_slug)}/{project_permalink}"
-    elif workspace_type == "personal":
-        prefix = project_permalink if include_project else ""
-    else:
+    if workspace_type not in {"organization", "personal"}:
        raise ValueError(f"Unsupported workspace_type for memory URL routing: {workspace_type}")

-    if not prefix:
-        return normalized_remainder
+    # Trigger: a caller supplied a workspace-qualified memory URL.
+    # Why: the first two path segments are the global route, even for Personal.
+    # Outcome: lookups preserve the complete workspace/project canonical permalink.
    if not normalized_remainder:
-        return prefix
-    return f"{prefix}/{normalized_remainder}"
+        normalized_remainder = project_permalink
+    return build_qualified_permalink_reference(
+        project_permalink,
+        normalized_remainder,
+        include_project=True,
+        workspace_permalink=workspace_slug,
+    )
+
+
+def _canonical_memory_path_for_active_route(
+    active_project: ProjectItem,
+    path: str,
+    *,
+    include_project: bool,
+    cached_workspace: WorkspaceInfo | None = None,
+) -> str:
+    """Return the canonical permalink path for the currently routed project/workspace."""
+    project_prefix = active_project.permalink
+    workspace_remainder = path
+    if include_project and (path == project_prefix or path.startswith(f"{project_prefix}/")):
+        # Trigger: the memory URL already names the active project root/prefix
+        # Why: workspace canonicalization adds the project prefix itself, so
+        #   keeping it in the remainder would produce <workspace>/<project>/<project>
+        # Outcome: keep project-root and project-prefixed URLs canonical once
+        workspace_remainder = (
+            "" if path == project_prefix else path.removeprefix(f"{project_prefix}/")
+        )
+
+    workspace_context = current_workspace_permalink_context()
+    if workspace_context is not None:
+        return _canonical_memory_path_for_workspace(
+            workspace_slug=workspace_context.workspace_slug,
+            workspace_type=workspace_context.workspace_type,
+            project_permalink=active_project.permalink,
+            remainder=workspace_remainder,
+        )
+
+    if cached_workspace is not None:
+        return _canonical_memory_path_for_workspace(
+            workspace_slug=cached_workspace.slug,
+            workspace_type=cached_workspace.workspace_type,
+            project_permalink=active_project.permalink,
+            remainder=workspace_remainder,
+        )
+
+    if not include_project:
+        return path
+
+    if path == project_prefix or path.startswith(f"{project_prefix}/"):
+        return path
+    return f"{project_prefix}/{path}"


 def _cloud_workspace_discovery_available(config: BasicMemoryConfig) -> bool:
@@ -476,6 +534,27 @@ async def resolve_workspace_qualified_memory_url(
    if segments is None:
        return None

+    return await _resolve_workspace_segments(identifier, segments, context=context)
+
+
+async def resolve_workspace_qualified_identifier(
+    identifier: str,
+    context: Optional[Context] = None,
+) -> WorkspaceMemoryUrlResolution | None:
+    """Resolve a workspace-qualified permalink or memory URL against accessible workspaces."""
+    segments = _split_workspace_identifier_segments(identifier)
+    if segments is None:
+        return None
+
+    return await _resolve_workspace_segments(identifier, segments, context=context)
+
+
+async def _resolve_workspace_segments(
+    identifier: str,
+    segments: tuple[str, str, str],
+    context: Optional[Context] = None,
+) -> WorkspaceMemoryUrlResolution | None:
+    """Resolve parsed workspace/project/path segments against accessible workspaces."""
    workspace_slug, project_identifier, remainder = segments
    index = await _ensure_workspace_project_index(context=context)
    workspace = next(
@@ -525,12 +604,11 @@ async def resolve_workspace_qualified_memory_url(
        workspace_type=entry.workspace.workspace_type,
        project_permalink=entry.project.permalink,
        remainder=remainder,
-        include_project=ConfigManager().config.permalinks_include_project,
    )
    return WorkspaceMemoryUrlResolution(entry=entry, canonical_path=canonical_path)


-def _format_qualified_choices(entries: tuple[WorkspaceProjectEntry, ...]) -> str:
+def _format_qualified_choices(entries: Sequence[WorkspaceProjectEntry]) -> str:
    """Format qualified project choices for collision errors."""
    return " or ".join(entry.qualified_name for entry in entries)

@@ -656,7 +734,7 @@ async def _ensure_workspace_project_index(
                )
            continue

-        workspace_entries = cast(tuple[WorkspaceProjectEntry, ...], result)
+        workspace_entries = result
        successful_fetches += 1
        entries_list.extend(workspace_entries)

@@ -759,7 +837,7 @@ async def resolve_workspace_project_identifier(
            )
        return matches[0]

-    matches = index.entries_by_permalink.get(project_permalink, ())
+    matches = list(index.entries_by_permalink.get(project_permalink, ()))
    if not matches:
        failed_note = ""
        if index.failed_workspaces:
@@ -893,7 +971,9 @@ async def resolve_workspace_parameter(
            cached_raw = await context.get_state("active_workspace")
            if isinstance(cached_raw, dict):
                cached_workspace = WorkspaceInfo.model_validate(cached_raw)
-                if workspace is None or _workspace_matches_identifier(cached_workspace, workspace):
+                if workspace is None or workspace_matches_exact_identifier(
+                    cached_workspace, workspace
+                ):
                    logger.debug(
                        f"Using cached workspace from context: {cached_workspace.tenant_id}"
                    )
@@ -909,19 +989,17 @@ async def resolve_workspace_parameter(
        selected_workspace: WorkspaceInfo | None = None

        if workspace:
-            matches = [
-                item for item in workspaces if _workspace_matches_identifier(item, workspace)
-            ]
+            matches = [item for item in workspaces if workspace_matches_identifier(item, workspace)]
            if not matches:
                raise ValueError(
                    f"Workspace '{workspace}' was not found.\n"
-                    f"Available workspaces:\n{_workspace_choices(workspaces)}"
+                    f"Available workspaces:\n{format_workspace_choices(workspaces)}"
                )
            if len(matches) > 1:
                raise ValueError(
-                    f"Workspace name '{workspace}' matches multiple workspaces. "
-                    "Use tenant_id instead.\n"
-                    f"Available workspaces:\n{_workspace_choices(workspaces)}"
+                    f"Workspace '{workspace}' matches multiple workspaces. "
+                    "Choose one of these matching workspaces by slug or tenant_id:\n"
+                    f"{format_workspace_selection_choices(matches)}"
                )
            selected_workspace = matches[0]
        elif len(workspaces) == 1:
@@ -929,8 +1007,8 @@ async def resolve_workspace_parameter(
        else:
            raise ValueError(
                "Multiple workspaces are available. Ask the user which workspace to use, then retry "
-                "with the 'workspace' argument set to the tenant_id or unique name.\n"
-                f"Available workspaces:\n{_workspace_choices(workspaces)}"
+                "with the 'workspace' argument set to the tenant_id or unique name/slug/type.\n"
+                f"Available workspaces:\n{format_workspace_choices(workspaces)}"
            )

        await _set_cached_active_workspace(context, selected_workspace)
@@ -1073,7 +1151,6 @@ async def resolve_project_and_path(
                    workspace_type=cached_workspace.workspace_type,
                    project_permalink=cached_project.permalink,
                    remainder=remainder,
-                    include_project=bool(include_project),
                )
                return cached_project, resolved_path, True

@@ -1096,7 +1173,6 @@ async def resolve_project_and_path(
                    workspace_type=workspace_context.workspace_type,
                    project_permalink=project_permalink,
                    remainder=remainder,
-                    include_project=bool(include_project),
                )
                return active_project, resolved_path, True

@@ -1115,8 +1191,11 @@ async def resolve_project_and_path(
                        f"Project is constrained to '{resolved_project}', cannot use '{project_prefix}'."
                    )

-                resolved_path = (
-                    f"{cached_project.permalink}/{remainder}" if include_project else remainder
+                resolved_path = _canonical_memory_path_for_active_route(
+                    cached_project,
+                    remainder,
+                    include_project=include_project,
+                    cached_workspace=cached_workspace,
                )
                return cached_project, resolved_path, True

@@ -1151,25 +1230,24 @@ async def resolve_project_and_path(
                )
                await _set_cached_active_project(context, active_project)

-                resolved_path = (
-                    f"{resolved.permalink}/{remainder}" if include_project else remainder
+                resolved_path = _canonical_memory_path_for_active_route(
+                    active_project,
+                    remainder,
+                    include_project=include_project,
+                    cached_workspace=cached_workspace,
                )
                return active_project, resolved_path, True

-        # Trigger: no resolvable project prefix in the memory URL
-        # Why: preserve existing memory URL behavior within the active project
-        # Outcome: use the active project and normalize the path for lookup
+        # Trigger: memory URL has no resolvable project route segment
+        # Why: preserve active-project behavior while honoring workspace paths
+        # Outcome: normalize against the already-selected local/cloud route
        active_project = await get_active_project(client, project, context, headers)
-        resolved_path = normalized_path
-        if include_project:
-            # Trigger: project-prefixed permalinks are enabled and the path lacks a prefix
-            # Why: ensure memory URL lookups align with canonical permalinks
-            # Outcome: prefix the path with the active project's permalink
-            project_prefix = active_project.permalink
-            if resolved_path != project_prefix and not resolved_path.startswith(
-                f"{project_prefix}/"
-            ):
-                resolved_path = f"{project_prefix}/{resolved_path}"
+        resolved_path = _canonical_memory_path_for_active_route(
+            active_project,
+            normalized_path,
+            include_project=include_project,
+            cached_workspace=cached_workspace,
+        )
        return active_project, resolved_path, True


@@ -1227,17 +1305,51 @@ async def detect_project_from_memory_url_prefix(
    if not identifier.strip().startswith("memory://"):
        return None

+    return await detect_project_from_identifier_prefix(identifier, config, context=context)
+
+
+async def detect_project_from_identifier_prefix(
+    identifier: str,
+    config: BasicMemoryConfig,
+    context: Optional[Context] = None,
+) -> Optional[str]:
+    """Resolve a project from a plain permalink, memory URL, or workspace route prefix."""
    local_project = detect_project_from_url_prefix(identifier, config)
    if local_project is not None:
        return local_project

+    normalized_identifier = normalize_project_reference(_identifier_path(identifier)).strip("/")
+    if "/" not in normalized_identifier:
+        # Trigger: plain text search query or single-segment title/permalink.
+        # Why: cloud project discovery can build a workspace index; only path-shaped
+        #   identifiers carry enough structure to justify that cost.
+        # Outcome: keep unqualified search/title input on the active/default project route.
+        return None
+
    if _cloud_workspace_discovery_available(config):
-        resolution = await resolve_workspace_qualified_memory_url(
+        workspace_resolution = await resolve_workspace_qualified_identifier(
            identifier,
            context=context,
        )
-        if resolution is not None:
-            return resolution.project_identifier
+        if workspace_resolution is not None:
+            return workspace_resolution.project_identifier
+
+        project_prefix, _ = _split_project_prefix(normalized_identifier)
+        if project_prefix is None:
+            return None
+
+        try:
+            project_resolution = await resolve_workspace_project_identifier(
+                project_prefix,
+                context=context,
+            )
+        except ValueError as exc:
+            message = str(exc).lower()
+            if "not found" in message or "no accessible workspaces" in message:
+                return None
+            raise
+
+        return project_resolution.qualified_name

    return None

@@ -1325,6 +1437,7 @@ async def get_project_client(
    # Outcome: route strictly based on explicit flag, no workspace network calls
    if _explicit_routing() and _force_local_mode():
        route_mode = "explicit_local"
+        await _clear_cached_active_workspace_for_local_route(context)
        with logfire.span(
            "routing.client_session",
            project_name=resolved_project,
@@ -1397,6 +1510,7 @@ async def get_project_client(

    # Step 4: Local routing (default)
    route_mode = "local_asgi"
+    await _clear_cached_active_workspace_for_local_route(context)
    with logfire.span(
        "routing.client_session",
        project_name=resolved_project,
@@ -6,7 +6,7 @@ a list containing a single `{"type": "text", "text": "{...json...}"}` item.
 """

 import json
-from typing import Any, Dict, List, Optional
+from typing import Any, Dict, List, Optional, cast

 from fastmcp import Context
 from loguru import logger
@@ -17,18 +17,30 @@ from basic_memory.mcp.tools.search import search_notes
 from basic_memory.schemas.search import SearchResponse, SearchResult


+def _identifier_for_read_note(identifier: str) -> str:
+    """Convert ChatGPT result ids into routable Basic Memory identifiers."""
+    stripped = identifier.strip()
+    if stripped.startswith("memory://") or "/" not in stripped:
+        return identifier
+    return f"memory://{stripped}"
+
+
 def _format_search_results_for_chatgpt(
-    results: SearchResponse | list[SearchResult] | list[dict[str, Any]] | dict[str, Any],
+    results: SearchResponse | list[SearchResult | dict[str, Any]] | dict[str, Any],
 ) -> List[Dict[str, Any]]:
    """Format search results according to ChatGPT's expected schema.

    Returns a list of result objects with id, title, and url fields.
    """
    if isinstance(results, SearchResponse):
-        raw_results: list[SearchResult] | list[dict[str, Any]] = results.results
+        raw_results: list[SearchResult | dict[str, Any]] = list(results.results)
    elif isinstance(results, dict):
        nested_results = results.get("results")
-        raw_results = nested_results if isinstance(nested_results, list) else []
+        raw_results = (
+            cast(list[SearchResult | dict[str, Any]], nested_results)
+            if isinstance(nested_results, list)
+            else []
+        )
    else:
        raw_results = results

@@ -113,8 +125,7 @@ async def search(
    logger.info(f"ChatGPT search request: query='{query}'")

    try:
-        # Let search_notes resolve the default project via get_project_client(),
-        # which works in both local mode (ConfigManager) and cloud mode (database).
+        # Keep this adapter tiny: the real search behavior lives in search_notes.
        results = await search_notes(
            query=query,
            page=1,
@@ -123,7 +134,6 @@ async def search(
            context=context,
        )

-        # Handle string error responses from search_notes
        if isinstance(results, str):
            logger.warning(f"Search failed with error: {results[:100]}...")
            search_results = {
@@ -131,16 +141,17 @@ async def search(
                "error": "Search failed",
                "error_details": results[:500],  # Truncate long error messages
            }
-        else:
-            # Format successful results for ChatGPT
-            raw_results = results.get("results", []) if isinstance(results, dict) else []
-            formatted_results = _format_search_results_for_chatgpt(raw_results)
-            search_results = {
-                "results": formatted_results,
-                "total_count": len(raw_results),  # Use actual count from results
-                "query": query,
-            }
-            logger.info(f"Search completed: {len(formatted_results)} results returned")
+            return [{"type": "text", "text": json.dumps(search_results, ensure_ascii=False)}]
+
+        raw_results = results.get("results", []) if isinstance(results, dict) else []
+
+        formatted_results = _format_search_results_for_chatgpt(raw_results)
+        search_results = {
+            "results": formatted_results,
+            "total_count": len(raw_results),  # Use actual count from results
+            "query": query,
+        }
+        logger.info(f"Search completed: {len(formatted_results)} results returned")

        # Return in MCP content array format as required by OpenAI
        return [{"type": "text", "text": json.dumps(search_results, ensure_ascii=False)}]
@@ -180,7 +191,7 @@ async def fetch(
        # which works in both local mode (ConfigManager) and cloud mode (database).
        content = str(
            await read_note(
-                identifier=id,
+                identifier=_identifier_for_read_note(id),
                context=context,
            )
        )
@@ -9,6 +9,7 @@ from pydantic import AliasChoices, Field

 from basic_memory.config import ConfigManager
 from basic_memory.mcp.project_context import (
+    _cloud_workspace_discovery_available,
    detect_project_from_memory_url_prefix,
    get_project_client,
    add_project_metadata,
@@ -17,7 +18,11 @@ from basic_memory.mcp.project_context import (
 from basic_memory.mcp.server import mcp
 from basic_memory.schemas.base import Entity
 from basic_memory.schemas.response import EntityResponse
-from basic_memory.utils import validate_project_path
+from basic_memory.services.link_resolver import (
+    detect_project_from_workspace_identifier_prefix,
+    is_workspace_qualified_plain_identifier,
+)
+from basic_memory.utils import normalize_project_reference, validate_project_path


 def _parse_identifier_to_title_and_directory(identifier: str) -> tuple[str, str]:
@@ -47,6 +52,58 @@ def _parse_identifier_to_title_and_directory(identifier: str) -> tuple[str, str]
    return title, directory


+def _compose_workspace_project_route(
+    *,
+    workspace: Optional[str],
+    project: Optional[str],
+    project_id: Optional[str],
+) -> Optional[str]:
+    """Return the explicit project route requested by workspace/project args."""
+    if workspace is None:
+        return project
+
+    cleaned_workspace = workspace.strip().strip("/")
+    if not cleaned_workspace:
+        raise ValueError("workspace must not be empty when provided")
+    if "/" in cleaned_workspace:
+        raise ValueError("workspace must be a single workspace slug, name, or tenant_id")
+    if project_id is not None:
+        raise ValueError("workspace cannot be combined with project_id; use project_id alone")
+    if project is None or not project.strip().strip("/"):
+        raise ValueError("workspace requires an explicit project argument")
+
+    cleaned_project = project.strip().strip("/")
+    if "/" in cleaned_project:
+        raise ValueError(
+            "Use either workspace='workspace' with project='project', "
+            "or project='workspace/project', not both"
+        )
+    return f"{cleaned_workspace}/{cleaned_project}"
+
+
+def _format_ambiguous_workspace_identifier_response(
+    *,
+    identifier: str,
+    detected_project: str,
+) -> str:
+    """Format the safe-stop response for ambiguous plain write identifiers."""
+    cleaned_identifier = identifier.strip()
+    normalized_identifier = normalize_project_reference(cleaned_identifier).strip("/")
+    workspace_hint, project_hint, note_identifier = normalized_identifier.split("/", 2)
+
+    return f"""# Edit Failed - Ambiguous Identifier
+
+`{cleaned_identifier}` could refer to a local note path in the active project, or to a note in `{detected_project}`.
+
+Because edit_note changes content, Basic Memory will not infer a workspace route from a plain path.
+
+Retry with one of these explicit routes:
+- `edit_note(identifier="{note_identifier}", project="{detected_project}", operation=..., content=...)`
+- `edit_note(identifier="{note_identifier}", workspace="{workspace_hint}", project="{project_hint}", operation=..., content=...)`
+- `edit_note(identifier="memory://{normalized_identifier}", operation=..., content=...)`
+- `edit_note(identifier="{note_identifier}", project_id="<project external_id>", operation=..., content=...)`"""
+
+
 def _format_error_response(
    error_message: str,
    operation: str,
@@ -181,6 +238,7 @@ async def edit_note(
        ),
    ],
    project: Optional[str] = None,
+    workspace: Optional[str] = None,
    project_id: Optional[str] = None,
    # Section/heading naming varies across tools; accept the descriptive forms.
    section: Annotated[
@@ -224,7 +282,10 @@ async def edit_note(
                  - "insert_after_section": Insert content after a section heading without consuming it (note must exist)
        content: The content to add or use for replacement
        project: Project name to edit in. Optional - server will resolve using hierarchy.
+                Use "workspace/project" to route to a project in a specific cloud workspace.
                If unknown, use list_memory_projects() to discover available projects.
+        workspace: Workspace slug, name, or tenant_id. When provided with `project`,
+                routes as `workspace/project`. Cannot be combined with `project_id`.
        project_id: Project external_id (UUID). Prefer this over `project` when known —
                it routes to the exact project regardless of name collisions across cloud
                workspaces. Takes precedence over `project`. Get from list_memory_projects().
@@ -287,18 +348,52 @@ async def edit_note(
    """
    # Resolve effective default: allow MCP clients to send null for optional int field
    effective_replacements = expected_replacements if expected_replacements is not None else 1
+    project = _compose_workspace_project_route(
+        workspace=workspace,
+        project=project,
+        project_id=project_id,
+    )

-    # Detect project from memory URL prefix before routing
-    # Trigger: identifier starts with memory:// and no explicit project/project_id was provided
-    # Why: only gate on memory:// to avoid misrouting plain paths like "research/note"
-    #      where "research" is a directory, not a project name
-    # Outcome: project is set from the URL prefix, routing goes to the correct project
-    if project is None and project_id is None and identifier.strip().startswith("memory://"):
-        detected = await detect_project_from_memory_url_prefix(
-            identifier,
-            ConfigManager().config,
-            context=context,
-        )
+    # Resolve or reject routable identifier prefixes before selecting a client.
+    # Trigger: no explicit project/project_id was provided.
+    # Why: memory:// URLs are explicit routes, but plain three-segment identifiers
+    #   are ambiguous for a mutating tool.
+    # Outcome: memory:// can route; plain workspace/project/path matches stop with
+    #   guidance instead of silently editing another project.
+    if project is None and project_id is None:
+        config = ConfigManager().config
+        if identifier.strip().startswith("memory://"):
+            detected = await detect_project_from_memory_url_prefix(
+                identifier,
+                config,
+                context=context,
+            )
+        elif _cloud_workspace_discovery_available(
+            config
+        ) and is_workspace_qualified_plain_identifier(identifier):
+            detected = await detect_project_from_workspace_identifier_prefix(
+                identifier,
+                config,
+                context=context,
+            )
+            if detected:
+                if output_format == "json":
+                    return {
+                        "title": None,
+                        "permalink": None,
+                        "file_path": None,
+                        "checksum": None,
+                        "operation": operation,
+                        "fileCreated": False,
+                        "error": "AMBIGUOUS_IDENTIFIER",
+                        "project": detected,
+                    }
+                return _format_ambiguous_workspace_identifier_response(
+                    identifier=identifier,
+                    detected_project=detected,
+                )
+        else:
+            detected = None
        if detected:
            project = detected

@@ -369,11 +369,11 @@ def _format_constrained_text(constrained_project: str) -> str:
    return result


-async def _resolve_create_project_workspace(
+async def _resolve_workspace_routing(
    workspace: str | None,
    context: Context | None,
 ) -> str | None:
-    """Resolve the create-project workspace selector to the routing tenant id."""
+    """Resolve an optional workspace selector to the routing tenant id."""
    if workspace is None:
        return None

@@ -389,7 +389,8 @@ async def _resolve_create_project_workspace(
    #   a friendly selector such as a slug, name, or tenant id.
    # Why: MCP callers should not need to paste UUIDs, but the transport still
    #   uses X-Workspace-ID with the tenant id as its routing authority.
-    # Outcome: resolve once at create time and pass only the tenant id downstream.
+    # Outcome: resolve once before the project-management request and pass only
+    #   the tenant id downstream.
    resolved_workspace = await resolve_workspace_parameter(workspace=workspace, context=context)
    return resolved_workspace.tenant_id

@@ -418,8 +419,8 @@ async def create_memory_project(
        workspace: Optional cloud workspace selector to create the project in. Slug is
            preferred for AI callers, but tenant_id and unique name are also accepted.
            When omitted, the connection's default workspace is used. Discover values
-            via `list_workspaces`. Only meaningful in cloud mode; ignored for local
-            projects.
+            via `list_workspaces`. In local mode the selector is passed through
+            without slug resolution.
        output_format: "text" returns the existing human-readable result text.
            "json" returns structured project creation metadata.
        context: Optional FastMCP context for progress/status logging.
@@ -432,31 +433,34 @@ async def create_memory_project(
        create_memory_project("work-notes", "/home/user/work", set_default=True)
        create_memory_project("team-notes", "/team/notes", workspace="team-paul")
    """
-    workspace_id = await _resolve_create_project_workspace(workspace, context)
+    # Trigger: MCP server is constrained to a single project.
+    # Why: constrained sessions cannot create projects, and workspace selectors
+    # may be invalid or unavailable in that locked context.
+    # Outcome: return the existing disabled response before opening a routed client.
+    constrained_project = os.environ.get("BASIC_MEMORY_MCP_PROJECT")
+    if constrained_project:
+        if output_format == "json":
+            return {
+                "name": project_name,
+                "path": project_path,
+                "is_default": False,
+                "created": False,
+                "already_exists": False,
+                "error": "PROJECT_CONSTRAINED",
+                "message": (
+                    f"Project creation disabled - MCP server is constrained to project "
+                    f"'{constrained_project}'."
+                ),
+            }
+        return f'# Error\n\nProject creation disabled - MCP server is constrained to project \'{constrained_project}\'.\nUse the CLI to create projects: `basic-memory project add "{project_name}" "{project_path}"`'
+
+    workspace_id = await _resolve_workspace_routing(workspace, context)

    # workspace targets a non-default cloud workspace at create time.
    # Trigger: caller passed workspace (e.g. a slug discovered via list_workspaces).
    # Why: there is no project_id yet for per-project routing — the project doesn't exist.
    # Outcome: cloud factory routes the create request to the resolved workspace tenant id.
    async with get_client(workspace=workspace_id) as client:
-        # Check if server is constrained to a specific project
-        constrained_project = os.environ.get("BASIC_MEMORY_MCP_PROJECT")
-        if constrained_project:
-            if output_format == "json":
-                return {
-                    "name": project_name,
-                    "path": project_path,
-                    "is_default": False,
-                    "created": False,
-                    "already_exists": False,
-                    "error": "PROJECT_CONSTRAINED",
-                    "message": (
-                        f"Project creation disabled - MCP server is constrained to project "
-                        f"'{constrained_project}'."
-                    ),
-                }
-            return f'# Error\n\nProject creation disabled - MCP server is constrained to project \'{constrained_project}\'.\nUse the CLI to create projects: `basic-memory project add "{project_name}" "{project_path}"`'
-
        if context:  # pragma: no cover
            await context.info(f"Creating project: {project_name} at {project_path}")

@@ -536,7 +540,11 @@ async def create_memory_project(
@mcp.tool(
    annotations={"destructiveHint": True, "openWorldHint": False},
 )
-async def delete_project(project_name: str, context: Context | None = None) -> str:
+async def delete_project(
+    project_name: str,
+    workspace: str | None = None,
+    context: Context | None = None,
+) -> str:
    """Delete a Basic Memory project.

    Removes a project from the configuration and database. This does NOT delete
@@ -545,23 +553,33 @@ async def delete_project(project_name: str, context: Context | None = None) -> s

    Args:
        project_name: Name of the project to delete
+        workspace: Optional cloud workspace selector to delete the project from.
+            Slug is preferred for AI callers, but tenant_id and unique name are
+            also accepted. When omitted, the connection's default workspace is
+            used. In local mode the selector is passed through without slug
+            resolution, matching create_memory_project behavior.

    Returns:
        Confirmation message about project deletion

    Example:
        delete_project("old-project")
+        delete_project("team-project", workspace="team-paul")

    Warning:
        This action cannot be undone. The project will need to be re-added
        to access its content through Basic Memory again.
    """
-    async with get_client() as client:
-        # Check if server is constrained to a specific project
-        constrained_project = os.environ.get("BASIC_MEMORY_MCP_PROJECT")
-        if constrained_project:
-            return f"# Error\n\nProject deletion disabled - MCP server is constrained to project '{constrained_project}'.\nUse the CLI to delete projects: `basic-memory project remove \"{project_name}\"`"
+    # Trigger: MCP server is constrained to a single project.
+    # Why: constrained sessions cannot delete projects, and workspace selectors
+    # may be invalid or unavailable in that locked context.
+    # Outcome: return the existing disabled message before opening a routed client.
+    constrained_project = os.environ.get("BASIC_MEMORY_MCP_PROJECT")
+    if constrained_project:
+        return f"# Error\n\nProject deletion disabled - MCP server is constrained to project '{constrained_project}'.\nUse the CLI to delete projects: `basic-memory project remove \"{project_name}\"`"

+    workspace_id = await _resolve_workspace_routing(workspace, context)
+    async with get_client(workspace=workspace_id) as client:
        if context:  # pragma: no cover
            await context.info(f"Deleting project: {project_name}")

@@ -11,7 +11,7 @@ from fastmcp import Context

 from basic_memory.config import ConfigManager
 from basic_memory.mcp.project_context import (
-    detect_project_from_memory_url_prefix,
+    detect_project_from_identifier_prefix,
    get_project_client,
    resolve_project_and_path,
 )
@@ -130,10 +130,10 @@ async def read_note(
        If the exact note isn't found, this tool provides helpful suggestions
        including related notes, search commands, and note creation templates.
    """
-    # Detect project from memory URL prefix before routing.
+    # Detect project from a memory URL or permalink prefix before routing.
    # project_id routes by external UUID, so it bypasses URL discovery entirely.
    if project is None and project_id is None:
-        detected = await detect_project_from_memory_url_prefix(
+        detected = await detect_project_from_identifier_prefix(
            identifier,
            ConfigManager().config,
            context=context,
@@ -287,7 +287,8 @@ async def read_note(
                # If successful, return the content
                if response.status_code == 200:
                    logger.info(
-                        "Returning read_note result from resource: {path}", path=entity_path
+                        "Returning read_note result from resource: {path}",
+                        path=entity_path,
                    )
                    if output_format == "json":
                        return await _read_json_payload(entity_id)
@@ -187,7 +187,9 @@ async def recent_activity(
    # project_id (UUID) takes precedence over project name — without this fallback,
    # callers passing only project_id would fall into Discovery Mode.
    effective_identifier = project_id if project_id else project
-    resolved_project = await resolve_project_parameter(effective_identifier, allow_discovery=True)
+    resolved_project = await resolve_project_parameter(
+        effective_identifier, allow_discovery=True, context=context
+    )

    if resolved_project is None:
        # Discovery Mode: Get activity across all projects
@@ -2,18 +2,24 @@

 import re
 from textwrap import dedent
-from typing import Annotated, List, Optional, Dict, Any, Literal
+from typing import Annotated, List, Optional, Dict, Any, Literal, cast
+from uuid import UUID

 import logfire
 from loguru import logger
 from fastmcp import Context
 from pydantic import AliasChoices, BeforeValidator, Field

-from basic_memory.config import ConfigManager
-from basic_memory.utils import coerce_dict, coerce_list
+from basic_memory.config import ConfigManager, has_cloud_credentials
+from basic_memory.utils import build_canonical_permalink, coerce_dict, coerce_list
+from basic_memory.mcp.async_client import (
+    _explicit_routing,
+    _force_local_mode,
+    is_factory_mode,
+)
 from basic_memory.mcp.container import get_container
 from basic_memory.mcp.project_context import (
-    detect_project_from_memory_url_prefix,
+    detect_project_from_identifier_prefix,
    get_project_client,
    resolve_project_and_path,
 )
@@ -22,6 +28,7 @@ from basic_memory.schemas.search import (
    SearchItemType,
    SearchQuery,
    SearchResponse,
+    SearchResult,
    SearchRetrievalMode,
 )

@@ -294,6 +301,266 @@ def _format_search_markdown(result: SearchResponse, project: str, query: str | N
    return "\n".join(parts)


+def _valid_project_id(value: object) -> str | None:
+    """Return a UUID project id string when one is present."""
+    if not isinstance(value, str) or not value.strip():
+        return None
+    try:
+        return str(UUID(value))
+    except ValueError:
+        return None
+
+
+def _matches_constrained_project(project: dict[str, Any], constrained_project: object) -> bool:
+    """Return True when a project list row satisfies BASIC_MEMORY_MCP_PROJECT."""
+    if not isinstance(constrained_project, str) or not constrained_project.strip():
+        return True
+
+    candidates = {
+        value
+        for value in (
+            project.get("name"),
+            project.get("qualified_name"),
+            project.get("external_id"),
+        )
+        if isinstance(value, str)
+    }
+    return constrained_project in candidates
+
+
+def _search_project_refs(projects_payload: object) -> list[dict[str, str | None]]:
+    """Extract project routing refs for optional account-scoped search."""
+    if not isinstance(projects_payload, dict):
+        return []
+
+    payload = cast(dict[str, Any], projects_payload)
+    projects = payload.get("projects")
+    if not isinstance(projects, list):
+        return []
+
+    refs: list[dict[str, str | None]] = []
+    seen: set[tuple[str | None, str | None]] = set()
+    constrained_project = payload.get("constrained_project")
+    for item in projects:
+        if not isinstance(item, dict) or not _matches_constrained_project(
+            item, constrained_project
+        ):
+            continue
+
+        project = item.get("qualified_name") or item.get("name")
+        project_name = project if isinstance(project, str) and project.strip() else None
+        project_id = _valid_project_id(item.get("external_id"))
+        if project_name is None and project_id is None:
+            continue
+
+        key = (project_name, project_id)
+        if key in seen:
+            continue
+        seen.add(key)
+        refs.append({"project": project_name, "project_id": project_id})
+    return refs
+
+
+async def _load_search_project_refs(context: Context | None = None) -> list[dict[str, str | None]]:
+    """Load accessible projects for search_all_projects without coupling the wrapper tool."""
+    from basic_memory.mcp.tools.project_management import list_memory_projects
+
+    return _search_project_refs(await list_memory_projects(output_format="json", context=context))
+
+
+def _raw_results_from_search_payload(
+    results: SearchResponse | list[SearchResult | dict[str, Any]] | dict[str, Any],
+) -> list[SearchResult | dict[str, Any]]:
+    """Return the result list from any search_notes JSON-compatible payload."""
+    if isinstance(results, SearchResponse):
+        return list(results.results)
+    if isinstance(results, dict):
+        nested_results = results.get("results")
+        return (
+            cast(list[SearchResult | dict[str, Any]], nested_results)
+            if isinstance(nested_results, list)
+            else []
+        )
+    return list(results)
+
+
+def _result_score(result: SearchResult | dict[str, Any]) -> float:
+    """Return a comparable search score for merged project results."""
+    if isinstance(result, SearchResult):
+        return result.score
+    score = result.get("score")
+    return float(score) if isinstance(score, int | float) else 0.0
+
+
+def _qualify_permalink_for_project(permalink: object, project: str | None) -> object:
+    """Return a workspace-qualified permalink when the project ref supplies one."""
+    if not isinstance(permalink, str) or not permalink.strip():
+        return permalink
+    if not isinstance(project, str) or "/" not in project.strip("/"):
+        return permalink
+
+    normalized_permalink = permalink.strip("/")
+    qualified_project = project.strip("/")
+    if normalized_permalink == qualified_project or normalized_permalink.startswith(
+        f"{qualified_project}/"
+    ):
+        return normalized_permalink
+
+    workspace_slug, project_permalink = qualified_project.split("/", 1)
+    return build_canonical_permalink(
+        project_permalink,
+        normalized_permalink,
+        include_project=True,
+        workspace_permalink=workspace_slug,
+    )
+
+
+def _qualify_results_for_project(
+    results: list[SearchResult | dict[str, Any]],
+    project_ref: dict[str, str | None],
+) -> list[dict[str, Any]]:
+    """Attach the searched workspace/project prefix to each result permalink."""
+    qualified: list[dict[str, Any]] = []
+    for result in results:
+        if isinstance(result, SearchResult):
+            result_data = result.model_dump()
+        else:
+            result_data = dict(result)
+        result_data["permalink"] = _qualify_permalink_for_project(
+            result_data.get("permalink"),
+            project_ref.get("project"),
+        )
+        qualified.append(result_data)
+    return qualified
+
+
+def _result_total(results: dict[str, Any], raw_results: list[SearchResult | dict[str, Any]]) -> int:
+    """Return the best available total for a per-project search payload."""
+    total = results.get("total")
+    if isinstance(total, int) and total > 0:
+        return total
+    return len(raw_results) + (1 if results.get("has_more") is True else 0)
+
+
+def _project_ref_label(project_ref: dict[str, str | None]) -> str:
+    """Return a stable log label for a project search ref."""
+    return project_ref.get("project") or project_ref.get("project_id") or "<unknown project>"
+
+
+async def _search_all_projects(
+    *,
+    query: str | None,
+    page: int,
+    page_size: int,
+    search_type: str | None,
+    output_format: Literal["text", "json"],
+    note_types: list[str],
+    entity_types: list[str],
+    after_date: str | None,
+    metadata_filters: dict[str, Any] | None,
+    tags: list[str] | None,
+    status: str | None,
+    min_similarity: float | None,
+    context: Context | None,
+) -> dict | str:
+    """Search every accessible project when the caller explicitly opts in."""
+    requested_page = max(page, 1)
+    requested_page_size = max(page_size, 1)
+    project_refs = await _load_search_project_refs(context=context)
+    if not project_refs:
+        response = SearchResponse(
+            results=[],
+            current_page=requested_page,
+            page_size=requested_page_size,
+            total=0,
+            has_more=False,
+        )
+        if output_format == "json":
+            return response.model_dump(mode="json", exclude_none=True)
+        return _format_search_markdown(response, "all projects", query)
+
+    per_project_page_size = requested_page * requested_page_size
+    merged_results: list[dict[str, Any]] = []
+    total = 0
+    any_project_has_more = False
+
+    # Trigger: caller asked for an account-wide search.
+    # Why: project_id (external UUID) routes through the cloud v2 API path,
+    #      which 401s on local installs because there's no JWT to present.
+    #      Project names route through the local-ASGI path and work for both
+    #      backends — cloud disambiguates names via the workspace/project
+    #      qualified_name already baked into project_ref["project"].
+    # Outcome: forward project_id only when the same signals get_project_client
+    #          uses to pick a cloud route are present. Mirrors the cloud_available
+    #          composite in project_context.get_project_client (single source of
+    #          truth for "can we route to cloud?").
+    config = ConfigManager().config
+    use_cloud_routing = (
+        is_factory_mode()
+        or (_explicit_routing() and not _force_local_mode())
+        or has_cloud_credentials(config)
+    )
+
+    for project_ref in project_refs:
+        recursive_project_id = project_ref["project_id"] if use_cloud_routing else None
+        try:
+            results = await search_notes(
+                query=query,
+                project=project_ref["project"],
+                project_id=recursive_project_id,
+                page=1,
+                page_size=per_project_page_size,
+                search_type=search_type,
+                output_format="json",
+                note_types=note_types or None,
+                entity_types=entity_types or None,
+                after_date=after_date,
+                metadata_filters=metadata_filters,
+                tags=tags,
+                status=status,
+                min_similarity=min_similarity,
+                search_all_projects=False,
+                context=context,
+            )
+        except Exception as exc:
+            logger.warning(
+                f"Multi-project search failed for project {_project_ref_label(project_ref)}: {exc}"
+            )
+            continue
+
+        if isinstance(results, str):
+            if not results.startswith("# Search Failed"):
+                return results
+            logger.warning(
+                "Multi-project search failed for project "
+                f"{_project_ref_label(project_ref)}: {results}"
+            )
+            continue
+
+        raw_results = _raw_results_from_search_payload(results)
+        total += _result_total(results, raw_results)
+        any_project_has_more = any_project_has_more or results.get("has_more") is True
+        merged_results.extend(_qualify_results_for_project(raw_results, project_ref))
+
+    sorted_results = sorted(merged_results, key=_result_score, reverse=True)
+    start = (requested_page - 1) * requested_page_size
+    end = start + requested_page_size
+    paged_results = sorted_results[start:end]
+    response = SearchResponse.model_validate(
+        {
+            "results": paged_results,
+            "current_page": requested_page,
+            "page_size": requested_page_size,
+            "total": total,
+            "has_more": any_project_has_more or total > end or len(sorted_results) > end,
+        }
+    )
+
+    if output_format == "json":
+        return response.model_dump(mode="json", exclude_none=True)
+    return _format_search_markdown(response, "all projects", query)
+
+
@mcp.tool(
    description="Search across all content in the knowledge base with advanced syntax support.",
    # TODO: re-enable once MCP client rendering is working
@@ -309,6 +576,13 @@ async def search_notes(
    ] = None,
    project: Optional[str] = None,
    project_id: Optional[str] = None,
+    search_all_projects: Annotated[
+        bool,
+        Field(
+            default=False,
+            validation_alias=AliasChoices("search_all_projects", "all_projects"),
+        ),
+    ] = False,
    # `offset` is intentionally NOT aliased to `page`: offset is item-indexed
    # (skip N items) while page is 1-indexed page-number. Direct aliasing would
    # silently return the wrong slice.
@@ -373,6 +647,8 @@ async def search_notes(
    Project Resolution:
    Server resolves projects in this order: Single Project Mode → project parameter → default project.
    If project unknown, use list_memory_projects() or recent_activity() first.
+    Set search_all_projects=True to search every accessible project; this is opt-in because it
+    performs one search per project.

    ## Search Syntax Examples

@@ -448,6 +724,8 @@ async def search_notes(
        project_id: Project external_id (UUID). Prefer this over `project` when known —
                it routes to the exact project regardless of name collisions across cloud
                workspaces. Takes precedence over `project`. Get from list_memory_projects().
+        search_all_projects: Optional opt-in to search every accessible project. Ignored when
+                `project` or `project_id` is supplied.
        page: The page number of results to return (default 1)
        page_size: The number of results to return per page (default 10)
        search_type: Type of search to perform, one of:
@@ -551,10 +829,10 @@ async def search_notes(
            remainder = re.sub(r"\b(AND|OR|NOT)\b", "", remainder).strip()
            query = remainder or None

-    # Detect project from memory URL prefix before routing.
+    # Detect project from a memory URL or permalink prefix before routing.
    # project_id routes by external UUID, so it bypasses URL discovery entirely.
    if project is None and project_id is None and query is not None:
-        detected = await detect_project_from_memory_url_prefix(
+        detected = await detect_project_from_identifier_prefix(
            query,
            ConfigManager().config,
            context=context,
@@ -562,12 +840,35 @@ async def search_notes(
        if detected:
            project = detected

+    # Trigger: caller explicitly requests account/workspace-wide search and did not
+    # already provide a concrete project route.
+    # Why: multi-project fan-out can be slow, so default search remains project-scoped.
+    # Outcome: run one normal search per accessible project and merge ranked results.
+    if search_all_projects and project is None and project_id is None:
+        all_projects_result = await _search_all_projects(
+            query=query,
+            page=page,
+            page_size=page_size,
+            search_type=search_type,
+            output_format=output_format,
+            note_types=note_types,
+            entity_types=entity_types,
+            after_date=after_date,
+            metadata_filters=metadata_filters,
+            tags=tags,
+            status=status,
+            min_similarity=min_similarity,
+            context=context,
+        )
+        return all_projects_result
+
    with logfire.span(
        "mcp.tool.search_notes",
        entrypoint="mcp",
        tool_name="search_notes",
        requested_project=project,
        requested_project_id=project_id,
+        search_all_projects=search_all_projects,
        search_type=search_type or "default",
        output_format=output_format,
        page=page,
@@ -8,7 +8,7 @@ import typing
 from typing import Any, Optional

 import logfire
-from httpx import Response, URL, AsyncClient, HTTPStatusError
+from httpx import Response, URL, AsyncClient, HTTPStatusError, Headers
 from httpx._client import UseClientDefault, USE_CLIENT_DEFAULT
 from httpx._types import (
    RequestContent,
@@ -58,6 +58,22 @@ def _transport_error_span_attrs(exc: Exception) -> dict[str, Any]:
    }


+def _request_headers(headers: HeaderTypes | None) -> HeaderTypes | None:
+    """Merge request-local workspace permalink headers into outbound API calls."""
+    from basic_memory.workspace_context import workspace_permalink_headers
+
+    workspace_headers = workspace_permalink_headers()
+    if not workspace_headers:
+        return headers
+
+    if headers is None:
+        return workspace_headers
+
+    merged_headers = Headers(headers)
+    merged_headers.update(workspace_headers)
+    return merged_headers
+
+
 def get_error_message(
    status_code: int, url: URL | str, method: str, msg: Optional[str] = None
 ) -> str:
@@ -224,7 +240,7 @@ async def call_get(
            response = await client.get(
                url,
                params=params,
-                headers=headers,
+                headers=_request_headers(headers),
                cookies=cookies,
                auth=auth,
                follow_redirects=follow_redirects,
@@ -328,7 +344,7 @@ async def call_put(
                files=files,
                json=json,
                params=params,
-                headers=headers,
+                headers=_request_headers(headers),
                cookies=cookies,
                auth=auth,
                follow_redirects=follow_redirects,
@@ -432,7 +448,7 @@ async def call_patch(
                files=files,
                json=json,
                params=params,
-                headers=headers,
+                headers=_request_headers(headers),
                cookies=cookies,
                auth=auth,
                follow_redirects=follow_redirects,
@@ -542,7 +558,7 @@ async def call_post(
                files=files,
                json=json,
                params=params,
-                headers=headers,
+                headers=_request_headers(headers),
                cookies=cookies,
                auth=auth,
                follow_redirects=follow_redirects,
@@ -667,7 +683,7 @@ async def call_delete(
            response = await client.delete(
                url=url,
                params=params,
-                headers=headers,
+                headers=_request_headers(headers),
                cookies=cookies,
                auth=auth,
                follow_redirects=follow_redirects,
@@ -66,10 +66,14 @@ async def write_note(

    Relations format:
        - Explicit: `- relation_type [[Entity]] (optional context)`
-        - Inline: Any `[[Entity]]` reference creates a relation
+        - Quoted: `- "multi word relation type" [[Entity]] (optional context)`
+        - Quoted: `- 'multi word relation type' [[Entity]] (optional context)`
+        - Inline: Any other `[[Entity]]` reference creates a `links_to` relation

        Examples:
        `- depends_on [[Content Parser]] (Need for semantic extraction)`
+        `- "based on" [[Design Notes]]`
+        `- 'in response to' [[Incident Review]]`
        `- implements [[Search Spec]] (Initial implementation)`
        `- This feature extends [[Base Design]] and uses [[Core Utils]]`

@@ -5,10 +5,10 @@ from typing import List, Optional, Sequence, Union, Any


 from loguru import logger
-from sqlalchemy import select, func
+from sqlalchemy import exists, func, select
 from sqlalchemy.exc import IntegrityError
 from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker
-from sqlalchemy.orm import selectinload
+from sqlalchemy.orm import load_only, selectinload
 from sqlalchemy.orm.interfaces import LoaderOption
 from sqlalchemy.engine import Row

@@ -178,6 +178,24 @@ class EntityRepository(Repository[Entity]):
        result = await self.execute_query(query, use_query_options=False)
        return list(result.scalars().all())

+    async def find_by_ids_for_hydration(self, ids: List[int]) -> Sequence[Entity]:
+        """Fetch minimal entity fields needed for context hydration.
+
+        Context hydration only needs an entity's primary key, title, and external
+        UUID. Keeping this separate from find_by_ids avoids the relationship eager
+        loads that are useful for full entity reads but expensive for response shaping.
+        """
+        if not ids:
+            return []
+
+        query = (
+            self.select()
+            .where(Entity.id.in_(ids))
+            .options(load_only(Entity.id, Entity.title, Entity.external_id))
+        )
+        result = await self.execute_query(query, use_query_options=False)
+        return list(result.scalars().all())
+
    async def get_permalink_to_file_path_map(self) -> dict[str, str]:
        """Get a mapping of permalink -> file_path for all entities.

@@ -436,6 +454,22 @@ class EntityRepository(Repository[Entity]):
        result = await self.execute_query(query, use_query_options=False)
        return list(result.scalars().all())

+    async def find_without_relations(self) -> Sequence[Entity]:
+        """Find entities that have no incoming or outgoing relations."""
+        # Trigger: entity appears as a source in any relation.
+        # Why: even unresolved outgoing links mean the entity references another node.
+        # Outcome: entities with outgoing relations are excluded from the orphan list.
+        has_outgoing = exists().where(Relation.from_id == Entity.id)
+
+        # Trigger: entity appears as the resolved target in any relation.
+        # Why: only resolved relation targets are graph nodes with an incoming edge.
+        # Outcome: entities referenced by resolved links are excluded from orphans.
+        has_incoming = exists().where(Relation.to_id == Entity.id)
+
+        query = self.select().where(~has_outgoing).where(~has_incoming).order_by(Entity.file_path)
+        result = await self.execute_query(query, use_query_options=False)
+        return list(result.scalars().all())
+
    async def get_distinct_directories(self) -> List[str]:
        """Extract unique directory paths from file_path column.

@@ -5,11 +5,17 @@ from __future__ import annotations
 from dataclasses import dataclass
 from datetime import date, datetime
 import re
-from typing import Any, Iterable, List
+from typing import Any, Iterable, List, cast


 _KEY_RE = re.compile(r"^[A-Za-z0-9_-]+(\.[A-Za-z0-9_-]+)*$")
 _NUMERIC_RE = re.compile(r"^-?\d+(\.\d+)?$")
+_COMPARISON_OPERATORS = {
+    "$gt": "gt",
+    "$gte": "gte",
+    "$lt": "lt",
+    "$lte": "lte",
+}


@dataclass(frozen=True)
@@ -48,6 +54,11 @@ def _normalize_scalar(value: Any) -> Any:
    return value


+def _normalize_numeric(value: object) -> float:
+    """Normalize a value already proven numeric by _is_numeric_value."""
+    return float(cast(str | int | float, value))
+
+
 def parse_metadata_filters(filters: dict[str, Any]) -> List[ParsedMetadataFilter]:
    """Parse metadata filters into normalized clauses.

@@ -73,7 +84,12 @@ def parse_metadata_filters(filters: dict[str, Any]) -> List[ParsedMetadataFilter
        if isinstance(raw_value, dict):
            if len(raw_value) != 1:
                raise ValueError(f"Invalid metadata filter for '{raw_key}': {raw_value}")
-            op, value = next(iter(raw_value.items()))
+            raw_op, value = next(iter(raw_value.items()))
+            if not isinstance(raw_op, str):
+                raise ValueError(
+                    f"Unsupported operator '{raw_op}' in metadata filter for '{raw_key}'"
+                )
+            op = raw_op

            if op == "$in":
                if not isinstance(value, list) or not value:
@@ -83,15 +99,20 @@ def parse_metadata_filters(filters: dict[str, Any]) -> List[ParsedMetadataFilter
                )
                continue

-            if op in {"$gt", "$gte", "$lt", "$lte"}:
+            if op in _COMPARISON_OPERATORS:
                if _is_numeric_value(value):
-                    normalized = float(value)
+                    normalized = _normalize_numeric(value)
                    comparison = "numeric"
                else:
                    normalized = _normalize_scalar(value)
                    comparison = "text"
                parsed.append(
-                    ParsedMetadataFilter(path_parts, op.lstrip("$"), normalized, comparison)
+                    ParsedMetadataFilter(
+                        path_parts,
+                        _COMPARISON_OPERATORS[op],
+                        normalized,
+                        comparison,
+                    )
                )
                continue

@@ -99,7 +120,7 @@ def parse_metadata_filters(filters: dict[str, Any]) -> List[ParsedMetadataFilter
                if not isinstance(value, list) or len(value) != 2:
                    raise ValueError(f"$between requires [min, max] for '{raw_key}'")
                if _is_numeric_collection(value):
-                    normalized = [float(v) for v in value]
+                    normalized = [_normalize_numeric(v) for v in value]
                    comparison = "numeric"
                else:
                    normalized = [_normalize_scalar(v) for v in value]
@@ -686,7 +686,17 @@ class PostgresSearchRepository(SearchRepositoryBase):
    # FTS search (Postgres-specific)
    # ------------------------------------------------------------------

-    async def search(
+    @staticmethod
+    def _is_tsquery_syntax_error(exc: Exception) -> bool:
+        msg = str(exc).lower()
+        return (
+            "syntax error in tsquery" in msg
+            or "invalid input syntax for type tsquery" in msg
+            or "no operand in tsquery" in msg
+            or "no operator in tsquery" in msg
+        )
+
+    async def _build_fts_query_parts(
        self,
        search_text: Optional[str] = None,
        permalink: Optional[str] = None,
@@ -696,31 +706,8 @@ class PostgresSearchRepository(SearchRepositoryBase):
        after_date: Optional[datetime] = None,
        search_item_types: Optional[List[SearchItemType]] = None,
        metadata_filters: Optional[dict] = None,
-        retrieval_mode: SearchRetrievalMode = SearchRetrievalMode.FTS,
-        min_similarity: Optional[float] = None,
-        limit: int = 10,
-        offset: int = 0,
-    ) -> List[SearchIndexRow]:
-        """Search across all indexed content using PostgreSQL tsvector."""
-        # --- Dispatch vector / hybrid modes (shared logic) ---
-        dispatched = await self._dispatch_retrieval_mode(
-            search_text=search_text,
-            permalink=permalink,
-            permalink_match=permalink_match,
-            title=title,
-            note_types=note_types,
-            after_date=after_date,
-            search_item_types=search_item_types,
-            metadata_filters=metadata_filters,
-            retrieval_mode=retrieval_mode,
-            min_similarity=min_similarity,
-            limit=limit,
-            offset=offset,
-        )
-        if dispatched is not None:
-            return dispatched
-
-        # --- FTS mode (Postgres-specific) ---
+    ) -> tuple[str, str, dict, str, str]:
+        """Build Postgres FTS FROM/WHERE params shared by search and count."""
        conditions = []
        params = {}
        order_by_clause = ""
@@ -787,7 +774,8 @@ class PostgresSearchRepository(SearchRepositoryBase):
        # Handle date filter
        if after_date:
            params["after_date"] = after_date
-            conditions.append("search_index.created_at > :after_date")
+            # Filter on updated_at so recently-edited notes are included even when created_at is old
+            conditions.append("search_index.updated_at > :after_date")
            # order by most recent first
            order_by_clause = ", search_index.updated_at DESC"

@@ -868,10 +856,6 @@ class PostgresSearchRepository(SearchRepositoryBase):
        params["project_id"] = self.project_id
        conditions.append("search_index.project_id = :project_id")

-        # set limit and offset
-        params["limit"] = limit
-        params["offset"] = offset
-
        # Build WHERE clause
        where_clause = " AND ".join(conditions) if conditions else "1=1"

@@ -884,6 +868,64 @@ class PostgresSearchRepository(SearchRepositoryBase):
        else:
            score_expr = "0"

+        return from_clause, where_clause, params, order_by_clause, score_expr
+
+    async def search(
+        self,
+        search_text: Optional[str] = None,
+        permalink: Optional[str] = None,
+        permalink_match: Optional[str] = None,
+        title: Optional[str] = None,
+        note_types: Optional[List[str]] = None,
+        after_date: Optional[datetime] = None,
+        search_item_types: Optional[List[SearchItemType]] = None,
+        metadata_filters: Optional[dict] = None,
+        retrieval_mode: SearchRetrievalMode = SearchRetrievalMode.FTS,
+        min_similarity: Optional[float] = None,
+        limit: int = 10,
+        offset: int = 0,
+    ) -> List[SearchIndexRow]:
+        """Search across all indexed content using PostgreSQL tsvector."""
+        # --- Dispatch vector / hybrid modes (shared logic) ---
+        dispatched = await self._dispatch_retrieval_mode(
+            search_text=search_text,
+            permalink=permalink,
+            permalink_match=permalink_match,
+            title=title,
+            note_types=note_types,
+            after_date=after_date,
+            search_item_types=search_item_types,
+            metadata_filters=metadata_filters,
+            retrieval_mode=retrieval_mode,
+            min_similarity=min_similarity,
+            limit=limit,
+            offset=offset,
+        )
+        if dispatched is not None:
+            return dispatched
+
+        # --- FTS mode (Postgres-specific) ---
+        (
+            from_clause,
+            where_clause,
+            params,
+            order_by_clause,
+            score_expr,
+        ) = await self._build_fts_query_parts(
+            search_text=search_text,
+            permalink=permalink,
+            permalink_match=permalink_match,
+            title=title,
+            note_types=note_types,
+            after_date=after_date,
+            search_item_types=search_item_types,
+            metadata_filters=metadata_filters,
+        )
+
+        # set limit and offset
+        params["limit"] = limit
+        params["offset"] = offset
+
        sql = f"""
            SELECT
                search_index.project_id,
@@ -904,7 +946,7 @@ class PostgresSearchRepository(SearchRepositoryBase):
                {score_expr} as score
            FROM {from_clause}
            WHERE {where_clause}
-            ORDER BY score DESC, search_index.id ASC {order_by_clause}
+            ORDER BY score DESC {order_by_clause}, search_index.id ASC
            LIMIT :limit
            OFFSET :offset
        """
@@ -915,17 +957,7 @@ class PostgresSearchRepository(SearchRepositoryBase):
                result = await session.execute(text(sql), params)
                rows = result.fetchall()
        except Exception as e:
-            # Handle tsquery syntax errors (and only those).
-            #
-            # Important: Postgres errors for other failures (e.g. missing table) will still mention
-            # `to_tsquery(...)` in the SQL text, so checking for the substring "tsquery" is too broad.
-            msg = str(e).lower()
-            if (
-                "syntax error in tsquery" in msg
-                or "invalid input syntax for type tsquery" in msg
-                or "no operand in tsquery" in msg
-                or "no operator in tsquery" in msg
-            ):
+            if self._is_tsquery_syntax_error(e):
                logger.warning(f"tsquery syntax error for search term: {search_text}, error: {e}")
                return []

@@ -966,3 +998,60 @@ class PostgresSearchRepository(SearchRepositoryBase):
            )

        return results
+
+    async def count(
+        self,
+        search_text: Optional[str] = None,
+        permalink: Optional[str] = None,
+        permalink_match: Optional[str] = None,
+        title: Optional[str] = None,
+        note_types: Optional[List[str]] = None,
+        after_date: Optional[datetime] = None,
+        search_item_types: Optional[List[SearchItemType]] = None,
+        metadata_filters: Optional[dict] = None,
+        retrieval_mode: SearchRetrievalMode = SearchRetrievalMode.FTS,
+        min_similarity: Optional[float] = None,
+    ) -> int:
+        """Count indexed content matching the Postgres FTS query."""
+        if retrieval_mode != SearchRetrievalMode.FTS:
+            return await super().count(
+                search_text=search_text,
+                permalink=permalink,
+                permalink_match=permalink_match,
+                title=title,
+                note_types=note_types,
+                after_date=after_date,
+                search_item_types=search_item_types,
+                metadata_filters=metadata_filters,
+                retrieval_mode=retrieval_mode,
+                min_similarity=min_similarity,
+            )
+
+        (
+            from_clause,
+            where_clause,
+            params,
+            _order_by_clause,
+            _score_expr,
+        ) = await self._build_fts_query_parts(
+            search_text=search_text,
+            permalink=permalink,
+            permalink_match=permalink_match,
+            title=title,
+            note_types=note_types,
+            after_date=after_date,
+            search_item_types=search_item_types,
+            metadata_filters=metadata_filters,
+        )
+        sql = f"SELECT COUNT(*) FROM {from_clause} WHERE {where_clause}"
+        logger.trace(f"Count {sql} params: {params}")
+        try:
+            async with db.scoped_session(self.session_maker) as session:
+                result = await session.execute(text(sql), params)
+                return int(result.scalar_one())
+        except Exception as e:
+            if self._is_tsquery_syntax_error(e):
+                logger.warning(f"tsquery syntax error for search term: {search_text}, error: {e}")
+                return 0
+            logger.error(f"Database error during search count: {e}")
+            raise
@@ -4,7 +4,9 @@ from pathlib import Path
 from typing import Optional, Sequence, Union


-from sqlalchemy import text
+from loguru import logger
+from sqlalchemy import inspect as sa_inspect, select, text
+from sqlalchemy.exc import NoResultFound, OperationalError
 from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker

 from basic_memory import db
@@ -12,6 +14,65 @@ from basic_memory.models.project import Project
 from basic_memory.repository.repository import Repository


+async def _load_sqlite_vec_on_session(session) -> bool:
+    """Ensure the sqlite-vec extension is loaded on this session's connection.
+
+    Returns True when vec0 is available after the call. Returns False when the
+    extension can't be loaded on this Python build (e.g., python.org macOS or
+    Windows interpreters without `enable_load_extension`) — every connection in
+    the pool shares the same interpreter, so a False here also means no
+    embedding row could ever have been written, and skipping the embeddings
+    purge is safe.
+
+    Mirrors SQLiteSearchRepository._ensure_sqlite_vec_loaded but as a free
+    function: we don't have a SearchRepository instance during project delete,
+    and the per-connection nature of extension loading means a pooled connection
+    routed to this session might not have vec loaded even when other
+    connections wrote embeddings.
+    """
+    try:
+        await session.execute(text("SELECT vec_version()"))
+        return True
+    except OperationalError:
+        pass
+
+    try:
+        import sqlite_vec  # type: ignore[import-not-found]
+    except ImportError:
+        logger.debug("sqlite-vec package not installed; skipping vec purge")
+        return False
+
+    async_connection = await session.connection()
+    raw_connection = await async_connection.get_raw_connection()
+    driver_connection = raw_connection.driver_connection
+
+    if not hasattr(driver_connection, "enable_load_extension"):
+        # Trigger: CPython build without sqlite extension support (#711).
+        # Why: load_extension is unavailable, so no connection in this pool
+        #      can host vec0. No embeddings exist anywhere.
+        # Outcome: skip the embeddings purge entirely.
+        logger.debug(
+            "Skipping search_vector_embeddings purge: this Python build does "
+            "not support SQLite extension loading"
+        )
+        return False
+
+    try:
+        await driver_connection.enable_load_extension(True)
+        await driver_connection.load_extension(sqlite_vec.loadable_path())
+        await driver_connection.enable_load_extension(False)
+        await session.execute(text("SELECT vec_version()"))
+    except Exception as exc:
+        logger.warning(
+            "Failed to load sqlite-vec for project delete cleanup; "
+            "skipping embeddings purge: {}",
+            exc,
+        )
+        return False
+
+    return True
+
+
 class ProjectRepository(Repository[Project]):
    """Repository for Project model.

@@ -121,6 +182,83 @@ class ProjectRepository(Repository[Project]):
                return target_project
            return None  # pragma: no cover

+    async def delete(self, entity_id: int) -> bool:
+        """Delete a project and its derived search rows in one transaction.
+
+        The cascade picture differs by backend:
+
+        - search_index → project: Postgres has ON DELETE CASCADE FK; SQLite
+          stores search_index as an FTS5 virtual table and can't carry FKs,
+          so it needs explicit cleanup.
+        - search_vector_chunks → project: neither backend has an FK here, so
+          both need an explicit DELETE.
+        - search_vector_embeddings → search_vector_chunks: Postgres has an FK
+          (chunk_id REFERENCES … ON DELETE CASCADE); SQLite stores embeddings
+          in a vec0 virtual table keyed by rowid with no cascade. On SQLite
+          the embeddings must be purged before the chunk rows, otherwise
+          `_run_vector_query` keeps returning stale vectors that crowd out
+          live results.
+
+        Each derived table is created lazily (search_index by
+        SearchRepository.init_search_index, the vector tables once semantic
+        search initializes), so any of them may be absent on minimal test DBs.
+        Inspect the connection once and skip whichever is missing.
+        """
+        logger.debug(f"Deleting Project and search rows for project_id: {entity_id}")
+        async with db.scoped_session(self.session_maker) as session:
+            try:
+                result = await session.execute(
+                    select(self.Model).filter(self.primary_key == entity_id)
+                )
+                project = result.scalars().one()
+            except NoResultFound:
+                logger.debug(f"No Project found to delete: {entity_id}")
+                return False
+
+            dialect_name = session.bind.dialect.name if session.bind else "sqlite"
+            is_sqlite = dialect_name == "sqlite"
+
+            existing_tables = await session.run_sync(
+                lambda sync_session: set(sa_inspect(sync_session.connection()).get_table_names())
+            )
+
+            # search_index: SQLite has no FK on the FTS5 virtual table; Postgres
+            # cascades from the project FK, so the explicit DELETE is redundant.
+            if is_sqlite and "search_index" in existing_tables:
+                await session.execute(
+                    text("DELETE FROM search_index WHERE project_id = :project_id"),
+                    {"project_id": entity_id},
+                )
+
+            # search_vector_chunks: no FK to project on either backend, so both
+            # backends need this. SQLite must purge vec0 embeddings first
+            # (rowid pseudocolumn — Postgres uses chunk_id and would 500 here);
+            # Postgres' chunk_id FK CASCADE handles its embeddings cleanup when
+            # we delete the chunk rows below.
+            if "search_vector_chunks" in existing_tables:
+                if is_sqlite and "search_vector_embeddings" in existing_tables:
+                    # Extension loading is per-connection. We must load vec0 on
+                    # *this* session before the DELETE; otherwise a different
+                    # pooled connection might have written embeddings that we'd
+                    # silently leave behind.
+                    if await _load_sqlite_vec_on_session(session):
+                        await session.execute(
+                            text(
+                                "DELETE FROM search_vector_embeddings WHERE rowid IN ("
+                                "SELECT id FROM search_vector_chunks "
+                                "WHERE project_id = :project_id)"
+                            ),
+                            {"project_id": entity_id},
+                        )
+                await session.execute(
+                    text("DELETE FROM search_vector_chunks WHERE project_id = :project_id"),
+                    {"project_id": entity_id},
+                )
+
+            await session.delete(project)
+            logger.debug(f"Deleted Project and search rows for project_id: {entity_id}")
+            return True
+
    async def update_path(self, project_id: int, new_path: str) -> Optional[Project]:
        """Update project path.

@@ -50,6 +50,22 @@ class SearchRepository(Protocol):
        """Search across indexed content."""
        ...

+    async def count(
+        self,
+        search_text: Optional[str] = None,
+        permalink: Optional[str] = None,
+        permalink_match: Optional[str] = None,
+        title: Optional[str] = None,
+        note_types: Optional[List[str]] = None,
+        after_date: Optional[datetime] = None,
+        search_item_types: Optional[List[SearchItemType]] = None,
+        metadata_filters: Optional[dict] = None,
+        retrieval_mode: SearchRetrievalMode = SearchRetrievalMode.FTS,
+        min_similarity: Optional[float] = None,
+    ) -> int:
+        """Count indexed content matching the same filters as search."""
+        ...
+
    async def index_item(self, search_index_row: SearchIndexRow) -> None:
        """Index a single item."""
        ...
@@ -247,6 +247,24 @@ class SearchRepositoryBase(ABC):
        """
        pass

+    async def count(
+        self,
+        search_text: Optional[str] = None,
+        permalink: Optional[str] = None,
+        permalink_match: Optional[str] = None,
+        title: Optional[str] = None,
+        note_types: Optional[List[str]] = None,
+        after_date: Optional[datetime] = None,
+        search_item_types: Optional[List[SearchItemType]] = None,
+        metadata_filters: Optional[Dict[str, Any]] = None,
+        retrieval_mode: SearchRetrievalMode = SearchRetrievalMode.FTS,
+        min_similarity: Optional[float] = None,
+    ) -> int:
+        """Count results when a backend-specific COUNT query is available."""
+        if retrieval_mode != SearchRetrievalMode.FTS:
+            raise ValueError("Exact counts are only supported for full-text search retrieval.")
+        raise NotImplementedError("Backend search repositories must implement full-text counts.")
+
    # ------------------------------------------------------------------
    # Abstract methods — semantic search (backend-specific DB operations)
    # ------------------------------------------------------------------
@@ -701,7 +701,11 @@ class SQLiteSearchRepository(SearchRepositoryBase):
    # FTS search (backend-specific)
    # ------------------------------------------------------------------

-    async def search(
+    @staticmethod
+    def _is_fts5_syntax_error(exc: Exception) -> bool:
+        return "fts5: syntax error" in str(exc).lower()
+
+    async def _build_fts_query_parts(
        self,
        search_text: Optional[str] = None,
        permalink: Optional[str] = None,
@@ -711,31 +715,8 @@ class SQLiteSearchRepository(SearchRepositoryBase):
        after_date: Optional[datetime] = None,
        search_item_types: Optional[List[SearchItemType]] = None,
        metadata_filters: Optional[dict] = None,
-        retrieval_mode: SearchRetrievalMode = SearchRetrievalMode.FTS,
-        min_similarity: Optional[float] = None,
-        limit: int = 10,
-        offset: int = 0,
-    ) -> List[SearchIndexRow]:
-        """Search across all indexed content using SQLite FTS5."""
-        # --- Dispatch vector / hybrid modes (shared logic) ---
-        dispatched = await self._dispatch_retrieval_mode(
-            search_text=search_text,
-            permalink=permalink,
-            permalink_match=permalink_match,
-            title=title,
-            note_types=note_types,
-            after_date=after_date,
-            search_item_types=search_item_types,
-            metadata_filters=metadata_filters,
-            retrieval_mode=retrieval_mode,
-            min_similarity=min_similarity,
-            limit=limit,
-            offset=offset,
-        )
-        if dispatched is not None:
-            return dispatched
-
-        # --- FTS mode (SQLite-specific) ---
+    ) -> tuple[str, str, dict, str]:
+        """Build SQLite FTS FROM/WHERE params shared by search and count."""
        conditions = []
        match_conditions = []
        params = {}
@@ -808,7 +789,8 @@ class SQLiteSearchRepository(SearchRepositoryBase):
        # Handle date filter using datetime() for proper comparison
        if after_date:
            params["after_date"] = after_date
-            conditions.append("datetime(search_index.created_at) > datetime(:after_date)")
+            # Filter on updated_at so recently-edited notes are included even when created_at is old
+            conditions.append("datetime(search_index.updated_at) > datetime(:after_date)")

            # order by most recent first
            order_by_clause = ", search_index.updated_at DESC"
@@ -911,13 +893,60 @@ class SQLiteSearchRepository(SearchRepositoryBase):
        params["project_id"] = self.project_id
        conditions.append("search_index.project_id = :project_id")

+        # Build WHERE clause
+        where_clause = " AND ".join(conditions) if conditions else "1=1"
+        return from_clause, where_clause, params, order_by_clause
+
+    async def search(
+        self,
+        search_text: Optional[str] = None,
+        permalink: Optional[str] = None,
+        permalink_match: Optional[str] = None,
+        title: Optional[str] = None,
+        note_types: Optional[List[str]] = None,
+        after_date: Optional[datetime] = None,
+        search_item_types: Optional[List[SearchItemType]] = None,
+        metadata_filters: Optional[dict] = None,
+        retrieval_mode: SearchRetrievalMode = SearchRetrievalMode.FTS,
+        min_similarity: Optional[float] = None,
+        limit: int = 10,
+        offset: int = 0,
+    ) -> List[SearchIndexRow]:
+        """Search across all indexed content using SQLite FTS5."""
+        # --- Dispatch vector / hybrid modes (shared logic) ---
+        dispatched = await self._dispatch_retrieval_mode(
+            search_text=search_text,
+            permalink=permalink,
+            permalink_match=permalink_match,
+            title=title,
+            note_types=note_types,
+            after_date=after_date,
+            search_item_types=search_item_types,
+            metadata_filters=metadata_filters,
+            retrieval_mode=retrieval_mode,
+            min_similarity=min_similarity,
+            limit=limit,
+            offset=offset,
+        )
+        if dispatched is not None:
+            return dispatched
+
+        # --- FTS mode (SQLite-specific) ---
+        from_clause, where_clause, params, order_by_clause = await self._build_fts_query_parts(
+            search_text=search_text,
+            permalink=permalink,
+            permalink_match=permalink_match,
+            title=title,
+            note_types=note_types,
+            after_date=after_date,
+            search_item_types=search_item_types,
+            metadata_filters=metadata_filters,
+        )
+
        # set limit on search query
        params["limit"] = limit
        params["offset"] = offset

-        # Build WHERE clause
-        where_clause = " AND ".join(conditions) if conditions else "1=1"
-
        sql = f"""
            SELECT
                search_index.project_id,
@@ -950,7 +979,7 @@ class SQLiteSearchRepository(SearchRepositoryBase):
                rows = result.fetchall()
        except Exception as e:
            # Handle FTS5 syntax errors and provide user-friendly feedback
-            if "fts5: syntax error" in str(e).lower():  # pragma: no cover
+            if self._is_fts5_syntax_error(e):  # pragma: no cover
                logger.warning(f"FTS5 syntax error for search term: {search_text}, error: {e}")
                # Return empty results rather than crashing
                return []
@@ -988,3 +1017,54 @@ class SQLiteSearchRepository(SearchRepositoryBase):
            )

        return results
+
+    async def count(
+        self,
+        search_text: Optional[str] = None,
+        permalink: Optional[str] = None,
+        permalink_match: Optional[str] = None,
+        title: Optional[str] = None,
+        note_types: Optional[List[str]] = None,
+        after_date: Optional[datetime] = None,
+        search_item_types: Optional[List[SearchItemType]] = None,
+        metadata_filters: Optional[dict] = None,
+        retrieval_mode: SearchRetrievalMode = SearchRetrievalMode.FTS,
+        min_similarity: Optional[float] = None,
+    ) -> int:
+        """Count indexed content matching the SQLite FTS query."""
+        if retrieval_mode != SearchRetrievalMode.FTS:
+            return await super().count(
+                search_text=search_text,
+                permalink=permalink,
+                permalink_match=permalink_match,
+                title=title,
+                note_types=note_types,
+                after_date=after_date,
+                search_item_types=search_item_types,
+                metadata_filters=metadata_filters,
+                retrieval_mode=retrieval_mode,
+                min_similarity=min_similarity,
+            )
+
+        from_clause, where_clause, params, _order_by_clause = await self._build_fts_query_parts(
+            search_text=search_text,
+            permalink=permalink,
+            permalink_match=permalink_match,
+            title=title,
+            note_types=note_types,
+            after_date=after_date,
+            search_item_types=search_item_types,
+            metadata_filters=metadata_filters,
+        )
+        sql = f"SELECT COUNT(*) FROM {from_clause} WHERE {where_clause}"
+        logger.trace(f"Count {sql} params: {params}")
+        try:
+            async with db.scoped_session(self.session_maker) as session:
+                result = await session.execute(text(sql), params)
+                return int(result.scalar_one())
+        except Exception as e:
+            if self._is_fts5_syntax_error(e):  # pragma: no cover
+                logger.warning(f"FTS5 syntax error for search term: {search_text}, error: {e}")
+                return 0
+            logger.error(f"Database error during search count: {e}")
+            raise
@@ -8,7 +8,9 @@ Syntax reference:
  field: type, description          # required field
  field?: type, description         # optional field
  field(array): type                # array of values
+  field(array, description): type   # array with description
  field?(enum): [val1, val2]        # enumeration
+  field?(enum, description): [val1, val2]  # enum with description
  field?(object):                   # nested object
    sub_field: type
  EntityName as type (capitalized)  # entity reference
@@ -58,46 +60,88 @@ class SchemaDefinition:
 # with an uppercase letter is treated as an entity reference.

 SCALAR_TYPES = frozenset({"string", "integer", "number", "boolean", "any"})
+MODIFIER_TYPES = frozenset({"array", "enum", "object"})


 # --- Field Name Parsing ---


-def _parse_field_key(key: str) -> tuple[str, bool, bool, bool, bool]:
+def _parse_field_key_parts(key: str) -> tuple[str, bool, bool, bool, bool, str | None]:
    """Parse a Picoschema field key into its components.

-    Returns (name, required, is_array, is_enum, is_object).
-    The key format is: name[?][(array|enum|object)]
+    Returns (name, required, is_array, is_enum, is_object, description).
+    The key format is: name[?][(array|enum|object[, description])]

    Examples:
-        "name"           -> ("name", True, False, False)
-        "role?"          -> ("role", False, False, False)
-        "tags?(array)"   -> ("tags", False, True, False)
-        "status?(enum)"  -> ("status", False, False, True)
-        "metadata?(object)" -> ("metadata", False, False, False) + children
+        "name"           -> ("name", True, False, False, False, None)
+        "role?"          -> ("role", False, False, False, False, None)
+        "tags?(array)"   -> ("tags", False, True, False, False, None)
+        "tags?(array, labels)" -> ("tags", False, True, False, False, "labels")
+        "status?(enum)"  -> ("status", False, False, True, False, None)
+        "metadata?(object)" -> ("metadata", False, False, False, True, None)
    """
    required = True
    is_array = False
    is_enum = False
    is_object = False
+    description = None

-    # Check for modifier suffix: (array), (enum), (object)
-    if key.endswith("(array)"):
+    key, modifier, description = _split_modifier_suffix(key)
+
+    if modifier == "array":
        is_array = True
-        key = key[: -len("(array)")]
-    elif key.endswith("(enum)"):
+    elif modifier == "enum":
        is_enum = True
-        key = key[: -len("(enum)")]
-    elif key.endswith("(object)"):
+    elif modifier == "object":
        is_object = True
-        key = key[: -len("(object)")]

    # Check for optional marker
    if key.endswith("?"):
        required = False
        key = key[:-1]

-    return key, required, is_array, is_enum, is_object
+    return key.strip(), required, is_array, is_enum, is_object, description
+
+
+def _parse_field_key(key: str) -> tuple[str, bool, bool, bool, bool]:
+    """Parse a Picoschema field key, discarding any modifier description."""
+    name, required, is_array, is_enum, is_object, _description = _parse_field_key_parts(key)
+    return name, required, is_array, is_enum, is_object
+
+
+def _split_modifier_suffix(key: str) -> tuple[str, str | None, str | None]:
+    """Split a trailing picoschema modifier from a field key."""
+    stripped_key = key.rstrip()
+    if not stripped_key.endswith(")"):
+        return key, None, None
+
+    # Trigger: field names and modifier descriptions may both contain parentheses
+    # Why: only the parenthesis paired with the final suffix can introduce a modifier
+    # Outcome: preserves names like "risk(score)" and descriptions like "labels (freeform)"
+    open_paren_index = -1
+    depth = 0
+    for index in range(len(stripped_key) - 1, -1, -1):
+        char = stripped_key[index]
+        if char == ")":
+            depth += 1
+        elif char == "(":
+            depth -= 1
+            if depth == 0:
+                open_paren_index = index
+                break
+
+    if open_paren_index == -1:
+        return key, None, None
+
+    modifier_text = stripped_key[open_paren_index + 1 : -1].strip()
+    modifier, separator, description = modifier_text.partition(",")
+    modifier = modifier.strip()
+    if modifier not in MODIFIER_TYPES:
+        return key, None, None
+
+    key_without_modifier = stripped_key[:open_paren_index].rstrip()
+    parsed_description = description.strip() if separator else None
+    return key_without_modifier, modifier, parsed_description or None


 def _parse_type_and_description(value: str) -> tuple[str, str | None]:
@@ -170,7 +214,7 @@ def parse_picoschema(yaml_dict: dict) -> list[SchemaField]:
    fields: list[SchemaField] = []

    for key, value in yaml_dict.items():
-        name, required, is_array, is_enum, is_object = _parse_field_key(key)
+        name, required, is_array, is_enum, is_object, key_description = _parse_field_key_parts(key)

        # --- Enum fields ---
        # Trigger: value is a list or a string containing bracketed enum values
@@ -179,11 +223,12 @@ def parse_picoschema(yaml_dict: dict) -> list[SchemaField]:
        #   in YAML to avoid parse errors)
        # Outcome: SchemaField with is_enum=True and enum_values populated
        if is_enum:
-            description = None
+            description = key_description
            if isinstance(value, list):
                enum_values = [str(v) for v in value]
            else:
-                enum_values, description = _parse_enum_string(str(value))
+                enum_values, value_description = _parse_enum_string(str(value))
+                description = description or value_description
            fields.append(
                SchemaField(
                    name=name,
@@ -207,13 +252,15 @@ def parse_picoschema(yaml_dict: dict) -> list[SchemaField]:
                    name=name,
                    type="object",
                    required=required,
+                    description=key_description,
                    children=children,
                )
            )
            continue

        # --- Scalar and entity ref fields ---
-        type_str, description = _parse_type_and_description(str(value))
+        type_str, value_description = _parse_type_and_description(str(value))
+        description = key_description or value_description
        is_entity_ref = _is_entity_ref_type(type_str)

        fields.append(
@@ -88,6 +88,51 @@ class WorkspaceListResponse(BaseModel):
    )


+def workspace_matches_exact_identifier(workspace: WorkspaceInfo, identifier: str) -> bool:
+    """Return True when identifier matches workspace tenant_id, slug, or name."""
+    if workspace.tenant_id == identifier:
+        return True
+    if workspace.slug.casefold() == identifier.casefold():
+        return True
+    return workspace.name.casefold() == identifier.casefold()
+
+
+def workspace_matches_identifier(workspace: WorkspaceInfo, identifier: str) -> bool:
+    """Return True when identifier matches workspace tenant_id, slug, name, or type."""
+    return (
+        workspace_matches_exact_identifier(workspace, identifier)
+        or workspace.workspace_type.casefold() == identifier.casefold()
+    )
+
+
+def format_workspace_choices(workspaces: list[WorkspaceInfo]) -> str:
+    """Format deterministic workspace choices for prompt-style errors."""
+    return "\n".join(
+        [
+            (
+                f"- {item.name} "
+                f"(slug={item.slug}, type={item.workspace_type}, "
+                f"role={item.role}, tenant_id={item.tenant_id})"
+            )
+            for item in workspaces
+        ]
+    )
+
+
+def format_workspace_selection_choices(workspaces: list[WorkspaceInfo]) -> str:
+    """Format matching workspaces with copyable unique identifiers first."""
+    return "\n".join(
+        [
+            (
+                f"- {item.name} ({item.workspace_type}, role={item.role})\n"
+                f"  workspace: {item.slug}\n"
+                f"  tenant_id: {item.tenant_id}"
+            )
+            for item in workspaces
+        ]
+    )
+
+
 class CloudProjectIndexStatus(BaseModel):
    """Index freshness summary for one cloud project."""

@@ -142,4 +142,5 @@ class SearchResponse(BaseModel):
    results: List[SearchResult]
    current_page: int
    page_size: int
+    total: int = 0
    has_more: bool = False
@@ -14,6 +14,7 @@ from basic_memory.schemas.v2.graph import (
    GraphEdge,
    GraphNode,
    GraphResponse,
+    OrphanEntitiesResponse,
 )
 from basic_memory.schemas.v2.resource import (
    CreateResourceRequest,
@@ -33,6 +34,7 @@ __all__ = [
    "GraphEdge",
    "GraphNode",
    "GraphResponse",
+    "OrphanEntitiesResponse",
    "CreateResourceRequest",
    "UpdateResourceRequest",
    "ResourceResponse",
@@ -29,3 +29,12 @@ class GraphResponse(BaseModel):
    edges: list[GraphEdge] = Field(
        default_factory=list, description="All resolved relations as edges"
    )
+
+
+class OrphanEntitiesResponse(BaseModel):
+    """Entities that have no incoming or outgoing relations in the knowledge graph."""
+
+    entities: list[GraphNode] = Field(
+        default_factory=list, description="Entities with no relations"
+    )
+    total: int = Field(..., description="Total count of orphan entities")
@@ -4,7 +4,7 @@ from __future__ import annotations

 from dataclasses import dataclass, field
 from datetime import datetime, timezone
-from typing import List, Optional, Tuple, TYPE_CHECKING
+from typing import Any, List, Optional, Tuple, TYPE_CHECKING


 from loguru import logger
@@ -307,7 +307,7 @@ class ContextService:
        entity_id_values = ", ".join([str(i) for i in entity_ids])

        # Parameters for bindings - include project_id for security filtering
-        params = {
+        params: dict[str, Any] = {
            "max_depth": max_depth,
            "max_results": max_results,
            "project_id": self.search_repository.project_id,
@@ -322,9 +322,9 @@ class ContextService:
                since_utc = (
                    since.astimezone(timezone.utc) if since.tzinfo else since
                )  # pragma: no cover
-                params["since_date"] = since_utc.replace(tzinfo=None)  # pyright: ignore  # pragma: no cover
+                params["since_date"] = since_utc.replace(tzinfo=None)  # pragma: no cover
            else:
-                params["since_date"] = since.isoformat()  # pyright: ignore
+                params["since_date"] = since.isoformat()
            date_filter = "AND e.created_at >= :since_date"
            relation_date_filter = "AND e_from.created_at >= :since_date"
            timeframe_condition = "AND eg.relation_date >= :since_date"
@@ -1042,9 +1042,9 @@ class EntityService(BaseService[EntityModel]):
            for rel, resolved in zip(markdown.relations, resolved_entities):
                # Handle exceptions from gather and None results
                target_entity: Optional[Entity] = None
-                if not isinstance(resolved, Exception):
-                    # Type narrowing: resolved is Optional[Entity] here, not Exception
-                    target_entity = resolved  # pyright: ignore [reportAssignmentType]
+                if not isinstance(resolved, BaseException):
+                    # asyncio.gather(..., return_exceptions=True) can return any BaseException.
+                    target_entity = resolved

                if target_entity is None and not resolve_targets:
                    target_entity = await self._resolve_deferred_self_relation(rel.target, entity)
@@ -1,7 +1,7 @@
-"""Service for resolving markdown links to permalinks."""
+"""Service and helpers for resolving markdown links and permalink-like identifiers."""

 import uuid as uuid_mod
-from typing import Optional, Tuple, Dict
+from typing import Any, Optional, Tuple, Dict

 from loguru import logger

@@ -13,10 +13,47 @@ from basic_memory.repository.search_repository import create_search_repository
 from basic_memory.schemas.search import SearchQuery, SearchItemType
 from basic_memory.services.search_service import SearchService
 from basic_memory.utils import (
-    build_canonical_permalink,
+    build_permalink_resolution_candidates,
    generate_permalink,
    normalize_project_reference,
 )
+from basic_memory.workspace_context import current_workspace_permalink_context
+
+
+def is_workspace_qualified_plain_identifier(identifier: str) -> bool:
+    """Return True for plain ``<workspace>/<project>/<path>`` identifiers."""
+    stripped = identifier.strip()
+    if stripped.startswith("memory://"):
+        return False
+
+    normalized = normalize_project_reference(stripped).strip("/")
+    return len(normalized.split("/", 2)) == 3
+
+
+async def detect_project_from_workspace_identifier_prefix(
+    identifier: str,
+    config: BasicMemoryConfig,
+    context: Any | None = None,
+) -> Optional[str]:
+    """Resolve a project route from a plain workspace-qualified identifier."""
+    if not is_workspace_qualified_plain_identifier(identifier):
+        return None
+
+    from basic_memory.mcp.project_context import (
+        _cloud_workspace_discovery_available,
+        resolve_workspace_qualified_identifier,
+    )
+
+    if not _cloud_workspace_discovery_available(config):
+        return None
+
+    workspace_resolution = await resolve_workspace_qualified_identifier(
+        identifier,
+        context=context,
+    )
+    if workspace_resolution is None:
+        return None
+    return workspace_resolution.project_identifier


 class LinkResolver:
@@ -189,25 +226,25 @@ class LinkResolver:
        """Resolve a link within a specific project scope."""
        clean_text = link_text
        include_project = self._include_project_permalinks()
+        workspace_context = current_workspace_permalink_context()
+        workspace_permalink = (
+            workspace_context.workspace_slug
+            if workspace_context and workspace_context.should_prefix_permalinks
+            else None
+        )

-        canonical_permalink: Optional[str] = None
-        legacy_permalink: Optional[str] = None
-        # Trigger: permalinks include project slug and project permalink is known
-        # Why: support globally addressable permalinks while keeping legacy links resolvable
-        # Outcome: include canonical and legacy candidates for resolution
-        if include_project and project_permalink:
-            canonical_permalink = build_canonical_permalink(
-                project_permalink, clean_text, include_project=True
-            )
-            if clean_text.startswith(f"{project_permalink}/"):
-                legacy_candidate = clean_text.removeprefix(f"{project_permalink}/")
-                if legacy_candidate:
-                    legacy_permalink = legacy_candidate
-
-        permalink_candidates = []
-        for candidate in (clean_text, canonical_permalink, legacy_permalink):
-            if candidate and candidate not in permalink_candidates:
-                permalink_candidates.append(candidate)
+        # Trigger: callers can pass title, short permalink, project/path, or
+        #   workspace/project/path identifiers to the same resolver.
+        # Why: search results and memory:// URLs should stay usable across read,
+        #   edit, delete, move, and API-level entity resolution.
+        # Outcome: resolve canonical workspace IDs and legacy project-prefixed rows
+        #   through one shared candidate builder.
+        permalink_candidates = build_permalink_resolution_candidates(
+            clean_text,
+            project_permalink,
+            include_project=include_project,
+            workspace_permalink=workspace_permalink,
+        )

        # --- Path Resolution ---
        # Note: All paths in Basic Memory are stored as POSIX strings (forward slashes)
@@ -3,6 +3,7 @@
 import asyncio
 import ast
 import re
+from dataclasses import dataclass
 from datetime import datetime
 from typing import List, Optional, Set, Dict, Any

@@ -64,6 +65,22 @@ FTS_RELAXED_STOPWORDS = {
 }


+@dataclass(frozen=True)
+class _PreparedSearchQuery:
+    """Normalized query inputs shared by search and count."""
+
+    search_text: str | None
+    permalink: str | None
+    permalink_match: str | None
+    title: str | None
+    note_types: list[str] | None
+    search_item_types: list[SearchItemType] | None
+    after_date: datetime | None
+    metadata_filters: dict[str, Any] | None
+    retrieval_mode: SearchRetrievalMode
+    min_similarity: float | None
+
+
 def _strip_nul(value: str) -> str:
    """Strip NUL bytes that PostgreSQL text columns cannot store.

@@ -132,27 +149,20 @@ class SearchService:

        logger.info("Reindex complete")

-    async def search(self, query: SearchQuery, limit=10, offset=0) -> List[SearchIndexRow]:
-        """Search across all indexed content.
+    def _prepare_query(self, query: SearchQuery) -> _PreparedSearchQuery | None:
+        """Normalize a SearchQuery into repository arguments."""
+        search_text = query.text
+        tags = query.tags

-        Supports three modes:
-        1. Exact permalink: finds direct matches for a specific path
-        2. Pattern match: handles * wildcards in paths
-        3. Text search: full-text search across title/content
-        """
-        # Support tag:<tag> shorthand by mapping to tags filter
-        if query.text:
-            text = query.text.strip()
-            if text.lower().startswith("tag:"):
-                tag_values = re.split(r"[,\s]+", text[4:].strip())
-                tags = [t for t in tag_values if t]
-                if tags:
-                    query.tags = tags
-                    query.text = None
-
-        if query.no_criteria():
-            logger.debug("no criteria passed to query")
-            return []
+        # Support tag:<tag> shorthand by mapping to tags filter.
+        if search_text is not None:
+            search_text = search_text.strip() or None
+            if search_text and search_text.lower().startswith("tag:"):
+                tag_values = re.split(r"[,\s]+", search_text[4:].strip())
+                parsed_tags = [t for t in tag_values if t]
+                if parsed_tags:
+                    tags = parsed_tags
+                    search_text = None

        after_date = (
            (
@@ -164,50 +174,124 @@ class SearchService:
            else None
        )

-        # Merge structured metadata filters (explicit + convenience fields)
+        # Merge structured metadata filters (explicit + convenience fields).
        metadata_filters: Optional[Dict[str, Any]] = None
-        if query.metadata_filters or query.tags or query.status:
+        if query.metadata_filters or tags or query.status:
            metadata_filters = dict(query.metadata_filters or {})
-            if query.tags:
-                metadata_filters.setdefault("tags", query.tags)
+            if tags:
+                metadata_filters.setdefault("tags", tags)
            if query.status:
                metadata_filters.setdefault("status", query.status)

-        retrieval_mode = query.retrieval_mode or SearchRetrievalMode.FTS
-        strict_search_text = query.text
+        prepared = _PreparedSearchQuery(
+            search_text=search_text,
+            permalink=query.permalink,
+            permalink_match=query.permalink_match,
+            title=query.title,
+            note_types=query.note_types,
+            search_item_types=query.entity_types,
+            after_date=after_date,
+            metadata_filters=metadata_filters,
+            retrieval_mode=query.retrieval_mode or SearchRetrievalMode.FTS,
+            min_similarity=query.min_similarity,
+        )
+
+        has_criteria = bool(
+            prepared.search_text
+            or prepared.permalink
+            or prepared.permalink_match
+            or prepared.title
+            or prepared.note_types
+            or prepared.search_item_types
+            or prepared.after_date
+            or prepared.metadata_filters
+        )
+        if not has_criteria:
+            logger.debug("no criteria passed to query")
+            return None
+        return prepared
+
+    @staticmethod
+    def _prepared_has_filters(prepared: _PreparedSearchQuery) -> bool:
+        return bool(
+            prepared.metadata_filters
+            or prepared.note_types
+            or prepared.search_item_types
+            or prepared.after_date
+        )
+
+    async def _search_repository(
+        self,
+        prepared: _PreparedSearchQuery,
+        *,
+        search_text: str | None,
+        limit: int,
+        offset: int,
+    ) -> List[SearchIndexRow]:
+        return await self.repository.search(
+            search_text=search_text,
+            permalink=prepared.permalink,
+            permalink_match=prepared.permalink_match,
+            title=prepared.title,
+            note_types=prepared.note_types,
+            search_item_types=prepared.search_item_types,
+            after_date=prepared.after_date,
+            metadata_filters=prepared.metadata_filters,
+            retrieval_mode=prepared.retrieval_mode,
+            min_similarity=prepared.min_similarity,
+            limit=limit,
+            offset=offset,
+        )
+
+    async def _count_repository(
+        self,
+        prepared: _PreparedSearchQuery,
+        *,
+        search_text: str | None,
+    ) -> int:
+        return await self.repository.count(
+            search_text=search_text,
+            permalink=prepared.permalink,
+            permalink_match=prepared.permalink_match,
+            title=prepared.title,
+            note_types=prepared.note_types,
+            search_item_types=prepared.search_item_types,
+            after_date=prepared.after_date,
+            metadata_filters=prepared.metadata_filters,
+            retrieval_mode=prepared.retrieval_mode,
+            min_similarity=prepared.min_similarity,
+        )
+
+    async def search(self, query: SearchQuery, limit=10, offset=0) -> List[SearchIndexRow]:
+        """Search across all indexed content.
+
+        Supports three modes:
+        1. Exact permalink: finds direct matches for a specific path
+        2. Pattern match: handles * wildcards in paths
+        3. Text search: full-text search across title/content
+        """
+        prepared = self._prepare_query(query)
+        if prepared is None:
+            return []
+
+        strict_search_text = prepared.search_text
        has_query = bool(
-            strict_search_text or query.title or query.permalink or query.permalink_match
-        )
-        has_filters = bool(
-            metadata_filters
-            or query.note_types
-            or query.entity_types
-            or after_date
-            or query.tags
-            or query.status
+            strict_search_text or prepared.title or prepared.permalink or prepared.permalink_match
        )
+        has_filters = self._prepared_has_filters(prepared)

        with logfire.span(
            "search.execute",
-            retrieval_mode=retrieval_mode.value,
+            retrieval_mode=prepared.retrieval_mode.value,
            has_query=has_query,
            has_filters=has_filters,
            limit=limit,
            offset=offset,
        ):
            logger.trace(f"Searching with query: {query}")
-            # First pass: preserve existing strict search behavior.
-            results = await self.repository.search(
+            results = await self._search_repository(
+                prepared,
                search_text=strict_search_text,
-                permalink=query.permalink,
-                permalink_match=query.permalink_match,
-                title=query.title,
-                note_types=query.note_types,
-                search_item_types=query.entity_types,
-                after_date=after_date,
-                metadata_filters=metadata_filters,
-                retrieval_mode=retrieval_mode,
-                min_similarity=query.min_similarity,
                limit=limit,
                offset=offset,
            )
@@ -217,7 +301,9 @@ class SearchService:
        # Outcome: retry once with relaxed OR terms while preserving explicit boolean intent.
        if results:
            return results
-        if not self._is_relaxed_fts_fallback_eligible(query, strict_search_text, retrieval_mode):
+        if not self._is_relaxed_fts_fallback_eligible(
+            query, strict_search_text, prepared.retrieval_mode
+        ):
            return results

        assert strict_search_text is not None
@@ -231,26 +317,57 @@ class SearchService:
        )
        with logfire.span(
            "search.relaxed_fts_retry",
-            retrieval_mode=retrieval_mode.value,
+            retrieval_mode=prepared.retrieval_mode.value,
            token_count=len(self._tokenize_fts_text(strict_search_text)),
            limit=limit,
            offset=offset,
        ):
-            return await self.repository.search(
+            return await self._search_repository(
+                prepared,
                search_text=relaxed_search_text,
-                permalink=query.permalink,
-                permalink_match=query.permalink_match,
-                title=query.title,
-                note_types=query.note_types,
-                search_item_types=query.entity_types,
-                after_date=after_date,
-                metadata_filters=metadata_filters,
-                retrieval_mode=retrieval_mode,
-                min_similarity=query.min_similarity,
                limit=limit,
                offset=offset,
            )

+    async def count(self, query: SearchQuery) -> int:
+        """Count all indexed rows matching a query."""
+        prepared = self._prepare_query(query)
+        if prepared is None:
+            return 0
+
+        strict_search_text = prepared.search_text
+        has_query = bool(
+            strict_search_text or prepared.title or prepared.permalink or prepared.permalink_match
+        )
+        has_filters = self._prepared_has_filters(prepared)
+
+        with logfire.span(
+            "search.count",
+            retrieval_mode=prepared.retrieval_mode.value,
+            has_query=has_query,
+            has_filters=has_filters,
+        ):
+            total = await self._count_repository(prepared, search_text=strict_search_text)
+
+        if total > 0:
+            return total
+        if not self._is_relaxed_fts_fallback_eligible(
+            query, strict_search_text, prepared.retrieval_mode
+        ):
+            return total
+
+        assert strict_search_text is not None
+        relaxed_search_text = self._build_relaxed_fts_query(strict_search_text)
+        if relaxed_search_text == strict_search_text:
+            return total
+
+        with logfire.span(
+            "search.count.relaxed_fts_retry",
+            retrieval_mode=prepared.retrieval_mode.value,
+            token_count=len(self._tokenize_fts_text(strict_search_text)),
+        ):
+            return await self._count_repository(prepared, search_text=relaxed_search_text)
+
    @staticmethod
    def _tokenize_fts_text(search_text: str) -> list[str]:
        """Tokenize text into alphanumeric terms for relaxed FTS fallback."""
@@ -1530,12 +1530,36 @@ class SyncService:
                count += 1
            return count

-        process = await asyncio.create_subprocess_shell(
-            f'find "{directory}" -type f | wc -l',
+        # Trigger: large-project scan optimization needs the OS `find` command.
+        # Why: passing argv directly avoids shell interpretation of configured project paths.
+        # Outcome: quotes and shell metacharacters in paths are treated as data.
+        process = await asyncio.create_subprocess_exec(
+            "find",
+            str(directory),
+            "-type",
+            "f",
+            "-print0",
            stdout=asyncio.subprocess.PIPE,
            stderr=asyncio.subprocess.PIPE,
        )
-        stdout, stderr = await process.communicate()
+
+        count = 0
+        stderr_task = None
+        if process.stderr is not None:
+            stderr_task = asyncio.create_task(process.stderr.read())
+
+        if process.stdout is None:
+            await process.wait()
+        else:
+            # Trigger: `find` can emit one path per file for very large projects.
+            # Why: collecting every path via communicate() scales memory with path bytes.
+            # Outcome: count null-delimited records in fixed-size chunks.
+            while chunk := await process.stdout.read(1024 * 1024):
+                count += chunk.count(b"\0")
+
+            await process.wait()
+
+        stderr = await stderr_task if stderr_task is not None else b""

        if process.returncode != 0:
            error_msg = stderr.decode().strip()
@@ -1550,7 +1574,7 @@ class SyncService:
                count += 1
            return count

-        return int(stdout.strip())
+        return count

    async def _scan_directory_modified_since(
        self, directory: Path, since_timestamp: float
@@ -1583,8 +1607,16 @@ class SyncService:
        # Convert timestamp to find-compatible format
        since_date = datetime.fromtimestamp(since_timestamp).strftime("%Y-%m-%d %H:%M:%S")

-        process = await asyncio.create_subprocess_shell(
-            f'find "{directory}" -type f -newermt "{since_date}"',
+        # Trigger: incremental scans ask `find` to filter by modification time.
+        # Why: passing argv directly avoids shell interpretation of paths and timestamps.
+        # Outcome: optimized scanning keeps its speed without a shell injection boundary.
+        process = await asyncio.create_subprocess_exec(
+            "find",
+            str(directory),
+            "-type",
+            "f",
+            "-newermt",
+            since_date,
            stdout=asyncio.subprocess.PIPE,
            stderr=asyncio.subprocess.PIPE,
        )
@@ -93,6 +93,7 @@ class WatchService:
        self.status_path = app_config.data_dir_path / WATCH_STATUS_JSON
        self.status_path.parent.mkdir(parents=True, exist_ok=True)
        self._ignore_patterns_cache: dict[Path, Set[str]] = {}
+        self._sorted_watch_filter_roots: tuple[Path, ...] | None = None
        self._sync_service_factory = sync_service_factory
        # When set (typically from BASIC_MEMORY_MCP_PROJECT), the watch cycle
        # only observes this project. Without it, each `basic-memory mcp --project X`
@@ -126,41 +127,54 @@ class WatchService:
    async def _watch_projects_cycle(self, projects: Sequence[Project], stop_event: asyncio.Event):
        """Run one cycle of watching the given projects until stop_event is set."""
        project_paths = [project.path for project in projects]
+        previous_filter_roots = self._sorted_watch_filter_roots
+        self._sorted_watch_filter_roots = tuple(
+            sorted(
+                (Path(project.path).expanduser().resolve() for project in projects),
+                # Trigger: configured project roots can overlap.
+                # Why: an enclosing project's hidden directory should still hide descendants.
+                # Outcome: choose the outermost matching root when checking hidden path parts.
+                key=lambda project_path: len(project_path.parts),
+            )
+        )

-        async for changes in awatch(
-            *project_paths,
-            debounce=self.app_config.sync_delay,
-            watch_filter=self.filter_changes,
-            recursive=True,
-            stop_event=stop_event,
-        ):
-            # group changes by project and filter using ignore patterns
-            project_changes = defaultdict(list)
-            for change, path in changes:
-                for project in projects:
-                    if self.is_project_path(project, path):
-                        # Check if the file should be ignored based on gitignore patterns
-                        project_path = Path(project.path)
-                        file_path = Path(path)
-                        ignore_patterns = self._get_ignore_patterns(project_path)
+        try:
+            async for changes in awatch(
+                *project_paths,
+                debounce=self.app_config.sync_delay,
+                watch_filter=self.filter_changes,
+                recursive=True,
+                stop_event=stop_event,
+            ):
+                # group changes by project and filter using ignore patterns
+                project_changes = defaultdict(list)
+                for change, path in changes:
+                    for project in projects:
+                        if self.is_project_path(project, path):
+                            # Check if the file should be ignored based on gitignore patterns
+                            project_path = Path(project.path)
+                            file_path = Path(path)
+                            ignore_patterns = self._get_ignore_patterns(project_path)

-                        if should_ignore_path(file_path, project_path, ignore_patterns):
-                            logger.trace(
-                                f"Ignoring watched file change: {file_path.relative_to(project_path)}"
-                            )
-                            continue
+                            if should_ignore_path(file_path, project_path, ignore_patterns):
+                                logger.trace(
+                                    f"Ignoring watched file change: {file_path.relative_to(project_path)}"
+                                )
+                                continue

-                        project_changes[project].append((change, path))
-                        break
+                            project_changes[project].append((change, path))
+                            break

-            # create coroutines to handle changes
-            change_handlers = [
-                self.handle_changes(project, set(changes))
-                for project, changes in project_changes.items()
-            ]
+                # create coroutines to handle changes
+                change_handlers = [
+                    self.handle_changes(project, set(changes))
+                    for project, changes in project_changes.items()
+                ]

-            # process changes
-            await asyncio.gather(*change_handlers)
+                # process changes
+                await asyncio.gather(*change_handlers)
+        finally:
+            self._sorted_watch_filter_roots = previous_filter_roots

    async def _select_projects_to_watch(self) -> list[Project]:
        """Return the set of projects this watch cycle should observe.
@@ -267,15 +281,43 @@ class WatchService:
            self.state.running = False
            await self.write_status()

-    def filter_changes(self, change: Change, path: str) -> bool:  # pragma: no cover
+    def filter_changes(self, change: Change, path: str) -> bool:
        """Filter to only watch non-hidden files and directories.

        Returns:
            True if the file should be watched, False if it should be ignored
        """

-        # Skip hidden directories and files
-        path_parts = Path(path).parts
+        path_obj = Path(path).expanduser().resolve()
+
+        project_paths = self._sorted_watch_filter_roots
+        if project_paths is None:
+            project_paths = tuple(
+                sorted(
+                    (
+                        Path(entry.path).expanduser().resolve()
+                        for entry in self.app_config.projects.values()
+                        if entry.path
+                    ),
+                    # Trigger: direct callers may not run inside a watch cycle.
+                    # Why: tests and one-off calls still need the same hidden-path semantics.
+                    # Outcome: compute the stable outermost-first order only for fallback calls.
+                    key=lambda project_path: len(project_path.parts),
+                )
+            )
+
+        relative_path = None
+        for project_path in project_paths:
+            try:
+                relative_path = path_obj.relative_to(project_path)
+                break
+            except ValueError:
+                continue
+
+        # Trigger: a project may live under a hidden parent such as ~/.claude.
+        # Why: only dotfiles and dot-directories inside the watched project should be ignored.
+        # Outcome: hidden parents outside the project root do not mute legitimate project changes.
+        path_parts = relative_path.parts if relative_path is not None else path_obj.parts
        for part in path_parts:
            if part.startswith("."):
                return False
@@ -276,6 +276,137 @@ def build_canonical_permalink(
    return project_path


+def build_qualified_permalink_reference(
+    project_permalink: Optional[str],
+    identifier: Union[Path, str, PathLike],
+    include_project: bool = True,
+    *,
+    workspace_permalink: Optional[str] = None,
+) -> str:
+    """Add workspace/project route prefixes while preserving lookup syntax.
+
+    Unlike ``build_canonical_permalink()``, this helper does not run the identifier
+    through permalink generation. It is for inbound references that may contain
+    lookup-only syntax such as ``.md`` extensions or ``*`` glob patterns.
+    """
+    normalized_path = normalize_project_reference(str(identifier)).strip("/")
+    normalized_workspace = generate_permalink(workspace_permalink) if workspace_permalink else None
+    normalized_project = generate_permalink(project_permalink) if project_permalink else None
+
+    if normalized_workspace:
+        if not normalized_project:
+            raise ValueError("workspace_permalink requires project_permalink")
+
+        workspace_project_prefix = f"{normalized_workspace}/{normalized_project}"
+        if not normalized_path:
+            return workspace_project_prefix
+        if normalized_path == workspace_project_prefix or normalized_path.startswith(
+            f"{workspace_project_prefix}/"
+        ):
+            return normalized_path
+        if normalized_path == normalized_project or normalized_path.startswith(
+            f"{normalized_project}/"
+        ):
+            return f"{normalized_workspace}/{normalized_path}"
+        return f"{workspace_project_prefix}/{normalized_path}"
+
+    if not include_project or not normalized_project:
+        return normalized_path
+
+    if not normalized_path:
+        return normalized_project
+    if normalized_path == normalized_project or normalized_path.startswith(
+        f"{normalized_project}/"
+    ):
+        return normalized_path
+    return f"{normalized_project}/{normalized_path}"
+
+
+def build_permalink_resolution_candidates(
+    identifier: Union[Path, str, PathLike],
+    project_permalink: Optional[str],
+    include_project: bool = True,
+    *,
+    workspace_permalink: Optional[str] = None,
+) -> list[str]:
+    """Return permalink candidates from most caller-specific to broadest legacy form.
+
+    The first candidate preserves the normalized identifier the caller supplied. Follow-up
+    candidates add the active workspace/project route and legacy project/path forms so
+    all resolver callers share the same compatibility behavior.
+    """
+    exact_path = normalize_project_reference(str(identifier)).strip("/")
+    normalized_path = generate_permalink(exact_path).strip("/")
+    normalized_project = generate_permalink(project_permalink) if project_permalink else None
+    normalized_workspace = generate_permalink(workspace_permalink) if workspace_permalink else None
+    candidates: list[str] = []
+
+    def add_candidate(value: str | None) -> None:
+        if value and value not in candidates:
+            candidates.append(value)
+
+    add_candidate(exact_path)
+    add_candidate(normalized_path)
+    if not normalized_project:
+        return candidates
+
+    workspace_project_prefix = (
+        f"{normalized_workspace}/{normalized_project}" if normalized_workspace else None
+    )
+    workspace_qualified = False
+    if workspace_project_prefix:
+        add_candidate(
+            build_canonical_permalink(
+                normalized_project,
+                normalized_path,
+                include_project=include_project,
+                workspace_permalink=normalized_workspace,
+            )
+        )
+        if normalized_path == workspace_project_prefix:
+            workspace_qualified = True
+            add_candidate(normalized_project)
+        elif normalized_path.startswith(f"{workspace_project_prefix}/"):
+            workspace_qualified = True
+            remainder = normalized_path.removeprefix(f"{workspace_project_prefix}/")
+            add_candidate(f"{normalized_project}/{remainder}")
+            add_candidate(remainder)
+
+    if workspace_project_prefix and not include_project and not workspace_qualified:
+        # Trigger: short lookup in a workspace where new canonical links omit project prefixes.
+        # Why: older rows in that same workspace may still be stored as `project/path`.
+        # Outcome: try the project-prefixed legacy form after the workspace-qualified form.
+        add_candidate(
+            build_canonical_permalink(
+                normalized_project,
+                normalized_path,
+                include_project=True,
+            )
+        )
+
+    if include_project and not workspace_qualified:
+        add_candidate(
+            build_canonical_permalink(
+                normalized_project,
+                normalized_path,
+                include_project=True,
+            )
+        )
+        if normalized_path == normalized_project:
+            return candidates
+        if normalized_path.startswith(f"{normalized_project}/"):
+            remainder = normalized_path.removeprefix(f"{normalized_project}/")
+            add_candidate(remainder)
+
+    if not include_project and normalized_path.startswith(f"{normalized_project}/"):
+        # Trigger: caller supplied `project/path` while legacy short permalinks are stored.
+        # Why: routing uses the project prefix, but strict lookup still needs the short row.
+        # Outcome: try `path` after the exact project-qualified candidate.
+        add_candidate(normalized_path.removeprefix(f"{normalized_project}/"))
+
+    return candidates
+
+
 def setup_logging(
    log_level: str = "INFO",
    log_to_file: bool = False,
@@ -14,14 +14,14 @@ _WORKSPACE_TYPES = {"personal", "organization"}

@dataclass(frozen=True)
 class WorkspacePermalinkContext:
-    """Workspace metadata needed to build canonical organization permalinks."""
+    """Workspace metadata needed to build canonical workspace permalinks."""

    workspace_slug: str
    workspace_type: str

    @property
    def should_prefix_permalinks(self) -> bool:
-        return self.workspace_type == "organization" and bool(self.workspace_slug)
+        return bool(self.workspace_slug)


 _workspace_permalink_context: ContextVar[WorkspacePermalinkContext | None] = ContextVar(
@@ -138,6 +138,17 @@ async def cleanup_global_db_after_test() -> AsyncGenerator[None, None]:
    await db.shutdown_db()


+@pytest.fixture(autouse=True)
+def clean_routing_env(monkeypatch) -> None:
+    """Keep CLI routing env mutations from leaking between integration tests."""
+    # Trigger: CLI integration tests exercise long-running MCP entrypoints that set routing env.
+    # Why: those commands normally own the process lifetime, but pytest keeps reusing it.
+    # Outcome: every integration test starts from neutral routing unless it opts in explicitly.
+    monkeypatch.delenv("BASIC_MEMORY_FORCE_LOCAL", raising=False)
+    monkeypatch.delenv("BASIC_MEMORY_FORCE_CLOUD", raising=False)
+    monkeypatch.delenv("BASIC_MEMORY_EXPLICIT_ROUTING", raising=False)
+
+
 POSTGRES_EPHEMERAL_TABLES = [
    "search_vector_embeddings",
    "search_vector_chunks",
@@ -1,34 +1,30 @@
-"""
-Integration test for long relation_type values (regression guard for issue #721).
+"""Integration test for long prose before inline wikilinks.

-When a markdown bullet contains an inline `[[wikilink]]` preceded by long prose,
-`parse_relation()` extracts ALL of that prose as the `relation_type`. Previously
-the response model `RelationType` had a `MaxLen(200)` constraint that caused
-edit_note (which round-trips through the response model when re-indexing) to
-fail with:
+Issue #721 was originally triggered by markdown bullets that contained inline
+`[[wikilinks]]` preceded by long prose. The parser treated all prose before the
+wikilink as `relation_type`, and the response model's former `MaxLen(200)`
+constraint caused edit_note to fail with:

    1 validation error for EntityResponseV2
    relations.0.relation_type
      String should have at most 200 characters

-Commit 01cbad1d removed the cap from `RelationType`. This test locks in that
-fix so a future contributor reintroducing `MaxLen` will see the test fail
-before shipping it.
-
-Out of scope: improving `parse_relation()` to fall back to a default relation
-type when the prose-before-link looks like a sentence rather than a label.
-That's a knowledge-graph-quality improvement, not a correctness fix, and is
-not required to keep edit_note working.
+The relation grammar now fixes the root ambiguity too: unquoted multi-word
+prefixes are prose, so this shape should index as a generic `links_to`
+relation rather than preserving prose as a custom relation type.
 """

 import pytest
 from fastmcp import Client

+from basic_memory.repository.relation_repository import RelationRepository
+

@pytest.mark.asyncio
-async def test_edit_note_handles_long_prose_around_wikilink(mcp_server, app, test_project):
-    """edit_note must succeed on notes whose inline wikilinks have >200 chars
-    of prose preceding them — that prose becomes the parsed relation_type."""
+async def test_edit_note_handles_long_prose_around_wikilink(
+    mcp_server, app, test_project, engine_factory
+):
+    """Long prose before an inline wikilink should not become a relation type."""
    long_prose = (
        "**Lorem ipsum dolor sit amet** — consectetur adipiscing elit, sed do eiusmod "
        "tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, "
@@ -75,3 +71,11 @@ async def test_edit_note_handles_long_prose_around_wikilink(mcp_server, app, tes
        )
        assert len(edit_result.content) == 1
        assert "Edited note (append)" in edit_result.content[0].text
+
+    _, session_maker = engine_factory
+    relation_repository = RelationRepository(session_maker, project_id=test_project.id)
+    links_to_relations = await relation_repository.find_by_type("links_to")
+    prose_type_relations = await relation_repository.find_by_type(long_prose)
+
+    assert any(relation.to_name == "Some Note Title" for relation in links_to_relations)
+    assert not prose_type_relations
@@ -28,6 +28,7 @@ async def test_search_notes_entity_types_as_string(mcp_server, app, test_project
            {
                "project": test_project.name,
                "query": "coercion",
+                "search_type": "text",
                "entity_types": '["entity"]',
            },
        )
@@ -54,6 +55,7 @@ async def test_search_notes_note_types_as_string(mcp_server, app, test_project):
            {
                "project": test_project.name,
                "query": "coercion",
+                "search_type": "text",
                "note_types": '["note"]',
            },
        )
@@ -81,6 +83,7 @@ async def test_search_notes_tags_as_string(mcp_server, app, test_project):
            {
                "project": test_project.name,
                "query": "tagged",
+                "search_type": "text",
                "tags": '["alpha"]',
            },
        )
@@ -107,6 +110,7 @@ async def test_search_notes_metadata_filters_as_string(mcp_server, app, test_pro
            {
                "project": test_project.name,
                "query": "metadata",
+                "search_type": "text",
                "metadata_filters": '{"type": "note"}',
            },
        )
@@ -0,0 +1,463 @@
+"""Integration coverage for local, cloud, and team permalink routing."""
+
+from __future__ import annotations
+
+import json
+from collections.abc import Iterable
+from contextlib import asynccontextmanager, contextmanager
+from pathlib import Path
+from typing import Any
+
+import pytest
+import pytest_asyncio
+from fastmcp import Client
+from httpx import ASGITransport, AsyncClient as HttpxAsyncClient
+
+from basic_memory.config import BasicMemoryConfig, ConfigManager, ProjectEntry
+from basic_memory.mcp import async_client
+from basic_memory.mcp import project_context
+from basic_memory.models import Project
+from basic_memory.repository.project_repository import ProjectRepository
+from basic_memory.schemas.cloud import WorkspaceInfo
+from basic_memory.workspace_context import workspace_permalink_headers
+
+
+def _json_content(tool_result) -> Any:
+    """Parse a FastMCP tool result content block into JSON."""
+    assert len(tool_result.content) == 1
+    assert tool_result.content[0].type == "text"
+    return json.loads(tool_result.content[0].text)  # pyright: ignore [reportAttributeAccessIssue]
+
+
+def _workspace(
+    *,
+    tenant_id: str,
+    slug: str,
+    workspace_type: str,
+    is_default: bool = True,
+) -> WorkspaceInfo:
+    return WorkspaceInfo(
+        tenant_id=tenant_id,
+        name=slug.replace("-", " ").title(),
+        workspace_type=workspace_type,
+        slug=slug,
+        role="owner",
+        organization_id=None,
+        is_default=is_default,
+        has_active_subscription=True,
+    )
+
+
+@pytest.fixture
+def personal_workspace() -> WorkspaceInfo:
+    return _workspace(
+        tenant_id="personal-tenant",
+        slug="personal",
+        workspace_type="personal",
+    )
+
+
+@pytest.fixture
+def team_workspace() -> WorkspaceInfo:
+    return _workspace(
+        tenant_id="team-tenant",
+        slug="team-paul",
+        workspace_type="organization",
+        is_default=False,
+    )
+
+
+@pytest.fixture
+def route_workspaces(app):
+    @contextmanager
+    def route(*workspaces: WorkspaceInfo):
+        with _workspace_routing(app, workspaces):
+            yield
+
+    return route
+
+
+@pytest_asyncio.fixture
+async def alternate_project(
+    config_home,
+    engine_factory,
+    app_config: BasicMemoryConfig,
+    config_manager: ConfigManager,
+) -> Project:
+    """Create a second project so no-project lookups cannot pass via the default."""
+    alternate_path = Path(config_home) / "alternate-project"
+    alternate_path.mkdir(parents=True, exist_ok=True)
+
+    _, session_maker = engine_factory
+    project_repository = ProjectRepository(session_maker)
+    project = await project_repository.create(
+        {
+            "name": "alternate-project",
+            "description": "Non-default project for prefix routing tests",
+            "path": str(alternate_path),
+            "is_active": True,
+            "is_default": False,
+        }
+    )
+
+    app_config.projects[project.name] = ProjectEntry(path=str(alternate_path))
+    config_manager.save_config(app_config)
+    return project
+
+
+def _save_permalink_config(
+    app_config: BasicMemoryConfig,
+    *,
+    include_project: bool,
+    default_project: str | None,
+) -> None:
+    app_config.permalinks_include_project = include_project
+    app_config.default_project = default_project
+    ConfigManager().save_config(app_config)
+
+
+@contextmanager
+def _workspace_routing(app, workspaces: Iterable[WorkspaceInfo]):
+    """Route MCP tool HTTP calls through an ASGI-backed cloud workspace seam."""
+    workspace_list = tuple(workspaces)
+    workspace_ids = {workspace.tenant_id for workspace in workspace_list}
+
+    async def workspace_provider():
+        return list(workspace_list)
+
+    @asynccontextmanager
+    async def factory(workspace: str | None = None):
+        assert workspace is None or workspace in workspace_ids
+        async with HttpxAsyncClient(
+            transport=ASGITransport(app=app),
+            base_url="http://test",
+            headers=workspace_permalink_headers(),
+        ) as inner:
+            yield inner
+
+    original_factory = async_client._client_factory
+    original_workspace_provider = project_context._workspace_provider
+    async_client.set_client_factory(factory)
+    project_context.set_workspace_provider(workspace_provider)
+    try:
+        yield
+    finally:
+        async_client._client_factory = original_factory
+        project_context._workspace_provider = original_workspace_provider
+
+
+async def _call_json(mcp_server, tool_name: str, arguments: dict[str, Any]) -> dict[str, Any]:
+    async with Client(mcp_server) as client:
+        result = await client.call_tool(tool_name, arguments)
+
+    payload = _json_content(result)
+    assert isinstance(payload, dict)
+    return payload
+
+
+async def _write_json(
+    mcp_server,
+    *,
+    project: str,
+    title: str,
+    directory: str = "permalink-suite",
+) -> dict[str, Any]:
+    return await _call_json(
+        mcp_server,
+        "write_note",
+        {
+            "project": project,
+            "title": title,
+            "directory": directory,
+            "content": f"# {title}\n\nUnique body for {title}.",
+            "output_format": "json",
+        },
+    )
+
+
+async def _read_json(
+    mcp_server,
+    *,
+    identifier: str,
+    project: str | None = None,
+) -> dict[str, Any]:
+    arguments = {
+        "identifier": identifier,
+        "output_format": "json",
+    }
+    if project is not None:
+        arguments["project"] = project
+    return await _call_json(mcp_server, "read_note", arguments)
+
+
+async def _search_single_permalink(
+    mcp_server,
+    *,
+    title: str,
+    project: str | None = None,
+) -> str:
+    arguments = {
+        "query": title,
+        "search_type": "text",
+        "output_format": "json",
+    }
+    if project is not None:
+        arguments["project"] = project
+
+    payload = await _call_json(mcp_server, "search_notes", arguments)
+    matching_results = [
+        item for item in payload["results"] if isinstance(item, dict) and item.get("title") == title
+    ]
+    assert len(matching_results) == 1
+    permalink = matching_results[0].get("permalink")
+    assert isinstance(permalink, str)
+    return permalink
+
+
+async def _search_permalink_exact(
+    mcp_server,
+    *,
+    permalink: str,
+    title: str,
+    project: str | None = None,
+) -> str:
+    arguments = {
+        "query": permalink,
+        "search_type": "permalink",
+        "output_format": "json",
+    }
+    if project is not None:
+        arguments["project"] = project
+
+    payload = await _call_json(mcp_server, "search_notes", arguments)
+    matching_results = [
+        item for item in payload["results"] if isinstance(item, dict) and item.get("title") == title
+    ]
+    assert len(matching_results) == 1
+    result_permalink = matching_results[0].get("permalink")
+    assert isinstance(result_permalink, str)
+    return result_permalink
+
+
+@pytest.mark.asyncio
+async def test_local_short_permalink_round_trips_when_project_is_supplied(
+    mcp_server,
+    test_project,
+    app_config,
+):
+    """Local short IDs need the project argument for write/search/read routing."""
+    _save_permalink_config(app_config, include_project=False, default_project=None)
+
+    title = "Local Short Permalink"
+    expected_permalink = "permalink-suite/local-short-permalink"
+
+    write_payload = await _write_json(mcp_server, project=test_project.name, title=title)
+    assert write_payload["permalink"] == expected_permalink
+
+    assert (
+        await _search_single_permalink(mcp_server, project=test_project.name, title=title)
+        == expected_permalink
+    )
+
+    short_read = await _read_json(
+        mcp_server,
+        project=test_project.name,
+        identifier=expected_permalink,
+    )
+    assert short_read["permalink"] == expected_permalink
+
+
+@pytest.mark.asyncio
+async def test_local_project_permalink_routes_without_project_argument(
+    mcp_server,
+    alternate_project,
+    app_config,
+):
+    """Local project-qualified IDs carry enough route context for search/read."""
+    _save_permalink_config(app_config, include_project=True, default_project=None)
+
+    title = "Local Project Permalink"
+    short_permalink = "permalink-suite/local-project-permalink"
+    expected_permalink = f"{alternate_project.name}/{short_permalink}"
+
+    write_payload = await _write_json(mcp_server, project=alternate_project.name, title=title)
+    assert write_payload["permalink"] == expected_permalink
+
+    assert (
+        await _search_permalink_exact(
+            mcp_server,
+            permalink=expected_permalink,
+            title=title,
+        )
+        == expected_permalink
+    )
+
+    project_read = await _read_json(mcp_server, identifier=expected_permalink)
+    assert project_read["permalink"] == expected_permalink
+
+
+@pytest.mark.asyncio
+async def test_personal_cloud_short_permalink_round_trips_when_project_is_supplied(
+    mcp_server,
+    test_project,
+    app_config,
+    personal_workspace,
+    route_workspaces,
+):
+    """Legacy short IDs remain readable/searchable in a personal cloud workspace."""
+    _save_permalink_config(app_config, include_project=False, default_project=None)
+
+    title = "Personal Cloud Short Permalink"
+    expected_permalink = "permalink-suite/personal-cloud-short-permalink"
+
+    write_payload = await _write_json(mcp_server, project=test_project.name, title=title)
+    assert write_payload["permalink"] == expected_permalink
+
+    with route_workspaces(personal_workspace):
+        assert (
+            await _search_single_permalink(
+                mcp_server,
+                project=test_project.name,
+                title=title,
+            )
+            == expected_permalink
+        )
+
+        short_read = await _read_json(
+            mcp_server,
+            project=test_project.name,
+            identifier=expected_permalink,
+        )
+        assert short_read["permalink"] == expected_permalink
+
+
+@pytest.mark.asyncio
+async def test_personal_cloud_project_permalink_routes_without_project_argument(
+    mcp_server,
+    alternate_project,
+    app_config,
+    personal_workspace,
+    route_workspaces,
+):
+    """Legacy project-qualified cloud IDs carry enough route context."""
+    _save_permalink_config(app_config, include_project=True, default_project=None)
+
+    title = "Personal Cloud Project Permalink"
+    short_permalink = "permalink-suite/personal-cloud-project-permalink"
+    expected_permalink = f"{alternate_project.name}/{short_permalink}"
+
+    write_payload = await _write_json(mcp_server, project=alternate_project.name, title=title)
+    assert write_payload["permalink"] == expected_permalink
+
+    with route_workspaces(personal_workspace):
+        assert (
+            await _search_permalink_exact(
+                mcp_server,
+                permalink=expected_permalink,
+                title=title,
+            )
+            == expected_permalink
+        )
+
+        project_read = await _read_json(mcp_server, identifier=expected_permalink)
+        assert project_read["permalink"] == expected_permalink
+
+
+@pytest.mark.asyncio
+async def test_team_short_permalink_round_trips_when_project_is_supplied(
+    mcp_server,
+    test_project,
+    app_config,
+    team_workspace,
+    route_workspaces,
+):
+    """Team short IDs need the qualified project argument for search/read routing."""
+    team_project = f"{team_workspace.slug}/{test_project.name}"
+
+    _save_permalink_config(app_config, include_project=False, default_project=None)
+    title = "Team Short Permalink"
+    expected_permalink = "permalink-suite/team-short-permalink"
+
+    write_payload = await _write_json(mcp_server, project=test_project.name, title=title)
+    assert write_payload["permalink"] == expected_permalink
+
+    with route_workspaces(team_workspace):
+        assert (
+            await _search_single_permalink(
+                mcp_server,
+                project=team_project,
+                title=title,
+            )
+            == expected_permalink
+        )
+        short_read = await _read_json(
+            mcp_server,
+            project=team_project,
+            identifier=expected_permalink,
+        )
+        assert short_read["permalink"] == expected_permalink
+
+
+@pytest.mark.asyncio
+async def test_team_project_permalink_routes_without_project_argument(
+    mcp_server,
+    alternate_project,
+    app_config,
+    team_workspace,
+    route_workspaces,
+):
+    """Team project-qualified IDs carry enough route context for search/read."""
+    _save_permalink_config(app_config, include_project=True, default_project=None)
+
+    title = "Team Project Permalink"
+    short_permalink = "permalink-suite/team-project-permalink"
+    expected_permalink = f"{alternate_project.name}/{short_permalink}"
+
+    write_payload = await _write_json(mcp_server, project=alternate_project.name, title=title)
+    assert write_payload["permalink"] == expected_permalink
+
+    with route_workspaces(team_workspace):
+        assert (
+            await _search_permalink_exact(
+                mcp_server,
+                permalink=expected_permalink,
+                title=title,
+            )
+            == expected_permalink
+        )
+        project_read = await _read_json(mcp_server, identifier=expected_permalink)
+        assert project_read["permalink"] == expected_permalink
+
+
+@pytest.mark.asyncio
+async def test_team_workspace_permalink_routes_to_specific_workspace(
+    mcp_server,
+    test_project,
+    app_config,
+    personal_workspace,
+    team_workspace,
+    route_workspaces,
+):
+    """Workspace-qualified IDs route to the project in that workspace."""
+    _save_permalink_config(app_config, include_project=True, default_project=None)
+    team_project = f"{team_workspace.slug}/{test_project.name}"
+
+    title = "Team Workspace Permalink"
+    short_permalink = "permalink-suite/team-workspace-permalink"
+    expected_permalink = f"{team_workspace.slug}/{test_project.name}/{short_permalink}"
+
+    with route_workspaces(personal_workspace, team_workspace):
+        write_payload = await _write_json(mcp_server, project=team_project, title=title)
+        assert write_payload["permalink"] == expected_permalink
+
+        assert (
+            await _search_permalink_exact(
+                mcp_server,
+                permalink=expected_permalink,
+                title=title,
+            )
+            == expected_permalink
+        )
+
+        workspace_read = await _read_json(mcp_server, identifier=expected_permalink)
+        assert workspace_read["permalink"] == expected_permalink
@@ -482,6 +482,23 @@ async def test_import_missing_file(client: AsyncClient, v2_project_url: str):
    assert response.status_code in [400, 422]  # Either bad request or unprocessable entity


+@pytest.mark.asyncio
+async def test_import_rejects_oversized_file(
+    client: AsyncClient, tmp_path, app_config, v2_project_url: str
+):
+    """Import endpoints should reject files before parsing unbounded JSON."""
+    app_config.import_upload_max_bytes = 8
+    file_path = tmp_path / "large.json"
+    file_path.write_text(json.dumps([{"message": "too large"}]), encoding="utf-8")
+
+    with open(file_path, "rb") as f:
+        files = {"file": ("large.json", f, "application/json")}
+        response = await client.post(f"{v2_project_url}/import/chatgpt", files=files)
+
+    assert response.status_code == 413
+    assert "maximum size" in response.json()["detail"]
+
+
@pytest.mark.asyncio
 async def test_import_empty_file(client: AsyncClient, tmp_path, v2_project_url: str):
    """Test importing an empty file via v2 endpoint."""
@@ -302,7 +302,7 @@ async def test_create_entity_with_observations_and_relations(

 ## Observations
 - [note] This is a test observation #tag1 (context)
- related to [[OtherEntity]]
+- "related to" [[OtherEntity]]
 """,
    }

@@ -55,6 +55,25 @@ class SpyEntityRepository:
        self.calls.append(ids)
        return [self.entities_by_id[i] for i in ids if i in self.entities_by_id]

+    async def find_by_ids_for_hydration(self, ids: list[int]):
+        self.calls.append(ids)
+        return [self.entities_by_id[i] for i in ids if i in self.entities_by_id]
+
+
+class LightweightOnlyEntityRepository:
+    """Raises if graph hydration uses the eager-loading repository method."""
+
+    def __init__(self, entities_by_id: dict[int, SimpleNamespace]):
+        self.entities_by_id = entities_by_id
+        self.hydration_calls: list[list[int]] = []
+
+    async def find_by_ids(self, ids: list[int]):
+        raise AssertionError("graph hydration must use the lightweight hydration lookup")
+
+    async def find_by_ids_for_hydration(self, ids: list[int]):
+        self.hydration_calls.append(ids)
+        return [self.entities_by_id[i] for i in ids if i in self.entities_by_id]
+

 # --- Single batch fetch (N+1 elimination) ---

@@ -198,3 +217,63 @@ async def test_to_graph_context_empty_results_skip_entity_lookup():

    assert repo.calls == []
    assert list(graph.results) == []
+
+
+@pytest.mark.asyncio
+async def test_to_graph_context_uses_lightweight_hydration_lookup():
+    """Hydration should not load observations/relations when only entity fields are needed."""
+    repo = LightweightOnlyEntityRepository(
+        {
+            1: _make_entity(1, "Root", "ext-root"),
+            2: _make_entity(2, "Child", "ext-child"),
+        }
+    )
+    now = datetime.now(timezone.utc)
+
+    context = ServiceContextResult(
+        results=[
+            ContextResultItem(
+                primary_result=_make_row(
+                    type="entity",
+                    id=1,
+                    root_id=1,
+                    title="Root",
+                    permalink="notes/root",
+                    file_path="notes/root.md",
+                    created_at=now,
+                ),
+                observations=[],
+                related_results=[
+                    _make_row(
+                        type="relation",
+                        id=20,
+                        root_id=1,
+                        title="links_to: Child",
+                        permalink="notes/root",
+                        file_path="notes/root.md",
+                        relation_type="links_to",
+                        from_id=1,
+                        to_id=2,
+                        depth=1,
+                        created_at=now,
+                    )
+                ],
+            )
+        ],
+        metadata=ContextMetadata(
+            types=[SearchItemType.ENTITY, SearchItemType.RELATION],
+            depth=1,
+            primary_count=1,
+            related_count=1,
+            total_relations=1,
+        ),
+    )
+
+    graph = await to_graph_context(context, entity_repository=repo)
+
+    assert len(repo.hydration_calls) == 1
+    assert set(repo.hydration_calls[0]) == {1, 2}
+    relation = graph.results[0].related_results[0]
+    assert isinstance(relation, RelationSummary)
+    assert relation.from_entity_external_id == "ext-root"
+    assert relation.to_entity_external_id == "ext-child"
@@ -0,0 +1,92 @@
+"""Tests for the /knowledge/orphans API endpoint."""
+
+import pytest
+from httpx import AsyncClient
+
+
+@pytest.mark.asyncio
+async def test_get_orphan_entities_empty_project(client: AsyncClient, v2_project_url):
+    """An empty project returns an empty orphans list."""
+    response = await client.get(f"{v2_project_url}/knowledge/orphans")
+
+    assert response.status_code == 200
+    assert response.json() == {"entities": [], "total": 0}
+
+
+@pytest.mark.asyncio
+async def test_get_orphan_entities_returns_unlinked_entities(client: AsyncClient, v2_project_url):
+    """Entities with no relations appear in the orphans endpoint."""
+    first = await client.post(
+        f"{v2_project_url}/knowledge/entities",
+        json={"title": "Orphan One", "directory": "orphan", "content": "No links here"},
+    )
+    second = await client.post(
+        f"{v2_project_url}/knowledge/entities",
+        json={"title": "Orphan Two", "directory": "orphan", "content": "Also no links"},
+    )
+    assert first.status_code == 200
+    assert second.status_code == 200
+
+    response = await client.get(f"{v2_project_url}/knowledge/orphans")
+
+    assert response.status_code == 200
+    data = response.json()
+    titles = {entity["title"] for entity in data["entities"]}
+    assert titles == {"Orphan One", "Orphan Two"}
+    assert data["total"] == 2
+
+
+@pytest.mark.asyncio
+async def test_get_orphan_entities_excludes_incoming_and_outgoing_relation_nodes(
+    client: AsyncClient, v2_project_url
+):
+    """Entities with either side of a resolved relation are excluded from orphans."""
+    target = await client.post(
+        f"{v2_project_url}/knowledge/entities",
+        json={
+            "title": "Target Note",
+            "directory": "linked",
+            "content": "Referenced entity",
+        },
+    )
+    source = await client.post(
+        f"{v2_project_url}/knowledge/entities",
+        json={
+            "title": "Source Note",
+            "directory": "linked",
+            "content": "- links_to [[Target Note]]",
+        },
+    )
+    standalone = await client.post(
+        f"{v2_project_url}/knowledge/entities",
+        json={"title": "Standalone Note", "directory": "linked", "content": "No links"},
+    )
+    assert source.status_code == 200
+    assert target.status_code == 200
+    assert standalone.status_code == 200
+
+    response = await client.get(f"{v2_project_url}/knowledge/orphans")
+
+    assert response.status_code == 200
+    titles = {entity["title"] for entity in response.json()["entities"]}
+    assert "Source Note" not in titles
+    assert "Target Note" not in titles
+    assert "Standalone Note" in titles
+
+
+@pytest.mark.asyncio
+async def test_get_orphan_entities_response_shape(client: AsyncClient, v2_project_url):
+    """Each orphan entity in the response has the expected graph-node fields."""
+    created = await client.post(
+        f"{v2_project_url}/knowledge/entities",
+        json={"title": "Shape Test", "directory": "shape", "content": "Testing shape"},
+    )
+    assert created.status_code == 200
+
+    response = await client.get(f"{v2_project_url}/knowledge/orphans")
+
+    assert response.status_code == 200
+    data = response.json()
+    entity = next(entity for entity in data["entities"] if entity["title"] == "Shape Test")
+    assert set(entity) == {"external_id", "title", "note_type", "file_path"}
+    assert entity["file_path"].endswith(".md")
@@ -321,6 +321,21 @@ async def test_resolve_project_by_permalink(
    assert resolved.resolution_method in ["name", "permalink"]


+@pytest.mark.asyncio
+async def test_resolve_project_by_workspace_qualified_permalink(
+    client: AsyncClient, test_project: Project, v2_projects_url
+):
+    """Resolve the workspace/project form shown by MCP disambiguation errors."""
+    resolve_data = {"identifier": f"personal/{test_project.name}"}
+    response = await client.post(f"{v2_projects_url}/resolve", json=resolve_data)
+
+    assert response.status_code == 200
+    resolved = ProjectResolveResponse.model_validate(response.json())
+    assert resolved.external_id == test_project.external_id
+    assert resolved.name == test_project.name
+    assert resolved.resolution_method == "permalink"
+
+
@pytest.mark.asyncio
 async def test_resolve_project_by_id(client: AsyncClient, test_project: Project, v2_projects_url):
    """Test resolving a project by external_id string returns correct project external_id."""
@@ -57,7 +57,7 @@ async def test_search_entities(
    )

    # Search for the entity
-    response = await client.post(f"{v2_project_url}/search/", json={"search_text": "Searchable"})
+    response = await client.post(f"{v2_project_url}/search/", json={"text": "Searchable"})

    assert response.status_code == 200
    data = response.json()
@@ -94,7 +94,7 @@ async def test_search_with_pagination(
    # Search with pagination
    response = await client.post(
        f"{v2_project_url}/search/",
-        json={"search_text": "Search Entity"},
+        json={"text": "Search Entity"},
        params={"page": 1, "page_size": 3},
    )

@@ -102,6 +102,57 @@ async def test_search_with_pagination(
    data = response.json()
    assert data["current_page"] == 1
    assert data["page_size"] == 3
+    assert data["total"] == 5
+    assert data["has_more"] is True
+
+    response = await client.post(
+        f"{v2_project_url}/search/",
+        json={"text": "Search Entity"},
+        params={"page": 2, "page_size": 3},
+    )
+
+    assert response.status_code == 200
+    data = response.json()
+    assert data["current_page"] == 2
+    assert data["page_size"] == 3
+    assert data["total"] == 5
+    assert data["has_more"] is False
+    assert len(data["results"]) == 2
+
+
+@pytest.mark.asyncio
+async def test_search_with_item_type_filter_returns_total(
+    client: AsyncClient,
+    test_project: Project,
+    v2_project_url: str,
+    entity_repository,
+    search_service,
+    file_service,
+):
+    """Metadata-only graph searches should include exact totals for pagination."""
+    for i in range(5):
+        entity_data = {
+            "title": f"Structured Entity {i}",
+            "note_type": "note",
+            "content_type": "text/markdown",
+            "file_path": f"structured_{i}.md",
+            "checksum": f"structuredsum{i}",
+        }
+        await create_test_entity(
+            test_project, entity_data, entity_repository, search_service, file_service
+        )
+
+    response = await client.post(
+        f"{v2_project_url}/search/",
+        json={"entity_types": ["entity"]},
+        params={"page": 1, "page_size": 3},
+    )
+
+    assert response.status_code == 200
+    data = response.json()
+    assert data["total"] == 5
+    assert data["has_more"] is True
+    assert len(data["results"]) == 3


@pytest.mark.asyncio
@@ -192,7 +243,7 @@ async def test_search_with_type_filter(

    # Search with type filter
    response = await client.post(
-        f"{v2_project_url}/search/", json={"search_text": "Type", "note_types": ["note"]}
+        f"{v2_project_url}/search/", json={"text": "Type", "note_types": ["note"]}
    )

    assert response.status_code == 200
@@ -225,7 +276,7 @@ async def test_search_with_date_filter(
    # Search with date filter
    response = await client.post(
        f"{v2_project_url}/search/",
-        json={"search_text": "Date Filtered", "after_date": "2024-01-01T00:00:00Z"},
+        json={"text": "Date Filtered", "after_date": "2024-01-01T00:00:00Z"},
    )

    assert response.status_code == 200
@@ -246,12 +297,42 @@ async def test_search_empty_query(
    assert response.status_code in [200, 422]


+@pytest.mark.asyncio
+async def test_search_whitespace_text_is_treated_as_empty(
+    client: AsyncClient,
+    test_project: Project,
+    v2_project_url: str,
+    entity_repository,
+    search_service,
+    file_service,
+):
+    """Whitespace-only text should not become an unfiltered project-wide search."""
+    entity_data = {
+        "title": "Whitespace Regression Entity",
+        "note_type": "note",
+        "content_type": "text/markdown",
+        "file_path": "whitespace_regression.md",
+        "checksum": "whitespace123",
+    }
+    await create_test_entity(
+        test_project, entity_data, entity_repository, search_service, file_service
+    )
+
+    response = await client.post(f"{v2_project_url}/search/", json={"text": "   "})
+
+    assert response.status_code == 200
+    data = response.json()
+    assert data["total"] == 0
+    assert data["has_more"] is False
+    assert data["results"] == []
+
+
@pytest.mark.asyncio
 async def test_search_invalid_project_id(
    client: AsyncClient,
 ):
    """Test searching with invalid project ID returns 404."""
-    response = await client.post("/v2/projects/999999/search/", json={"search_text": "test"})
+    response = await client.post("/v2/projects/999999/search/", json={"text": "test"})

    assert response.status_code == 404

@@ -291,7 +372,7 @@ async def test_v2_search_endpoints_use_project_id_not_name(
 ):
    """Test that v2 search endpoints reject string project names."""
    # Try to use project name instead of ID - should fail
-    response = await client.post(f"/v2/{test_project.name}/search/", json={"search_text": "test"})
+    response = await client.post(f"/v2/{test_project.name}/search/", json={"text": "test"})

    # FastAPI path validation should reject non-integer project_id
    assert response.status_code in [404, 422]
@@ -307,11 +388,14 @@ async def test_search_router_returns_400_for_semantic_disabled(
        async def search(self, *args, **kwargs):
            raise SemanticSearchDisabledError("Semantic search is disabled for this project.")

+        async def count(self, *args, **kwargs):
+            raise SemanticSearchDisabledError("Semantic search is disabled for this project.")
+
    app.dependency_overrides[get_search_service_v2_external] = lambda: RaisingSearchService()
    try:
        response = await client.post(
            f"{v2_project_url}/search/",
-            json={"search_text": "semantic query", "retrieval_mode": "vector"},
+            json={"text": "semantic query", "retrieval_mode": "vector"},
        )
    finally:
        app.dependency_overrides.pop(get_search_service_v2_external, None)
@@ -330,11 +414,14 @@ async def test_search_router_returns_400_for_semantic_missing_deps(
        async def search(self, *args, **kwargs):
            raise SemanticDependenciesMissingError("Semantic dependencies are missing.")

+        async def count(self, *args, **kwargs):
+            raise SemanticDependenciesMissingError("Semantic dependencies are missing.")
+
    app.dependency_overrides[get_search_service_v2_external] = lambda: RaisingSearchService()
    try:
        response = await client.post(
            f"{v2_project_url}/search/",
-            json={"search_text": "semantic query", "retrieval_mode": "hybrid"},
+            json={"text": "semantic query", "retrieval_mode": "hybrid"},
        )
    finally:
        app.dependency_overrides.pop(get_search_service_v2_external, None)
@@ -353,6 +440,9 @@ async def test_search_router_returns_400_for_invalid_vector_query(
        async def search(self, *args, **kwargs):
            raise ValueError("Vector retrieval requires a text query.")

+        async def count(self, *args, **kwargs):
+            raise ValueError("Vector retrieval requires a text query.")
+
    app.dependency_overrides[get_search_service_v2_external] = lambda: RaisingSearchService()
    try:
        response = await client.post(
@@ -366,6 +456,56 @@ async def test_search_router_returns_400_for_invalid_vector_query(
    assert "Vector retrieval requires a text query" in response.json()["detail"]


+@pytest.mark.asyncio
+async def test_semantic_search_uses_probe_pagination_without_count(
+    client: AsyncClient,
+    app,
+    v2_project_url: str,
+):
+    """Semantic searches should not run an extra count query."""
+    now = datetime.now(timezone.utc)
+    fake_rows = [
+        SearchIndexRow(
+            project_id=1,
+            id=row_id,
+            type="entity",
+            file_path=f"notes/semantic-{row_id}.md",
+            created_at=now,
+            updated_at=now,
+            title=f"Semantic Result {row_id}",
+            permalink=f"notes/semantic-{row_id}",
+            score=1.0 - (row_id / 10),
+        )
+        for row_id in range(1, 4)
+    ]
+
+    class FakeSearchService:
+        async def search(self, query, *, limit, offset):
+            assert query.retrieval_mode.value == "vector"
+            assert limit == 3
+            assert offset == 0
+            return fake_rows
+
+        async def count(self, *args, **kwargs):
+            raise AssertionError("semantic search must not run count")
+
+    app.dependency_overrides[get_search_service_v2_external] = lambda: FakeSearchService()
+    try:
+        response = await client.post(
+            f"{v2_project_url}/search/",
+            json={"text": "semantic query", "retrieval_mode": "vector"},
+            params={"page": 1, "page_size": 2},
+        )
+    finally:
+        app.dependency_overrides.pop(get_search_service_v2_external, None)
+
+    assert response.status_code == 200
+    data = response.json()
+    assert data["total"] == 0
+    assert data["has_more"] is True
+    assert len(data["results"]) == 2
+
+
@pytest.mark.asyncio
 async def test_search_has_more_when_more_results_exist(
    client: AsyncClient,
@@ -459,11 +599,14 @@ async def test_search_result_includes_matched_chunk(
        async def search(self, *args, **kwargs):
            return [fake_row]

+        async def count(self, *args, **kwargs):
+            return 1
+
    app.dependency_overrides[get_search_service_v2_external] = lambda: FakeSearchService()
    try:
        response = await client.post(
            f"{v2_project_url}/search/",
-            json={"search_text": "pricing"},
+            json={"text": "pricing"},
        )
    finally:
        app.dependency_overrides.pop(get_search_service_v2_external, None)
@@ -500,11 +643,14 @@ async def test_search_result_omits_matched_chunk_when_none(
        async def search(self, *args, **kwargs):
            return [fake_row]

+        async def count(self, *args, **kwargs):
+            return 1
+
    app.dependency_overrides[get_search_service_v2_external] = lambda: FakeSearchService()
    try:
        response = await client.post(
            f"{v2_project_url}/search/",
-            json={"search_text": "general"},
+            json={"text": "general"},
        )
    finally:
        app.dependency_overrides.pop(get_search_service_v2_external, None)
@@ -23,6 +23,9 @@ async def test_search_router_wraps_request_in_manual_operation(monkeypatch) -> N
        async def search(self, query, *, limit, offset):
            return []

+        async def count(self, query):
+            return 0
+
    @contextmanager
    def fake_span(name: str, **attrs):
        operations.append((name, attrs))
@@ -32,13 +32,48 @@ def test_convert_bmignore_to_rclone_filters_creates_and_converts(config_home):
    # Comments/empties preserved
    assert "# comment" in content
    assert "" in content
-    # Directory pattern becomes recursive exclude
+    # Plain and wildcard patterns exclude direct matches and recursive contents.
+    assert "- node_modules" in content
    assert "- node_modules/**" in content
-    # Wildcard pattern becomes simple exclude
    assert "- *.pyc" in content
+    assert "- *.pyc/**" in content
+    assert "- .git" in content
    assert "- .git/**" in content


+def test_convert_bmignore_to_rclone_filters_excludes_files_and_hidden_directory_contents(
+    config_home,
+):
+    bmignore = get_bmignore_path()
+    bmignore.parent.mkdir(parents=True, exist_ok=True)
+    bmignore.write_text("config.json\n.*\nnode_modules/**\n", encoding="utf-8")
+
+    rclone_filter = convert_bmignore_to_rclone_filters()
+    content = rclone_filter.read_text(encoding="utf-8").splitlines()
+
+    assert "- config.json" in content
+    assert "- config.json/**" in content
+    assert "- .*" in content
+    assert "- .*/**" in content
+    assert "- node_modules" in content
+    assert "- node_modules/**" in content
+
+
+def test_convert_bmignore_to_rclone_filters_preserves_directory_only_patterns(config_home):
+    bmignore = get_bmignore_path()
+    bmignore.parent.mkdir(parents=True, exist_ok=True)
+    bmignore.write_text("cache/\nconfig.json/**\n", encoding="utf-8")
+
+    rclone_filter = convert_bmignore_to_rclone_filters()
+    content = rclone_filter.read_text(encoding="utf-8").splitlines()
+
+    assert "- cache/" in content
+    assert "- cache/**" in content
+    assert "- cache" not in content
+    assert "- config.json" in content
+    assert "- config.json/**" in content
+
+
 def test_convert_bmignore_to_rclone_filters_is_cached_when_up_to_date(config_home):
    bmignore = get_bmignore_path()
    bmignore.parent.mkdir(parents=True, exist_ok=True)
@@ -0,0 +1,54 @@
+"""Tests for secure rclone installer fallbacks."""
+
+import pytest
+
+from basic_memory.cli.commands.cloud import rclone_installer
+
+
+def test_macos_installer_does_not_fallback_to_remote_script(monkeypatch):
+    """Homebrew failure should produce manual guidance, not curl-piped sudo bash."""
+    commands: list[list[str]] = []
+
+    def fake_which(command: str) -> str | None:
+        return "/opt/homebrew/bin/brew" if command == "brew" else None
+
+    def fake_run(command: list[str], check: bool = True):
+        commands.append(command)
+        raise rclone_installer.RcloneInstallError("brew failed")
+
+    monkeypatch.setattr(rclone_installer.shutil, "which", fake_which)
+    monkeypatch.setattr(rclone_installer, "run_command", fake_run)
+
+    with pytest.raises(rclone_installer.RcloneInstallError) as exc_info:
+        rclone_installer.install_rclone_macos()
+
+    assert commands == [["brew", "install", "rclone"]]
+    assert "curl" not in str(exc_info.value)
+    assert "sudo bash" not in str(exc_info.value)
+    assert "brew install rclone" in str(exc_info.value)
+
+
+def test_linux_installer_uses_package_managers_only(monkeypatch):
+    """Linux package-manager failures should not fall through to remote script execution."""
+    commands: list[list[str]] = []
+
+    def fake_which(command: str) -> str | None:
+        return f"/usr/bin/{command}" if command in {"apt", "snap"} else None
+
+    def fake_run(command: list[str], check: bool = True):
+        commands.append(command)
+        raise rclone_installer.RcloneInstallError("install failed")
+
+    monkeypatch.setattr(rclone_installer.shutil, "which", fake_which)
+    monkeypatch.setattr(rclone_installer, "run_command", fake_run)
+
+    with pytest.raises(rclone_installer.RcloneInstallError) as exc_info:
+        rclone_installer.install_rclone_linux()
+
+    assert commands == [
+        ["sudo", "apt", "update"],
+        ["sudo", "snap", "install", "rclone"],
+    ]
+    assert all("curl" not in token for command in commands for token in command)
+    assert "sudo bash" not in str(exc_info.value)
+    assert "sudo apt install rclone" in str(exc_info.value)
@@ -80,3 +80,26 @@ def test_bm_version_does_not_import_heavy_modules():
    assert "CLEAN" in result.stdout, (
        f"Heavy modules loaded during --version: {result.stdout.strip()}"
    )
+
+
+def test_bm_help_does_not_import_api_app():
+    """Regression test: 'bm --help' must not build the FastAPI app graph."""
+    check_script = (
+        "import sys; "
+        "sys.argv = ['bm', '--help']; "
+        "import basic_memory.cli.main; "
+        "heavy = [m for m in sys.modules "
+        "if m == 'basic_memory.api.app' or m.startswith('basic_memory.api.v2.routers')]; "
+        "print(','.join(heavy) if heavy else 'CLEAN')"
+    )
+    result = subprocess.run(
+        ["uv", "run", "python", "-c", check_script],
+        capture_output=True,
+        text=True,
+        timeout=10,
+        cwd=Path(__file__).parent.parent.parent,
+    )
+    assert result.returncode == 0
+    assert "CLEAN" in result.stdout, (
+        f"API app modules loaded during --help: {result.stdout.strip()}"
+    )
@@ -0,0 +1,150 @@
+"""Tests for the 'basic-memory orphans' CLI command."""
+
+import json
+from contextlib import asynccontextmanager, nullcontext
+from unittest.mock import AsyncMock, MagicMock, patch
+
+from mcp.server.fastmcp.exceptions import ToolError
+from typer.testing import CliRunner
+
+from basic_memory.cli.main import app as cli_app
+from basic_memory.schemas.v2.graph import GraphNode
+
+import basic_memory.cli.commands.orphans as orphans_cmd  # noqa: F401
+
+runner = CliRunner()
+
+_MOCK_PROJECT_ITEM = MagicMock()
+_MOCK_PROJECT_ITEM.name = "test-project"
+_MOCK_PROJECT_ITEM.external_id = "11111111-1111-1111-1111-111111111111"
+
+_ORPHAN_ENTITIES = [
+    GraphNode(
+        external_id="aaaa-1111",
+        title="Isolated Note",
+        file_path="notes/isolated.md",
+        note_type="note",
+    ),
+    GraphNode(
+        external_id="bbbb-2222",
+        title="Dangling Spec",
+        file_path="specs/dangling.md",
+        note_type="spec",
+    ),
+]
+
+
+def _mock_config_manager():
+    mock_config = MagicMock()
+    mock_config.default_project = "test-project"
+    return mock_config
+
+
+@asynccontextmanager
+async def _fake_get_client(project_name=None):
+    yield MagicMock()
+
+
+@patch("basic_memory.cli.commands.orphans.run_orphans", new_callable=AsyncMock)
+@patch("basic_memory.cli.commands.orphans.force_routing")
+def test_orphans_preserves_project_routing_by_default(mock_force_routing, mock_run_orphans):
+    """Default invocation keeps routing implicit so project mode can choose local/cloud."""
+    mock_force_routing.return_value = nullcontext()
+    mock_run_orphans.return_value = ("test-project", [])
+
+    result = runner.invoke(cli_app, ["orphans"])
+
+    assert result.exit_code == 0, f"CLI failed: {result.output}"
+    mock_force_routing.assert_called_once_with(local=False, cloud=False)
+
+
+@patch("basic_memory.cli.commands.orphans.ConfigManager")
+@patch("basic_memory.cli.commands.orphans.get_active_project", new_callable=AsyncMock)
+@patch("basic_memory.cli.commands.orphans.get_client")
+@patch("basic_memory.cli.commands.orphans.KnowledgeClient")
+def test_orphans_json_output(mock_knowledge_cls, mock_get_client, mock_get_active, mock_config_cls):
+    """basic-memory orphans --json outputs a JSON array of orphan entity objects."""
+    mock_config_cls.return_value = _mock_config_manager()
+    mock_get_active.return_value = _MOCK_PROJECT_ITEM
+    mock_get_client.side_effect = _fake_get_client
+    mock_knowledge = AsyncMock()
+    mock_knowledge.get_orphans.return_value = _ORPHAN_ENTITIES
+    mock_knowledge_cls.return_value = mock_knowledge
+
+    result = runner.invoke(cli_app, ["orphans", "--json"])
+
+    assert result.exit_code == 0, f"CLI failed: {result.output}"
+    json_start = result.output.rfind("[\n")
+    data = json.loads(result.output[json_start:])
+    titles = {entity["title"] for entity in data}
+    assert titles == {"Isolated Note", "Dangling Spec"}
+    mock_get_client.assert_called_once_with(project_name="test-project")
+
+
+@patch("basic_memory.cli.commands.orphans.ConfigManager")
+@patch("basic_memory.cli.commands.orphans.get_active_project", new_callable=AsyncMock)
+@patch("basic_memory.cli.commands.orphans.get_client")
+@patch("basic_memory.cli.commands.orphans.KnowledgeClient")
+def test_orphans_table_output(
+    mock_knowledge_cls, mock_get_client, mock_get_active, mock_config_cls
+):
+    """basic-memory orphans renders a table with orphan titles and paths."""
+    mock_config_cls.return_value = _mock_config_manager()
+    mock_get_active.return_value = _MOCK_PROJECT_ITEM
+    mock_get_client.side_effect = _fake_get_client
+    mock_knowledge = AsyncMock()
+    mock_knowledge.get_orphans.return_value = _ORPHAN_ENTITIES
+    mock_knowledge_cls.return_value = mock_knowledge
+
+    result = runner.invoke(cli_app, ["orphans"])
+
+    assert result.exit_code == 0, f"CLI failed: {result.output}"
+    assert "Isolated Note" in result.output
+    assert "Dangling Spec" in result.output
+    assert "notes/isolated.md" in result.output
+
+
+@patch("basic_memory.cli.commands.orphans.ConfigManager")
+@patch("basic_memory.cli.commands.orphans.get_active_project", new_callable=AsyncMock)
+@patch("basic_memory.cli.commands.orphans.get_client")
+@patch("basic_memory.cli.commands.orphans.KnowledgeClient")
+def test_orphans_no_results(mock_knowledge_cls, mock_get_client, mock_get_active, mock_config_cls):
+    """basic-memory orphans prints a success message when no orphans are found."""
+    mock_config_cls.return_value = _mock_config_manager()
+    mock_get_active.return_value = _MOCK_PROJECT_ITEM
+    mock_get_client.side_effect = _fake_get_client
+    mock_knowledge = AsyncMock()
+    mock_knowledge.get_orphans.return_value = []
+    mock_knowledge_cls.return_value = mock_knowledge
+
+    result = runner.invoke(cli_app, ["orphans"])
+
+    assert result.exit_code == 0, f"CLI failed: {result.output}"
+    assert "No orphan entities" in result.output
+
+
+@patch("basic_memory.cli.commands.orphans.run_orphans", new_callable=AsyncMock)
+@patch("basic_memory.cli.commands.orphans.force_routing")
+def test_orphans_value_error(mock_force_routing, mock_run_orphans):
+    """User-facing command errors are printed and exit with failure."""
+    mock_force_routing.return_value = nullcontext()
+    mock_run_orphans.side_effect = ValueError("project not found")
+
+    result = runner.invoke(cli_app, ["orphans"])
+
+    assert result.exit_code == 1
+    assert "Error: project not found" in result.output
+
+
+@patch("basic_memory.cli.commands.orphans.run_orphans", new_callable=AsyncMock)
+@patch("basic_memory.cli.commands.orphans.force_routing")
+def test_orphans_tool_error_json_output(mock_force_routing, mock_run_orphans):
+    """User-facing command errors are JSON formatted when requested."""
+    mock_force_routing.return_value = nullcontext()
+    mock_run_orphans.side_effect = ToolError("cloud request failed")
+
+    result = runner.invoke(cli_app, ["orphans", "--json"])
+
+    assert result.exit_code == 1
+    json_start = result.output.rfind("{\n")
+    assert json.loads(result.output[json_start:]) == {"error": "cloud request failed"}
@@ -10,6 +10,7 @@ from typer.testing import CliRunner

 from basic_memory.cli.app import app
 from basic_memory.mcp.clients.project import ProjectClient
+from basic_memory.schemas.cloud import WorkspaceInfo
 from basic_memory.schemas.project_info import ProjectList

 # Importing registers project subcommands on the shared app instance.
@@ -53,6 +54,26 @@ def mock_client(monkeypatch):
    monkeypatch.setattr(project_cmd, "get_client", fake_get_client)


+def _workspace(
+    *,
+    tenant_id: str,
+    slug: str,
+    name: str,
+    workspace_type: str,
+    is_default: bool = False,
+) -> WorkspaceInfo:
+    return WorkspaceInfo(
+        tenant_id=tenant_id,
+        workspace_type=workspace_type,
+        slug=slug,
+        name=name,
+        role="owner",
+        is_default=is_default,
+        organization_id=None,
+        has_active_subscription=True,
+    )
+
+
 def test_project_list_shows_local_cloud_presence_and_routes(
    runner: CliRunner, write_config, mock_client, tmp_path, monkeypatch
 ):
@@ -215,6 +236,680 @@ def test_project_list_shows_display_name_for_private_projects(
    assert private_project["display_name"] == "My Project"


+def test_project_list_cloud_fetches_all_workspaces_and_labels_duplicate_permalinks(
+    runner: CliRunner, write_config, monkeypatch
+):
+    """Cloud project list should include every workspace without collapsing matching names."""
+    write_config(
+        {
+            "env": "dev",
+            "projects": {},
+            "default_project": None,
+            "cloud_api_key": "bmc_test_key_123",
+        }
+    )
+
+    personal = _workspace(
+        tenant_id="tenant-personal",
+        slug="personal",
+        name="Personal",
+        workspace_type="personal",
+        is_default=True,
+    )
+    team = _workspace(
+        tenant_id="tenant-team",
+        slug="team",
+        name="Team",
+        workspace_type="organization",
+    )
+
+    async def fake_get_available_workspaces():
+        return [personal, team]
+
+    class FakeClient:
+        def __init__(self, workspace: str | None):
+            self.workspace = workspace
+
+    @asynccontextmanager
+    async def fake_get_client(workspace=None):
+        yield FakeClient(workspace)
+
+    payloads_by_workspace = {
+        None: {"projects": [], "default_project": None},
+        "tenant-personal": {
+            "projects": [
+                {
+                    "id": 1,
+                    "external_id": "11111111-1111-1111-1111-111111111111",
+                    "name": "shared",
+                    "path": "/personal/shared",
+                    "is_default": True,
+                }
+            ],
+            "default_project": "shared",
+        },
+        "tenant-team": {
+            "projects": [
+                {
+                    "id": 2,
+                    "external_id": "22222222-2222-2222-2222-222222222222",
+                    "name": "shared",
+                    "path": "/team/shared",
+                    "is_default": False,
+                }
+            ],
+            "default_project": None,
+        },
+    }
+    seen_workspaces: list[str | None] = []
+
+    async def fake_list_projects(self):
+        workspace = self.http_client.workspace
+        seen_workspaces.append(workspace)
+        return ProjectList.model_validate(payloads_by_workspace[workspace])
+
+    monkeypatch.setattr(
+        "basic_memory.mcp.project_context.get_available_workspaces",
+        fake_get_available_workspaces,
+    )
+    monkeypatch.setattr(project_cmd, "get_client", fake_get_client)
+    monkeypatch.setattr(ProjectClient, "list_projects", fake_list_projects)
+
+    result = runner.invoke(app, ["project", "list", "--json"], env={"COLUMNS": "240"})
+
+    assert result.exit_code == 0, f"Exit code: {result.exit_code}, output: {result.stdout}"
+    # The initial None call is the local project fetch before cloud workspaces are listed.
+    assert seen_workspaces == [None, "tenant-personal", "tenant-team"]
+
+    data = json.loads(result.stdout)
+    shared_projects = [project for project in data["projects"] if project["name"] == "shared"]
+    assert len(shared_projects) == 2
+    assert {project["cloud_path"] for project in shared_projects} == {
+        "/personal/shared",
+        "/team/shared",
+    }
+    assert {project["workspace"] for project in shared_projects} == {"Personal", "Team"}
+    assert {project["workspace_type"] for project in shared_projects} == {
+        "personal",
+        "organization",
+    }
+
+    table_result = runner.invoke(app, ["project", "list"], env={"COLUMNS": "240"})
+
+    assert table_result.exit_code == 0
+    assert "Personal (personal)" in table_result.stdout
+    assert "Team (organization)" in table_result.stdout
+
+
+def test_project_list_workspace_discovery_failure_warns_and_uses_fallback(
+    runner: CliRunner, write_config, monkeypatch
+):
+    """Workspace discovery failures should fall back and explain the degraded result."""
+    write_config(
+        {
+            "env": "dev",
+            "projects": {},
+            "default_project": None,
+            "default_workspace": "tenant-default",
+            "cloud_api_key": "bmc_test_key_123",
+        }
+    )
+
+    class FakeClient:
+        def __init__(self, workspace: str | None):
+            self.workspace = workspace
+
+    @asynccontextmanager
+    async def fake_get_client(workspace=None):
+        yield FakeClient(workspace)
+
+    async def fail_get_available_workspaces():
+        raise RuntimeError("workspace service unavailable")
+
+    payloads_by_workspace = {
+        None: {"projects": [], "default_project": None},
+        "tenant-default": {
+            "projects": [
+                {
+                    "id": 1,
+                    "external_id": "11111111-1111-1111-1111-111111111111",
+                    "name": "fallback-project",
+                    "path": "/fallback-project",
+                    "is_default": False,
+                }
+            ],
+            "default_project": None,
+        },
+    }
+
+    async def fake_list_projects(self):
+        return ProjectList.model_validate(payloads_by_workspace[self.http_client.workspace])
+
+    monkeypatch.setattr(
+        "basic_memory.mcp.project_context.get_available_workspaces",
+        fail_get_available_workspaces,
+    )
+    monkeypatch.setattr(project_cmd, "get_client", fake_get_client)
+    monkeypatch.setattr(ProjectClient, "list_projects", fake_list_projects)
+
+    result = runner.invoke(app, ["project", "list"], env={"COLUMNS": "240"})
+
+    assert result.exit_code == 0, f"Exit code: {result.exit_code}, output: {result.stdout}"
+    assert "fallback-project" in result.stdout
+    assert "Cloud workspace discovery failed: workspace service unavailable" in result.stdout
+    assert "Showing cloud projects from the configured/default workspace only" in result.stdout
+
+
+def test_project_list_partial_workspace_failure_warns_and_keeps_successes(
+    runner: CliRunner, write_config, monkeypatch
+):
+    """A failed workspace fetch should not hide projects from successful workspaces."""
+    write_config(
+        {
+            "env": "dev",
+            "projects": {},
+            "default_project": None,
+            "cloud_api_key": "bmc_test_key_123",
+        }
+    )
+
+    personal = _workspace(
+        tenant_id="tenant-personal",
+        slug="personal",
+        name="Personal",
+        workspace_type="personal",
+        is_default=True,
+    )
+    team = _workspace(
+        tenant_id="tenant-team",
+        slug="team",
+        name="Team",
+        workspace_type="organization",
+    )
+
+    async def fake_get_available_workspaces():
+        return [personal, team]
+
+    class FakeClient:
+        def __init__(self, workspace: str | None):
+            self.workspace = workspace
+
+    @asynccontextmanager
+    async def fake_get_client(workspace=None):
+        yield FakeClient(workspace)
+
+    payloads_by_workspace = {
+        None: {"projects": [], "default_project": None},
+        "tenant-personal": {
+            "projects": [
+                {
+                    "id": 1,
+                    "external_id": "11111111-1111-1111-1111-111111111111",
+                    "name": "personal-project",
+                    "path": "/personal-project",
+                    "is_default": False,
+                }
+            ],
+            "default_project": None,
+        },
+    }
+
+    async def fake_list_projects(self):
+        if self.http_client.workspace == "tenant-team":
+            raise RuntimeError("team unavailable")
+        return ProjectList.model_validate(payloads_by_workspace[self.http_client.workspace])
+
+    monkeypatch.setattr(
+        "basic_memory.mcp.project_context.get_available_workspaces",
+        fake_get_available_workspaces,
+    )
+    monkeypatch.setattr(project_cmd, "get_client", fake_get_client)
+    monkeypatch.setattr(ProjectClient, "list_projects", fake_list_projects)
+
+    result = runner.invoke(app, ["project", "list"], env={"COLUMNS": "240"})
+
+    assert result.exit_code == 0, f"Exit code: {result.exit_code}, output: {result.stdout}"
+    assert "personal-project" in result.stdout
+    assert "Cloud project discovery failed for workspace Team: team unavailable" in result.stdout
+
+
+def test_project_list_workspace_type_filter_selects_unique_workspace(
+    runner: CliRunner, write_config, monkeypatch
+):
+    """--workspace can use a workspace type when it resolves to one workspace."""
+    write_config(
+        {
+            "env": "dev",
+            "projects": {},
+            "default_project": None,
+            "cloud_api_key": "bmc_test_key_123",
+        }
+    )
+
+    personal = _workspace(
+        tenant_id="tenant-personal",
+        slug="personal",
+        name="Personal",
+        workspace_type="personal",
+        is_default=True,
+    )
+    team = _workspace(
+        tenant_id="tenant-team",
+        slug="team",
+        name="Team",
+        workspace_type="organization",
+    )
+
+    async def fake_get_available_workspaces():
+        return [personal, team]
+
+    class FakeClient:
+        def __init__(self, workspace: str | None):
+            self.workspace = workspace
+
+    @asynccontextmanager
+    async def fake_get_client(workspace=None):
+        yield FakeClient(workspace)
+
+    payloads_by_workspace = {
+        None: {"projects": [], "default_project": None},
+        "tenant-team": {
+            "projects": [
+                {
+                    "id": 1,
+                    "external_id": "11111111-1111-1111-1111-111111111111",
+                    "name": "team-project",
+                    "path": "/team-project",
+                    "is_default": True,
+                }
+            ],
+            "default_project": "team-project",
+        },
+    }
+    seen_workspaces: list[str | None] = []
+
+    async def fake_list_projects(self):
+        workspace = self.http_client.workspace
+        seen_workspaces.append(workspace)
+        return ProjectList.model_validate(payloads_by_workspace[workspace])
+
+    monkeypatch.setattr(
+        "basic_memory.mcp.project_context.get_available_workspaces",
+        fake_get_available_workspaces,
+    )
+    monkeypatch.setattr(project_cmd, "get_client", fake_get_client)
+    monkeypatch.setattr(ProjectClient, "list_projects", fake_list_projects)
+
+    result = runner.invoke(
+        app,
+        ["project", "list", "--workspace", "organization", "--json"],
+        env={"COLUMNS": "240"},
+    )
+
+    assert result.exit_code == 0, f"Exit code: {result.exit_code}, output: {result.stdout}"
+    assert seen_workspaces == [None, "tenant-team"]
+    data = json.loads(result.stdout)
+    assert [project["name"] for project in data["projects"]] == ["team-project"]
+    assert data["projects"][0]["workspace"] == "Team"
+
+
+def test_project_list_workspace_type_filter_lists_ambiguous_matches(
+    runner: CliRunner, write_config, monkeypatch
+):
+    """Ambiguous workspace type filters should list copyable matching slugs."""
+    write_config(
+        {
+            "env": "dev",
+            "projects": {},
+            "default_project": None,
+            "cloud_api_key": "bmc_test_key_123",
+        }
+    )
+
+    async def fake_get_available_workspaces():
+        return [
+            _workspace(
+                tenant_id="tenant-personal",
+                slug="personal",
+                name="Personal",
+                workspace_type="personal",
+                is_default=True,
+            ),
+            _workspace(
+                tenant_id="tenant-team-alpha",
+                slug="team-alpha",
+                name="Team Alpha",
+                workspace_type="organization",
+            ),
+            _workspace(
+                tenant_id="tenant-team-beta",
+                slug="team-beta",
+                name="Team Beta",
+                workspace_type="organization",
+            ),
+        ]
+
+    @asynccontextmanager
+    async def fake_get_client(workspace=None):
+        yield object()
+
+    async def fake_list_projects(self):
+        return ProjectList.model_validate({"projects": [], "default_project": None})
+
+    monkeypatch.setattr(
+        "basic_memory.mcp.project_context.get_available_workspaces",
+        fake_get_available_workspaces,
+    )
+    monkeypatch.setattr(project_cmd, "get_client", fake_get_client)
+    monkeypatch.setattr(ProjectClient, "list_projects", fake_list_projects)
+
+    result = runner.invoke(
+        app,
+        ["project", "list", "--workspace", "organization"],
+        env={"COLUMNS": "240"},
+    )
+
+    assert result.exit_code == 1
+    assert "Workspace 'organization' matches multiple workspaces" in result.stdout
+    assert "Choose one of these matching workspaces by slug" in result.stdout
+    assert "workspace: team-alpha" in result.stdout
+    assert "workspace: team-beta" in result.stdout
+    assert "tenant_id: tenant-team-alpha" in result.stdout
+    assert "tenant_id: tenant-team-beta" in result.stdout
+    assert "workspace: personal" not in result.stdout
+
+
+def test_project_list_invalid_workspace_exits_without_local_fallback(
+    runner: CliRunner, write_config, tmp_path, monkeypatch
+):
+    """Invalid explicit workspace filters should stop instead of showing local-only rows."""
+    local_path = (tmp_path / "main").as_posix()
+    write_config(
+        {
+            "env": "dev",
+            "projects": {"main": {"path": local_path, "mode": "local"}},
+            "default_project": "main",
+            "cloud_api_key": "bmc_test_key_123",
+        }
+    )
+
+    personal = _workspace(
+        tenant_id="tenant-personal",
+        slug="personal",
+        name="Personal",
+        workspace_type="personal",
+        is_default=True,
+    )
+
+    async def fake_get_available_workspaces():
+        return [personal]
+
+    class FakeClient:
+        def __init__(self, workspace: str | None):
+            self.workspace = workspace
+
+    @asynccontextmanager
+    async def fake_get_client(workspace=None):
+        yield FakeClient(workspace)
+
+    async def fake_list_projects(self):
+        return ProjectList.model_validate(
+            {
+                "projects": [
+                    {
+                        "id": 1,
+                        "external_id": "11111111-1111-1111-1111-111111111111",
+                        "name": "main",
+                        "path": local_path,
+                        "is_default": True,
+                    }
+                ],
+                "default_project": "main",
+            }
+        )
+
+    monkeypatch.setattr(
+        "basic_memory.mcp.project_context.get_available_workspaces",
+        fake_get_available_workspaces,
+    )
+    monkeypatch.setattr(project_cmd, "get_client", fake_get_client)
+    monkeypatch.setattr(ProjectClient, "list_projects", fake_list_projects)
+
+    result = runner.invoke(
+        app,
+        ["project", "list", "--workspace", "missing"],
+        env={"COLUMNS": "240"},
+    )
+
+    assert result.exit_code == 1
+    assert "Workspace 'missing' not found" in result.stdout
+    assert "Basic Memory Projects" not in result.stdout
+    assert "Cloud project discovery failed" not in result.stdout
+
+
+def test_project_list_attaches_local_state_to_one_duplicate_cloud_project(
+    runner: CliRunner, write_config, tmp_path, monkeypatch
+):
+    """Local path/default/sync state should not appear on every matching workspace."""
+    local_path = (tmp_path / "main").as_posix()
+    write_config(
+        {
+            "env": "dev",
+            "projects": {
+                "main": {
+                    "path": local_path,
+                    "mode": "local",
+                    "local_sync_path": local_path,
+                }
+            },
+            "default_project": "main",
+            "cloud_api_key": "bmc_test_key_123",
+        }
+    )
+
+    personal = _workspace(
+        tenant_id="tenant-personal",
+        slug="personal",
+        name="Personal",
+        workspace_type="personal",
+        is_default=True,
+    )
+    team = _workspace(
+        tenant_id="tenant-team",
+        slug="team",
+        name="Team",
+        workspace_type="organization",
+    )
+
+    async def fake_get_available_workspaces():
+        return [personal, team]
+
+    class FakeClient:
+        def __init__(self, workspace: str | None):
+            self.workspace = workspace
+
+    @asynccontextmanager
+    async def fake_get_client(workspace=None):
+        yield FakeClient(workspace)
+
+    payloads_by_workspace = {
+        None: {
+            "projects": [
+                {
+                    "id": 1,
+                    "external_id": "11111111-1111-1111-1111-111111111111",
+                    "name": "main",
+                    "path": local_path,
+                    "is_default": True,
+                }
+            ],
+            "default_project": "main",
+        },
+        "tenant-personal": {
+            "projects": [
+                {
+                    "id": 2,
+                    "external_id": "22222222-2222-2222-2222-222222222222",
+                    "name": "main",
+                    "path": "/basic-memory",
+                    "is_default": True,
+                }
+            ],
+            "default_project": "main",
+        },
+        "tenant-team": {
+            "projects": [
+                {
+                    "id": 3,
+                    "external_id": "33333333-3333-3333-3333-333333333333",
+                    "name": "main",
+                    "path": "/basic-memory",
+                    "is_default": True,
+                }
+            ],
+            "default_project": "main",
+        },
+    }
+
+    async def fake_list_projects(self):
+        return ProjectList.model_validate(payloads_by_workspace[self.http_client.workspace])
+
+    monkeypatch.setattr(
+        "basic_memory.mcp.project_context.get_available_workspaces",
+        fake_get_available_workspaces,
+    )
+    monkeypatch.setattr(project_cmd, "get_client", fake_get_client)
+    monkeypatch.setattr(ProjectClient, "list_projects", fake_list_projects)
+
+    result = runner.invoke(app, ["project", "list", "--json"], env={"COLUMNS": "240"})
+
+    assert result.exit_code == 0, f"Exit code: {result.exit_code}, output: {result.stdout}"
+    data = json.loads(result.stdout)
+    main_rows = [project for project in data["projects"] if project["name"] == "main"]
+    assert len(main_rows) == 2
+
+    personal_row = next(project for project in main_rows if project["workspace"] == "Personal")
+    team_row = next(project for project in main_rows if project["workspace"] == "Team")
+
+    assert personal_row["local_path"] == project_cmd.format_path(local_path)
+    assert personal_row["cli_route"] == "local"
+    assert personal_row["mcp_stdio"] == "stdio"
+    assert personal_row["sync"] is True
+    assert personal_row["is_default"] is True
+
+    assert team_row["local_path"] == ""
+    assert team_row["cli_route"] == "cloud"
+    assert team_row["mcp_stdio"] == "https"
+    assert team_row["sync"] is False
+    assert team_row["is_default"] is False
+
+    filtered_result = runner.invoke(
+        app,
+        ["project", "list", "--workspace", "organization", "--json"],
+        env={"COLUMNS": "240"},
+    )
+
+    assert filtered_result.exit_code == 0, (
+        f"Exit code: {filtered_result.exit_code}, output: {filtered_result.stdout}"
+    )
+    filtered_data = json.loads(filtered_result.stdout)
+    assert len(filtered_data["projects"]) == 1
+    filtered_team_row = filtered_data["projects"][0]
+    assert filtered_team_row["workspace"] == "Team"
+    assert filtered_team_row["local_path"] == ""
+    assert filtered_team_row["cli_route"] == "cloud"
+    assert filtered_team_row["mcp_stdio"] == "https"
+    assert filtered_team_row["sync"] is False
+    assert filtered_team_row["is_default"] is False
+
+
+def test_project_list_hides_bisync_flag_for_attached_team_workspace(
+    runner: CliRunner, write_config, tmp_path, monkeypatch
+):
+    """Bisync is only supported for personal workspaces."""
+    local_path = (tmp_path / "team-main").as_posix()
+    write_config(
+        {
+            "env": "dev",
+            "projects": {
+                "main": {
+                    "path": local_path,
+                    "mode": "cloud",
+                    "workspace_id": "tenant-team",
+                    "local_sync_path": local_path,
+                }
+            },
+            "default_project": "main",
+            "cloud_api_key": "bmc_test_key_123",
+        }
+    )
+
+    personal = _workspace(
+        tenant_id="tenant-personal",
+        slug="personal",
+        name="Personal",
+        workspace_type="personal",
+        is_default=True,
+    )
+    team = _workspace(
+        tenant_id="tenant-team",
+        slug="team",
+        name="Team",
+        workspace_type="organization",
+    )
+
+    async def fake_get_available_workspaces():
+        return [personal, team]
+
+    class FakeClient:
+        def __init__(self, workspace: str | None):
+            self.workspace = workspace
+
+    @asynccontextmanager
+    async def fake_get_client(workspace=None):
+        yield FakeClient(workspace)
+
+    project_payload = {
+        "projects": [
+            {
+                "id": 1,
+                "external_id": "11111111-1111-1111-1111-111111111111",
+                "name": "main",
+                "path": "/basic-memory",
+                "is_default": True,
+            }
+        ],
+        "default_project": "main",
+    }
+    payloads_by_workspace = {
+        None: {"projects": [], "default_project": None},
+        "tenant-personal": project_payload,
+        "tenant-team": project_payload,
+    }
+
+    async def fake_list_projects(self):
+        return ProjectList.model_validate(payloads_by_workspace[self.http_client.workspace])
+
+    monkeypatch.setattr(
+        "basic_memory.mcp.project_context.get_available_workspaces",
+        fake_get_available_workspaces,
+    )
+    monkeypatch.setattr(project_cmd, "get_client", fake_get_client)
+    monkeypatch.setattr(ProjectClient, "list_projects", fake_list_projects)
+
+    result = runner.invoke(app, ["project", "list", "--json"], env={"COLUMNS": "240"})
+
+    assert result.exit_code == 0, f"Exit code: {result.exit_code}, output: {result.stdout}"
+    data = json.loads(result.stdout)
+    main_rows = [project for project in data["projects"] if project["name"] == "main"]
+    team_row = next(project for project in main_rows if project["workspace"] == "Team")
+
+    assert team_row["cli_route"] == "cloud"
+    assert team_row["mcp_stdio"] == "https"
+    assert team_row["sync"] is False
+    assert team_row["is_default"] is True
+
+
 def test_project_ls_local_mode_defaults_to_local_route(
    runner: CliRunner, write_config, mock_client, tmp_path, monkeypatch
 ):
@@ -182,6 +182,46 @@ class TestWorkspaceSetDefault:
        assert result.exit_code == 1
        assert "not found" in result.stdout

+    def test_set_default_workspace_ambiguous_type_lists_matching_choices(self, runner, monkeypatch):
+        async def fake_get_available_workspaces(context=None):
+            return [
+                _workspace(
+                    tenant_id="11111111-1111-1111-1111-111111111111",
+                    workspace_type="personal",
+                    slug="personal",
+                    name="Personal",
+                    role="owner",
+                    is_default=True,
+                ),
+                _workspace(
+                    tenant_id="22222222-2222-2222-2222-222222222222",
+                    workspace_type="organization",
+                    slug="team-alpha",
+                    name="Team Alpha",
+                    role="editor",
+                ),
+                _workspace(
+                    tenant_id="33333333-3333-3333-3333-333333333333",
+                    workspace_type="organization",
+                    slug="team-beta",
+                    name="Team Beta",
+                    role="owner",
+                ),
+            ]
+
+        monkeypatch.setattr(
+            workspace_cmd, "get_available_workspaces", fake_get_available_workspaces
+        )
+
+        result = runner.invoke(app, ["cloud", "workspace", "set-default", "organization"])
+
+        assert result.exit_code == 1
+        assert "Workspace 'organization' matches multiple workspaces" in result.stdout
+        assert "Choose one of these matching workspaces by slug" in result.stdout
+        assert "workspace: team-alpha" in result.stdout
+        assert "workspace: team-beta" in result.stdout
+        assert "workspace: personal" not in result.stdout
+
    def test_set_default_workspace_no_workspaces(self, runner, monkeypatch):
        async def fake_get_available_workspaces(context=None):
            return []
@@ -128,3 +128,51 @@ def test_unicode_targets():
    assert relation.type == "type"
    assert relation.target == "Target"
    assert relation.context == "测试"
+
+
+def test_quoted_multi_word_relation_type_parses_as_explicit_relation():
+    """Quoted relation labels allow explicit multi-word relation types."""
+    md = MarkdownIt().use(relation_plugin)
+
+    tokens = md.parse('- "some type" [[Target]] (context)')
+    token = next(t for t in tokens if t.type == "inline")
+
+    assert token.meta["relations"] == [
+        {"type": "some type", "target": "Target", "context": "context"}
+    ]
+    assert parse_relation(token) == {"type": "some type", "target": "Target", "context": "context"}
+
+
+def test_single_quoted_multi_word_relation_type_parses_as_explicit_relation():
+    """Single-quoted relation labels also allow explicit multi-word relation types."""
+    md = MarkdownIt().use(relation_plugin)
+
+    tokens = md.parse("- 'some type' [[Target]] (context)")
+    token = next(t for t in tokens if t.type == "inline")
+
+    assert token.meta["relations"] == [
+        {"type": "some type", "target": "Target", "context": "context"}
+    ]
+    assert parse_relation(token) == {"type": "some type", "target": "Target", "context": "context"}
+
+
+def test_unquoted_multi_word_prefix_is_inline_link_not_relation_type():
+    """Unquoted prose before a wikilink is an inline link, not a relation type."""
+    md = MarkdownIt().use(relation_plugin)
+
+    tokens = md.parse("- some other thing [[Target]]")
+    token = next(t for t in tokens if t.type == "inline")
+
+    assert token.meta["relations"] == [{"type": "links_to", "target": "Target", "context": None}]
+    assert parse_relation(token) is None
+
+
+def test_bare_list_wikilink_is_inline_link_not_default_explicit_relation():
+    """A list item containing only a wikilink is still a generic inline link."""
+    md = MarkdownIt().use(relation_plugin)
+
+    tokens = md.parse("- [[Target]]")
+    token = next(t for t in tokens if t.type == "inline")
+
+    assert token.meta["relations"] == [{"type": "links_to", "target": "Target", "context": None}]
+    assert parse_relation(token) is None
@@ -133,6 +133,39 @@ class TestKnowledgeClient:
        result = await client.resolve_entity("my-note")
        assert result == "entity-uuid-123"

+    @pytest.mark.asyncio
+    async def test_get_orphans_validates_response(self, monkeypatch):
+        """Orphan responses are validated into GraphNode objects."""
+        from basic_memory.mcp.clients import knowledge as knowledge_mod
+        from basic_memory.schemas.v2.graph import GraphNode
+
+        mock_response = MagicMock()
+        mock_response.json.return_value = {
+            "entities": [
+                {
+                    "external_id": "entity-uuid-123",
+                    "title": "Orphan Note",
+                    "file_path": "notes/orphan.md",
+                    "note_type": "note",
+                }
+            ],
+            "total": 1,
+        }
+
+        async def mock_call_get(client, url, **kwargs):
+            assert "/v2/projects/proj-123/knowledge/orphans" in url
+            return mock_response
+
+        monkeypatch.setattr(knowledge_mod, "call_get", mock_call_get)
+
+        mock_http = MagicMock()
+        client = KnowledgeClient(mock_http, "proj-123")
+        result = await client.get_orphans()
+
+        assert len(result) == 1
+        assert isinstance(result[0], GraphNode)
+        assert result[0].title == "Orphan Note"
+

 class TestSearchClient:
    """Tests for SearchClient."""
@@ -340,6 +340,106 @@ async def test_workspace_invalid_selection_lists_choices(monkeypatch):
        await resolve_workspace_parameter(workspace="missing-workspace")


+@pytest.mark.asyncio
+async def test_workspace_ambiguous_type_selection_lists_matching_choices(monkeypatch):
+    from basic_memory.mcp.project_context import resolve_workspace_parameter
+
+    workspaces = [
+        _workspace(
+            tenant_id="11111111-1111-1111-1111-111111111111",
+            workspace_type="personal",
+            slug="personal",
+            name="Personal",
+            role="owner",
+            is_default=True,
+        ),
+        _workspace(
+            tenant_id="22222222-2222-2222-2222-222222222222",
+            workspace_type="organization",
+            slug="team-alpha",
+            name="Team Alpha",
+            role="editor",
+        ),
+        _workspace(
+            tenant_id="33333333-3333-3333-3333-333333333333",
+            workspace_type="organization",
+            slug="team-beta",
+            name="Team Beta",
+            role="owner",
+        ),
+    ]
+
+    async def fake_get_available_workspaces(context=None):
+        return workspaces
+
+    monkeypatch.setattr(
+        "basic_memory.mcp.project_context.get_available_workspaces",
+        fake_get_available_workspaces,
+    )
+
+    with pytest.raises(ValueError) as exc_info:
+        await resolve_workspace_parameter(workspace="organization")
+
+    message = str(exc_info.value)
+    assert "Workspace 'organization' matches multiple workspaces" in message
+    assert "workspace: team-alpha" in message
+    assert "workspace: team-beta" in message
+    assert "workspace: personal" not in message
+
+
+@pytest.mark.asyncio
+async def test_workspace_type_selection_ignores_cached_workspace_for_ambiguity(monkeypatch):
+    from basic_memory.mcp.project_context import resolve_workspace_parameter
+
+    cached_workspace = _workspace(
+        tenant_id="22222222-2222-2222-2222-222222222222",
+        workspace_type="organization",
+        slug="team-alpha",
+        name="Team Alpha",
+        role="editor",
+    )
+    workspaces = [
+        _workspace(
+            tenant_id="11111111-1111-1111-1111-111111111111",
+            workspace_type="personal",
+            slug="personal",
+            name="Personal",
+            role="owner",
+            is_default=True,
+        ),
+        cached_workspace,
+        _workspace(
+            tenant_id="33333333-3333-3333-3333-333333333333",
+            workspace_type="organization",
+            slug="team-beta",
+            name="Team Beta",
+            role="owner",
+        ),
+    ]
+    context = _ContextState()
+    await context.set_state("active_workspace", cached_workspace.model_dump())
+    fetches = 0
+
+    async def fake_get_available_workspaces(context=None):
+        nonlocal fetches
+        fetches += 1
+        return workspaces
+
+    monkeypatch.setattr(
+        "basic_memory.mcp.project_context.get_available_workspaces",
+        fake_get_available_workspaces,
+    )
+
+    with pytest.raises(ValueError) as exc_info:
+        await resolve_workspace_parameter(workspace="organization", context=_ctx(context))
+
+    message = str(exc_info.value)
+    assert fetches == 1
+    assert "Workspace 'organization' matches multiple workspaces" in message
+    assert "workspace: team-alpha" in message
+    assert "workspace: team-beta" in message
+
+
@pytest.mark.asyncio
 async def test_workspace_uses_cached_workspace_without_fetch(monkeypatch):
    from basic_memory.mcp.project_context import resolve_workspace_parameter
@@ -826,7 +926,7 @@ async def test_resolve_workspace_qualified_memory_url_uses_personal_canonical_pa
    resolved = await resolve_workspace_qualified_memory_url("memory://personal/main/notes/foo")

    assert resolved is not None
-    assert resolved.canonical_path == "main/notes/foo"
+    assert resolved.canonical_path == "personal/main/notes/foo"


@pytest.mark.asyncio
@@ -1373,7 +1473,7 @@ async def test_resolve_project_and_path_keeps_workspace_qualified_canonical_path


@pytest.mark.asyncio
-async def test_resolve_project_and_path_strips_personal_workspace_prefix(
+async def test_resolve_project_and_path_preserves_personal_workspace_prefix(
    config_manager,
    monkeypatch,
 ):
@@ -1417,7 +1517,7 @@ async def test_resolve_project_and_path_strips_personal_workspace_prefix(
    )

    assert active_project == cached_project
-    assert resolved_path == "main/notes/foo"
+    assert resolved_path == "personal/main/notes/foo"
    assert is_memory_url is True


@@ -1453,6 +1553,225 @@ async def test_resolve_project_and_path_preserves_existing_project_prefixed_memo
    assert is_memory_url is True


+@pytest.mark.asyncio
+async def test_resolve_project_and_path_uses_cached_workspace_for_active_route(
+    config_manager,
+    monkeypatch,
+):
+    from mcp.server.fastmcp.exceptions import ToolError
+
+    import basic_memory.mcp.project_context as project_context
+    from basic_memory.mcp.project_context import resolve_project_and_path
+    from basic_memory.schemas.project_info import ProjectItem
+
+    config = config_manager.load_config()
+    config.permalinks_include_project = True
+    config_manager.save_config(config)
+
+    context = _ContextState()
+    cached_project = ProjectItem(
+        id=1,
+        external_id="11111111-1111-1111-1111-111111111111",
+        name="main",
+        path="/tmp/main",
+        is_default=False,
+    )
+    team_workspace = _workspace(
+        tenant_id="team-tenant",
+        workspace_type="organization",
+        slug="team-paul",
+        name="Team Paul",
+        role="editor",
+    )
+    await context.set_state("active_project", cached_project.model_dump())
+    await context.set_state("active_workspace", team_workspace.model_dump())
+
+    async def fake_call_post(*args, **kwargs):
+        raise ToolError("project not found")
+
+    async def fake_get_active_project(*args, **kwargs):
+        return cached_project
+
+    monkeypatch.setattr("basic_memory.mcp.tools.utils.call_post", fake_call_post)
+    monkeypatch.setattr(project_context, "get_active_project", fake_get_active_project)
+
+    active_project, resolved_path, is_memory_url = await resolve_project_and_path(
+        client=cast(Any, None),
+        identifier="memory://notes/foo",
+        project="main",
+        context=_ctx(context),
+    )
+
+    assert active_project == cached_project
+    assert resolved_path == "team-paul/main/notes/foo"
+    assert is_memory_url is True
+
+    active_project, resolved_path, is_memory_url = await resolve_project_and_path(
+        client=cast(Any, None),
+        identifier="memory://main",
+        project="main",
+        context=_ctx(context),
+    )
+
+    assert active_project == cached_project
+    assert resolved_path == "team-paul/main"
+    assert is_memory_url is True
+
+
+@pytest.mark.asyncio
+async def test_resolve_project_and_path_uses_workspace_context_for_project_root(
+    config_manager,
+    monkeypatch,
+):
+    import basic_memory.mcp.project_context as project_context
+    from basic_memory.mcp.project_context import resolve_project_and_path
+    from basic_memory.schemas.project_info import ProjectItem
+    from basic_memory.workspace_context import workspace_permalink_context
+
+    config = config_manager.load_config()
+    config.permalinks_include_project = True
+    config_manager.save_config(config)
+
+    active = ProjectItem(
+        id=1,
+        external_id="11111111-1111-1111-1111-111111111111",
+        name="main",
+        path="/tmp/main",
+        is_default=False,
+    )
+
+    async def fake_get_active_project(*args, **kwargs):
+        return active
+
+    monkeypatch.setattr(project_context, "get_active_project", fake_get_active_project)
+
+    with workspace_permalink_context(workspace_slug="team-paul", workspace_type="organization"):
+        active_project, resolved_path, is_memory_url = await resolve_project_and_path(
+            client=cast(Any, None),
+            identifier="memory://main",
+            project="main",
+            context=_ctx(_ContextState()),
+        )
+
+    assert active_project == active
+    assert resolved_path == "team-paul/main"
+    assert is_memory_url is True
+
+
+@pytest.mark.asyncio
+async def test_resolve_project_and_path_uses_cached_workspace_for_cached_project_prefix(
+    config_manager,
+    monkeypatch,
+):
+    import basic_memory.mcp.project_context as project_context
+    from basic_memory.mcp.project_context import resolve_project_and_path
+    from basic_memory.schemas.project_info import ProjectItem
+
+    config = config_manager.load_config()
+    config.permalinks_include_project = True
+    config_manager.save_config(config)
+
+    context = _ContextState()
+    cached_project = ProjectItem(
+        id=1,
+        external_id="11111111-1111-1111-1111-111111111111",
+        name="main",
+        path="/tmp/main",
+        is_default=False,
+    )
+    team_workspace = _workspace(
+        tenant_id="team-tenant",
+        workspace_type="organization",
+        slug="team-paul",
+        name="Team Paul",
+        role="editor",
+    )
+    await context.set_state("active_project", cached_project.model_dump())
+    await context.set_state("active_workspace", team_workspace.model_dump())
+
+    async def fail_call_post(*args, **kwargs):  # pragma: no cover
+        raise AssertionError("Cached project prefix should not call project resolve API")
+
+    async def fake_resolve_project_parameter(project=None, **kwargs):
+        return cached_project.name if project else cached_project.name
+
+    monkeypatch.setattr("basic_memory.mcp.tools.utils.call_post", fail_call_post)
+    monkeypatch.setattr(
+        project_context,
+        "resolve_project_parameter",
+        fake_resolve_project_parameter,
+    )
+
+    active_project, resolved_path, is_memory_url = await resolve_project_and_path(
+        client=cast(Any, None),
+        identifier="memory://main/notes/foo",
+        context=_ctx(context),
+    )
+
+    assert active_project == cached_project
+    assert resolved_path == "team-paul/main/notes/foo"
+    assert is_memory_url is True
+
+
+@pytest.mark.asyncio
+async def test_resolve_project_and_path_uses_cached_workspace_for_resolved_project_prefix(
+    config_manager,
+    monkeypatch,
+):
+    import basic_memory.mcp.project_context as project_context
+    from basic_memory.mcp.project_context import resolve_project_and_path
+
+    config = config_manager.load_config()
+    config.permalinks_include_project = True
+    config_manager.save_config(config)
+
+    context = _ContextState()
+    team_workspace = _workspace(
+        tenant_id="team-tenant",
+        workspace_type="organization",
+        slug="team-paul",
+        name="Team Paul",
+        role="editor",
+    )
+    await context.set_state("active_workspace", team_workspace.model_dump())
+
+    class FakeResponse:
+        def json(self):
+            return {
+                "external_id": "22222222-2222-2222-2222-222222222222",
+                "project_id": 2,
+                "name": "Research",
+                "permalink": "research",
+                "path": "/tmp/research",
+                "is_active": True,
+                "is_default": False,
+                "resolution_method": "permalink",
+            }
+
+    async def fake_call_post(*args, **kwargs):
+        return FakeResponse()
+
+    async def fake_resolve_project_parameter(project=None, **kwargs):
+        return "Research" if project else "Research"
+
+    monkeypatch.setattr("basic_memory.mcp.tools.utils.call_post", fake_call_post)
+    monkeypatch.setattr(
+        project_context,
+        "resolve_project_parameter",
+        fake_resolve_project_parameter,
+    )
+
+    active_project, resolved_path, is_memory_url = await resolve_project_and_path(
+        client=cast(Any, None),
+        identifier="memory://research/notes/foo",
+        context=_ctx(context),
+    )
+
+    assert active_project.name == "Research"
+    assert resolved_path == "team-paul/research/notes/foo"
+    assert is_memory_url is True
+
+
 class TestDetectProjectFromUrlPrefix:
    """Test detect_project_from_url_prefix for URL-based project detection."""

@@ -1556,6 +1875,92 @@ class TestGetProjectClientRoutingOrder:
        # The error should NOT be about workspaces
        assert "workspace" not in str(exc_info.value).lower()

+    @pytest.mark.asyncio
+    async def test_local_route_clears_stale_cached_workspace(self, config_manager, monkeypatch):
+        """A previous cloud workspace must not decorate later local memory URLs."""
+        from contextlib import asynccontextmanager
+
+        from mcp.server.fastmcp.exceptions import ToolError
+
+        import basic_memory.mcp.project_context as project_context
+        from basic_memory.config import ProjectEntry
+        from basic_memory.mcp.project_context import get_project_client, resolve_project_and_path
+        from basic_memory.schemas.project_info import ProjectItem
+        from basic_memory.workspace_context import current_workspace_permalink_context
+
+        config = config_manager.load_config()
+        config.permalinks_include_project = True
+        config.projects["local-proj"] = ProjectEntry(
+            path=str(config_manager.config_dir.parent / "local-proj")
+        )
+        config_manager.save_config(config)
+
+        context = _ContextState()
+        stale_workspace = _workspace(
+            tenant_id="team-tenant",
+            workspace_type="organization",
+            slug="team-paul",
+            name="Team Paul",
+            role="editor",
+        )
+        await context.set_state("active_workspace", stale_workspace.model_dump())
+
+        seen: dict[str, object] = {}
+        active = ProjectItem(
+            id=1,
+            external_id="local-project-id",
+            name="local-proj",
+            path="/local-proj",
+            is_default=False,
+        )
+
+        async def fail_ensure_workspace_project_index(context=None):  # pragma: no cover
+            raise AssertionError("Local routing must not discover cloud workspaces")
+
+        @asynccontextmanager
+        async def fake_get_client(project_name=None, workspace=None):
+            seen["project_name"] = project_name
+            seen["workspace"] = workspace
+            seen["permalink_context"] = current_workspace_permalink_context()
+            yield object()
+
+        async def fake_get_active_project(client, project_name, context=None, headers=None):
+            assert project_name == "local-proj"
+            return active
+
+        async def fake_call_post(*args, **kwargs):
+            raise ToolError("project not found")
+
+        monkeypatch.setattr(
+            project_context,
+            "_ensure_workspace_project_index",
+            fail_ensure_workspace_project_index,
+        )
+        monkeypatch.setattr("basic_memory.mcp.async_client.get_client", fake_get_client)
+        monkeypatch.setattr(project_context, "get_active_project", fake_get_active_project)
+        monkeypatch.setattr("basic_memory.mcp.tools.utils.call_post", fake_call_post)
+
+        async with get_project_client(
+            project="local-proj",
+            context=_ctx(context),
+        ) as (client, active_project):
+            _, resolved_path, is_memory_url = await resolve_project_and_path(
+                client=cast(Any, client),
+                identifier="memory://notes/foo",
+                project="local-proj",
+                context=_ctx(context),
+            )
+
+        assert active_project == active
+        assert seen == {
+            "project_name": "local-proj",
+            "workspace": None,
+            "permalink_context": None,
+        }
+        assert resolved_path == "local-proj/notes/foo"
+        assert is_memory_url is True
+        assert await context.get_state("active_workspace") is None
+
    @pytest.mark.asyncio
    async def test_cloud_project_uses_per_project_workspace_id(self, config_manager, monkeypatch):
        """Cloud project with workspace_id uses cached workspace permalink context."""
@@ -4,7 +4,7 @@ import pytest

 from mcp.server.fastmcp.exceptions import ToolError

-from basic_memory.mcp.tools import build_context
+from basic_memory.mcp.tools import build_context, write_note


@pytest.mark.asyncio
@@ -75,6 +75,36 @@ async def test_get_discussion_context_pattern(client, test_graph, test_project):
    assert result["metadata"]["depth"] == 1


+@pytest.mark.asyncio
+async def test_build_context_project_id_preserves_workspace_contextvar_canonical_path(
+    app, test_project
+):
+    """project_id routing keeps ContextVar workspace prefixes in memory URL lookups."""
+    from basic_memory.workspace_context import workspace_permalink_context
+
+    with workspace_permalink_context(workspace_slug="team-paul", workspace_type="organization"):
+        await write_note(
+            project_id=test_project.external_id,
+            title="Workspace Build Context Note",
+            directory="tests",
+            content="Build context should find this workspace note",
+        )
+
+        result = await build_context(
+            project_id=test_project.external_id,
+            url="memory://tests/*",
+            timeframe="30d",
+        )
+
+    assert isinstance(result, dict)
+    assert len(result["results"]) == 1
+    primary = result["results"][0]["primary_result"]
+    assert primary["permalink"] == (
+        f"team-paul/{test_project.name}/tests/workspace-build-context-note"
+    )
+    assert primary["content"] == "Build context should find this workspace note"
+
+
@pytest.mark.asyncio
 async def test_get_discussion_context_timeframe(client, test_graph, test_project):
    """Test timeframe parameter filtering."""
@@ -31,12 +31,13 @@ EXPECTED_TOOL_SIGNATURES: dict[str, list[str]] = {
        "output_format",
    ],
    "delete_note": ["identifier", "is_directory", "project", "project_id", "output_format"],
-    "delete_project": ["project_name"],
+    "delete_project": ["project_name", "workspace"],
    "edit_note": [
        "identifier",
        "operation",
        "content",
        "project",
+        "workspace",
        "project_id",
        "section",
        "find_text",
@@ -83,6 +84,7 @@ EXPECTED_TOOL_SIGNATURES: dict[str, list[str]] = {
        "query",
        "project",
        "project_id",
+        "search_all_projects",
        "page",
        "page_size",
        "search_type",
@@ -9,6 +9,68 @@ from basic_memory.mcp.tools.read_note import read_note
 from basic_memory.mcp.tools.write_note import write_note


+def test_edit_note_workspace_project_route_helper():
+    """workspace/project routing should be explicit and deterministic."""
+    import importlib
+
+    edit_note_module = importlib.import_module("basic_memory.mcp.tools.edit_note")
+
+    assert (
+        edit_note_module._compose_workspace_project_route(
+            workspace=None,
+            project="docs/setup",
+            project_id=None,
+        )
+        == "docs/setup"
+    )
+    assert (
+        edit_note_module._compose_workspace_project_route(
+            workspace="docs",
+            project="setup",
+            project_id=None,
+        )
+        == "docs/setup"
+    )
+
+
+@pytest.mark.parametrize(
+    ("route_kwargs", "message"),
+    [
+        (
+            {"workspace": " ", "project": "setup", "project_id": None},
+            "workspace must not be empty",
+        ),
+        (
+            {"workspace": "docs/setup", "project": "setup", "project_id": None},
+            "workspace must be a single workspace",
+        ),
+        (
+            {"workspace": "docs", "project": "setup", "project_id": "project-id"},
+            "workspace cannot be combined with project_id",
+        ),
+        (
+            {"workspace": "docs", "project": None, "project_id": None},
+            "workspace requires an explicit project",
+        ),
+        (
+            {"workspace": "docs", "project": "setup/install", "project_id": None},
+            "not both",
+        ),
+    ],
+)
+def test_edit_note_workspace_project_route_helper_rejects_invalid_inputs(
+    route_kwargs,
+    message,
+):
+    """Ambiguous workspace/project argument combinations should fail before routing."""
+    import importlib
+
+    edit_note_module = importlib.import_module("basic_memory.mcp.tools.edit_note")
+
+    with pytest.raises(ValueError, match=message):
+        edit_note_module._compose_workspace_project_route(**route_kwargs)
+
+
@pytest.mark.asyncio
 async def test_edit_note_append_operation(client, test_project):
    """Test appending content to an existing note."""
@@ -827,6 +889,221 @@ async def test_edit_note_workspace_qualified_memory_url_keeps_complete_permalink
    assert f"permalink: {expected_permalink}" in result


+@pytest.mark.asyncio
+async def test_edit_note_workspace_qualified_plain_permalink_requires_explicit_route(
+    monkeypatch,
+    test_project,
+):
+    """Plain workspace-qualified write identifiers should stop before mutating."""
+    import importlib
+    from contextlib import asynccontextmanager
+
+    edit_note_module = importlib.import_module("basic_memory.mcp.tools.edit_note")
+    workspace_slug = "team-acme"
+    qualified_identifier = f"{workspace_slug}/{test_project.name}/team/plain-edit-note"
+    detected_identifiers: list[str] = []
+
+    async def detect_workspace_project(identifier, config, context=None):
+        detected_identifiers.append(identifier)
+        return f"{workspace_slug}/{test_project.name}"
+
+    @asynccontextmanager
+    async def fail_if_called(*args, **kwargs):
+        raise AssertionError("ambiguous plain identifiers should not select a project client")
+        yield
+
+    monkeypatch.setattr(
+        edit_note_module,
+        "_cloud_workspace_discovery_available",
+        lambda config: True,
+    )
+    monkeypatch.setattr(
+        edit_note_module,
+        "detect_project_from_workspace_identifier_prefix",
+        detect_workspace_project,
+        raising=False,
+    )
+    monkeypatch.setattr(edit_note_module, "get_project_client", fail_if_called)
+
+    result = await edit_note(
+        identifier=qualified_identifier,
+        operation="append",
+        content="\nAppended via plain workspace-qualified permalink.",
+        project=None,
+    )
+
+    assert detected_identifiers == [qualified_identifier]
+    assert isinstance(result, str)
+    assert "# Edit Failed - Ambiguous Identifier" in result
+    assert f"`{qualified_identifier}` could refer to a local note path" in result
+    assert f'project="{workspace_slug}/{test_project.name}"' in result
+    assert f"memory://{qualified_identifier}" in result
+
+
+@pytest.mark.asyncio
+async def test_edit_note_workspace_qualified_plain_permalink_json_error(
+    monkeypatch,
+    test_project,
+):
+    """Ambiguous plain write identifiers should stay machine-readable in JSON mode."""
+    import importlib
+
+    edit_note_module = importlib.import_module("basic_memory.mcp.tools.edit_note")
+    workspace_slug = "team-acme"
+    qualified_identifier = f"{workspace_slug}/{test_project.name}/team/plain-edit-note"
+
+    async def detect_workspace_project(identifier, config, context=None):
+        assert identifier == qualified_identifier
+        return f"{workspace_slug}/{test_project.name}"
+
+    monkeypatch.setattr(
+        edit_note_module,
+        "_cloud_workspace_discovery_available",
+        lambda config: True,
+    )
+    monkeypatch.setattr(
+        edit_note_module,
+        "detect_project_from_workspace_identifier_prefix",
+        detect_workspace_project,
+        raising=False,
+    )
+
+    result = await edit_note(
+        identifier=qualified_identifier,
+        operation="append",
+        content="\nAppended via plain workspace-qualified permalink.",
+        output_format="json",
+        project=None,
+    )
+
+    assert isinstance(result, dict)
+    assert result["error"] == "AMBIGUOUS_IDENTIFIER"
+    assert result["project"] == f"{workspace_slug}/{test_project.name}"
+    assert result["fileCreated"] is False
+
+
+@pytest.mark.asyncio
+async def test_edit_note_ambiguous_namespace_identifier_returns_guidance(
+    monkeypatch,
+    test_project,
+):
+    """Namespace-style workspace identifiers should still return ambiguity guidance."""
+    import importlib
+
+    edit_note_module = importlib.import_module("basic_memory.mcp.tools.edit_note")
+    workspace_slug = "team-acme"
+    identifier = f"{workspace_slug}::{test_project.name}/team/plain-edit-note"
+    normalized_identifier = f"{workspace_slug}/{test_project.name}/team/plain-edit-note"
+
+    async def detect_workspace_project(raw_identifier, config, context=None):
+        assert raw_identifier == identifier
+        return f"{workspace_slug}/{test_project.name}"
+
+    monkeypatch.setattr(
+        edit_note_module,
+        "_cloud_workspace_discovery_available",
+        lambda config: True,
+    )
+    monkeypatch.setattr(
+        edit_note_module,
+        "detect_project_from_workspace_identifier_prefix",
+        detect_workspace_project,
+        raising=False,
+    )
+
+    result = await edit_note(
+        identifier=identifier,
+        operation="append",
+        content="\nAppended via namespace-style plain identifier.",
+        project=None,
+    )
+
+    assert isinstance(result, str)
+    assert "# Edit Failed - Ambiguous Identifier" in result
+    assert f"`{identifier}` could refer to a local note path" in result
+    assert f"memory://{normalized_identifier}" in result
+
+
+@pytest.mark.asyncio
+async def test_edit_note_workspace_project_args_compose_explicit_route(monkeypatch):
+    """workspace plus project should route like project='workspace/project'."""
+    from contextlib import asynccontextmanager
+    from types import SimpleNamespace
+
+    import importlib
+
+    edit_note_module = importlib.import_module("basic_memory.mcp.tools.edit_note")
+    captured_routes: list[tuple[str | None, str | None]] = []
+
+    @asynccontextmanager
+    async def fake_get_project_client(project, context=None, project_id=None):
+        captured_routes.append((project, project_id))
+        yield object(), SimpleNamespace(name="setup")
+
+    monkeypatch.setattr(edit_note_module, "get_project_client", fake_get_project_client)
+
+    with pytest.raises(ValueError, match="Invalid operation"):
+        await edit_note(
+            identifier="install",
+            operation="invalid",
+            content="content",
+            workspace="docs",
+            project="setup",
+        )
+
+    assert captured_routes == [("docs/setup", None)]
+
+
+@pytest.mark.asyncio
+async def test_edit_note_three_segment_plain_path_stays_local_without_workspace_discovery(
+    monkeypatch,
+    client,
+    test_project,
+):
+    """Three-segment local paths should stay on the active project without discovery."""
+    import importlib
+
+    edit_note_module = importlib.import_module("basic_memory.mcp.tools.edit_note")
+
+    await write_note(
+        project=test_project.name,
+        title="Local Three Segment",
+        directory="folder/subdir",
+        content="# Local Three Segment\nOriginal content.",
+    )
+
+    async def fail_if_called(*args, **kwargs):
+        raise AssertionError("local three-segment paths should not trigger workspace detection")
+
+    monkeypatch.setattr(
+        edit_note_module,
+        "_cloud_workspace_discovery_available",
+        lambda config: False,
+    )
+    monkeypatch.setattr(
+        edit_note_module,
+        "detect_project_from_workspace_identifier_prefix",
+        fail_if_called,
+    )
+
+    result = await edit_note(
+        identifier="folder/subdir/local-three-segment",
+        operation="append",
+        content="\nAppended locally.",
+        project=None,
+    )
+
+    assert isinstance(result, str)
+    assert "Edited note (append)" in result
+    assert f"project: {test_project.name}" in result
+
+    updated = await read_note(
+        identifier="folder/subdir/local-three-segment",
+        project=test_project.name,
+    )
+    assert "Appended locally." in updated
+
+
@pytest.mark.asyncio
 async def test_edit_note_skips_detection_for_plain_path(client, test_project):
    """edit_note should NOT call detect_project_from_url_prefix for plain path identifiers.
@@ -834,9 +1111,12 @@ async def test_edit_note_skips_detection_for_plain_path(client, test_project):
    A plain path like 'research/note' should not be misrouted to a project
    named 'research' — the 'research' segment is a directory, not a project.
    """
-    with patch(
-        "basic_memory.mcp.tools.edit_note.detect_project_from_memory_url_prefix"
-    ) as mock_detect:
+    with (
+        patch("basic_memory.mcp.tools.edit_note.detect_project_from_memory_url_prefix") as mock_url,
+        patch(
+            "basic_memory.mcp.tools.edit_note.detect_project_from_workspace_identifier_prefix"
+        ) as mock_workspace,
+    ):
        # Use a plain path (no memory:// prefix) — detection should not be called
        await edit_note(
            identifier="test/some-note",
@@ -845,15 +1125,19 @@ async def test_edit_note_skips_detection_for_plain_path(client, test_project):
            project=None,
        )

-        mock_detect.assert_not_called()
+        mock_url.assert_not_called()
+        mock_workspace.assert_not_called()


@pytest.mark.asyncio
 async def test_edit_note_skips_detection_when_project_provided(client, test_project):
    """edit_note should skip URL detection when project is explicitly provided."""
-    with patch(
-        "basic_memory.mcp.tools.edit_note.detect_project_from_memory_url_prefix"
-    ) as mock_detect:
+    with (
+        patch("basic_memory.mcp.tools.edit_note.detect_project_from_memory_url_prefix") as mock_url,
+        patch(
+            "basic_memory.mcp.tools.edit_note.detect_project_from_workspace_identifier_prefix"
+        ) as mock_workspace,
+    ):
        await edit_note(
            identifier=f"memory://{test_project.name}/test/some-note",
            operation="append",
@@ -861,7 +1145,8 @@ async def test_edit_note_skips_detection_when_project_provided(client, test_proj
            project=test_project.name,
        )

-        mock_detect.assert_not_called()
+        mock_url.assert_not_called()
+        mock_workspace.assert_not_called()


@pytest.mark.asyncio
@@ -885,6 +1170,11 @@ async def test_edit_note_skips_detection_when_project_id_provided(

    edit_note_module = importlib.import_module("basic_memory.mcp.tools.edit_note")
    monkeypatch.setattr(edit_note_module, "detect_project_from_memory_url_prefix", fail_if_called)
+    monkeypatch.setattr(
+        edit_note_module,
+        "detect_project_from_workspace_identifier_prefix",
+        fail_if_called,
+    )

    result = await edit_note(
        identifier=f"memory://{test_project.name}/test/project-id-memory-url-edit",
@@ -1,7 +1,9 @@
 """Tests for MCP project management tools."""

+from contextlib import asynccontextmanager
 from unittest.mock import AsyncMock, patch

+import httpx
 import pytest
 from sqlalchemy import select

@@ -136,9 +138,6 @@ async def test_create_and_delete_project_and_name_match_branch(
@pytest.mark.asyncio
 async def test_create_memory_project_resolves_workspace_slug(app, tmp_path_factory):
    """A friendly workspace slug resolves to the tenant id used for cloud routing."""
-    from contextlib import asynccontextmanager
-    import httpx
-
    from basic_memory.mcp.clients import ProjectClient
    from basic_memory.schemas.project_info import ProjectStatusResponse

@@ -207,9 +206,6 @@ async def test_create_memory_project_resolves_workspace_slug(app, tmp_path_facto
@pytest.mark.asyncio
 async def test_create_memory_project_workspace_is_local_noop(app, tmp_path_factory):
    """Local create accepts workspace without requiring cloud workspace discovery."""
-    from contextlib import asynccontextmanager
-    import httpx
-
    from basic_memory.mcp.clients import ProjectClient
    from basic_memory.schemas.project_info import ProjectStatusResponse

@@ -276,9 +272,6 @@ async def test_create_memory_project_workspace_is_local_noop(app, tmp_path_facto
@pytest.mark.asyncio
 async def test_create_memory_project_default_workspace_is_none(app, tmp_path_factory):
    """When workspace is omitted, get_client receives workspace=None (default workspace)."""
-    from contextlib import asynccontextmanager
-    import httpx
-
    from basic_memory.mcp.clients import ProjectClient
    from basic_memory.schemas.project_info import ProjectStatusResponse

@@ -328,6 +321,248 @@ async def test_create_memory_project_default_workspace_is_none(app, tmp_path_fac
    assert captured["workspace"] is None


+@pytest.mark.asyncio
+async def test_create_memory_project_constrained_with_workspace_returns_disabled_message(
+    monkeypatch, tmp_path_factory
+):
+    """A constrained MCP session rejects creation before resolving a workspace selector."""
+    monkeypatch.setenv("BASIC_MEMORY_MCP_PROJECT", "locked-project")
+    project_root = tmp_path_factory.mktemp("constrained-create-project-home")
+
+    with (
+        patch(
+            "basic_memory.mcp.tools.project_management.is_factory_mode",
+            return_value=True,
+        ),
+        patch(
+            "basic_memory.mcp.tools.project_management.resolve_workspace_parameter",
+            new_callable=AsyncMock,
+            side_effect=RuntimeError("bad workspace"),
+        ) as mock_resolve_workspace,
+    ):
+        result = await create_memory_project(
+            project_name="Any Project",
+            project_path=str(project_root),
+            workspace="missing-team",
+        )
+
+    mock_resolve_workspace.assert_not_awaited()
+    assert "Project creation disabled" in result
+    assert "locked-project" in result
+
+
+@pytest.mark.asyncio
+async def test_delete_project_resolves_workspace_slug(app):
+    """A friendly workspace slug resolves to the tenant id used for delete routing."""
+    from basic_memory.mcp.clients import ProjectClient
+    from basic_memory.schemas.project_info import ProjectStatusResponse
+
+    target_project = _make_project(
+        "WS Project",
+        "/ws-project",
+        external_id="project-uuid",
+    )
+    captured: dict[str, str | None] = {}
+
+    @asynccontextmanager
+    async def fake_get_client(*, workspace=None, project_name=None):
+        captured["workspace"] = workspace
+        async with httpx.AsyncClient(base_url="http://testserver") as client:
+            yield client
+
+    fake_status = ProjectStatusResponse(
+        message="Project deleted",
+        status="success",
+        default=False,
+        old_project=target_project,
+    )
+
+    with (
+        patch(
+            "basic_memory.mcp.tools.project_management.get_client",
+            new=fake_get_client,
+        ),
+        patch(
+            "basic_memory.mcp.tools.project_management.is_factory_mode",
+            return_value=True,
+        ),
+        patch(
+            "basic_memory.mcp.tools.project_management.resolve_workspace_parameter",
+            new_callable=AsyncMock,
+            return_value=_make_workspace(
+                "tenant-abc-123",
+                "Team Paul",
+                workspace_type="organization",
+                slug="team-paul",
+            ),
+        ) as mock_resolve_workspace,
+        patch.object(
+            ProjectClient,
+            "list_projects",
+            new_callable=AsyncMock,
+            return_value=_make_list([target_project], default=None),
+        ),
+        patch.object(
+            ProjectClient,
+            "delete_project",
+            new_callable=AsyncMock,
+            return_value=fake_status,
+        ) as mock_delete_project,
+        patch(
+            "basic_memory.mcp.project_context.invalidate_workspace_project_index",
+            new_callable=AsyncMock,
+        ),
+    ):
+        result = await delete_project("WS Project", workspace="team-paul")
+
+    mock_resolve_workspace.assert_awaited_once_with(workspace="team-paul", context=None)
+    assert captured["workspace"] == "tenant-abc-123"
+    mock_delete_project.assert_awaited_once_with("project-uuid")
+    assert result.startswith("✓")
+
+
+@pytest.mark.asyncio
+async def test_delete_project_workspace_is_local_noop(app):
+    """Local delete accepts workspace without requiring cloud workspace discovery."""
+    from basic_memory.mcp.clients import ProjectClient
+    from basic_memory.schemas.project_info import ProjectStatusResponse
+
+    target_project = _make_project(
+        "Local WS Project",
+        "/local-ws-project",
+        external_id="local-project-uuid",
+    )
+    captured: dict[str, str | None] = {}
+
+    @asynccontextmanager
+    async def fake_get_client(*, workspace=None, project_name=None):
+        captured["workspace"] = workspace
+        async with httpx.AsyncClient(base_url="http://testserver") as client:
+            yield client
+
+    fake_status = ProjectStatusResponse(
+        message="Project deleted",
+        status="success",
+        default=False,
+        old_project=target_project,
+    )
+
+    with (
+        patch(
+            "basic_memory.mcp.tools.project_management.get_client",
+            new=fake_get_client,
+        ),
+        patch(
+            "basic_memory.mcp.tools.project_management.is_factory_mode",
+            return_value=False,
+        ),
+        patch(
+            "basic_memory.mcp.tools.project_management.has_cloud_credentials",
+            return_value=False,
+        ),
+        patch(
+            "basic_memory.mcp.tools.project_management.resolve_workspace_parameter",
+            new_callable=AsyncMock,
+        ) as mock_resolve_workspace,
+        patch.object(
+            ProjectClient,
+            "list_projects",
+            new_callable=AsyncMock,
+            return_value=_make_list([target_project], default=None),
+        ),
+        patch.object(
+            ProjectClient,
+            "delete_project",
+            new_callable=AsyncMock,
+            return_value=fake_status,
+        ),
+        patch(
+            "basic_memory.mcp.project_context.invalidate_workspace_project_index",
+            new_callable=AsyncMock,
+        ),
+    ):
+        await delete_project("Local WS Project", workspace="team-paul")
+
+    mock_resolve_workspace.assert_not_awaited()
+    assert captured["workspace"] == "team-paul"
+
+
+@pytest.mark.asyncio
+async def test_delete_project_default_workspace_is_none(app):
+    """When workspace is omitted, delete_project routes through the default workspace."""
+    from basic_memory.mcp.clients import ProjectClient
+    from basic_memory.schemas.project_info import ProjectStatusResponse
+
+    target_project = _make_project(
+        "Default WS Project",
+        "/default-ws-project",
+        external_id="default-project-uuid",
+    )
+    captured: dict[str, str | None] = {"workspace": "sentinel"}
+
+    @asynccontextmanager
+    async def fake_get_client(*, workspace=None, project_name=None):
+        captured["workspace"] = workspace
+        async with httpx.AsyncClient(base_url="http://testserver") as client:
+            yield client
+
+    fake_status = ProjectStatusResponse(
+        message="Project deleted",
+        status="success",
+        default=False,
+        old_project=target_project,
+    )
+
+    with (
+        patch(
+            "basic_memory.mcp.tools.project_management.get_client",
+            new=fake_get_client,
+        ),
+        patch.object(
+            ProjectClient,
+            "list_projects",
+            new_callable=AsyncMock,
+            return_value=_make_list([target_project], default=None),
+        ),
+        patch.object(
+            ProjectClient,
+            "delete_project",
+            new_callable=AsyncMock,
+            return_value=fake_status,
+        ),
+        patch(
+            "basic_memory.mcp.project_context.invalidate_workspace_project_index",
+            new_callable=AsyncMock,
+        ),
+    ):
+        await delete_project("Default WS Project")
+
+    assert captured["workspace"] is None
+
+
+@pytest.mark.asyncio
+async def test_delete_project_constrained_with_workspace_returns_disabled_message(monkeypatch):
+    """A constrained MCP session rejects deletion before resolving a workspace selector."""
+    monkeypatch.setenv("BASIC_MEMORY_MCP_PROJECT", "locked-project")
+
+    with (
+        patch(
+            "basic_memory.mcp.tools.project_management.is_factory_mode",
+            return_value=True,
+        ),
+        patch(
+            "basic_memory.mcp.tools.project_management.resolve_workspace_parameter",
+            new_callable=AsyncMock,
+            side_effect=RuntimeError("bad workspace"),
+        ) as mock_resolve_workspace,
+    ):
+        result = await delete_project("Any Project", workspace="missing-team")
+
+    mock_resolve_workspace.assert_not_awaited()
+    assert "Project deletion disabled" in result
+    assert "locked-project" in result
+
+
 # --- Cloud merge tests ---


@@ -292,7 +292,7 @@ async def test_read_note_skips_url_detection_when_project_id_provided(
    import importlib

    read_note_module = importlib.import_module("basic_memory.mcp.tools.read_note")
-    monkeypatch.setattr(read_note_module, "detect_project_from_memory_url_prefix", fail_if_called)
+    monkeypatch.setattr(read_note_module, "detect_project_from_identifier_prefix", fail_if_called)

    result = await read_note(
        f"memory://{test_project.name}/test/project-id-memory-url-read",
@@ -380,14 +380,14 @@ async def test_team_workspace_write_stores_complete_permalink_when_project_prefi


@pytest.mark.asyncio
-async def test_personal_workspace_write_keeps_project_scoped_permalink(
+async def test_personal_workspace_write_stores_complete_canonical_permalink(
    app,
    test_project,
    entity_repository,
 ):
    from basic_memory.workspace_context import workspace_permalink_context

-    expected_permalink = f"{test_project.name}/personal/personal-workspace-note"
+    expected_permalink = f"personal/{test_project.name}/personal/personal-workspace-note"

    with workspace_permalink_context(workspace_slug="personal", workspace_type="personal"):
        write_result = await write_note(
@@ -404,6 +404,68 @@ async def test_personal_workspace_write_keeps_project_scoped_permalink(
    assert stored.permalink == expected_permalink


+@pytest.mark.asyncio
+async def test_read_note_personal_workspace_keeps_short_project_permalink_working(
+    app,
+    test_project,
+):
+    from basic_memory.workspace_context import workspace_permalink_context
+
+    legacy_permalink = f"{test_project.name}/personal/short-personal-note"
+
+    await write_note(
+        project=test_project.name,
+        title="Short Personal Note",
+        directory="personal",
+        content="Short personal workspace content",
+    )
+
+    with workspace_permalink_context(workspace_slug="personal", workspace_type="personal"):
+        read_result = await read_note(
+            f"memory://{legacy_permalink}",
+            project=test_project.name,
+            output_format="json",
+        )
+
+    assert isinstance(read_result, dict)
+    assert read_result["permalink"] == legacy_permalink
+    assert read_result["content"].strip() == "Short personal workspace content"
+
+
+@pytest.mark.asyncio
+async def test_read_note_workspace_qualified_personal_url_finds_legacy_short_permalink(
+    app,
+    test_project,
+    entity_repository,
+):
+    from basic_memory.workspace_context import workspace_permalink_context
+
+    legacy_permalink = f"{test_project.name}/personal/legacy-personal-note"
+    qualified_permalink = f"personal/{legacy_permalink}"
+
+    await write_note(
+        project=test_project.name,
+        title="Legacy Personal Note",
+        directory="personal",
+        content="Legacy personal workspace content",
+    )
+
+    stored = await entity_repository.get_by_permalink(legacy_permalink)
+    assert stored is not None
+    assert stored.permalink == legacy_permalink
+
+    with workspace_permalink_context(workspace_slug="personal", workspace_type="personal"):
+        read_result = await read_note(
+            f"memory://{qualified_permalink}",
+            project=test_project.name,
+            output_format="json",
+        )
+
+    assert isinstance(read_result, dict)
+    assert read_result["permalink"] == legacy_permalink
+    assert read_result["content"].strip() == "Legacy personal workspace content"
+
+
@pytest.mark.asyncio
 async def test_read_note_workspace_qualified_memory_url_uses_complete_permalink(
    app,
@@ -116,6 +116,71 @@ async def test_schema_validate_json_output(app, test_project, sync_service):
    assert result["results"][0]["passed"] is True


+@pytest.mark.asyncio
+async def test_schema_validate_picoschema_modifier_descriptions(app, test_project, sync_service):
+    """Modifier descriptions should not become literal field names."""
+    project_path = Path(test_project.path)
+
+    _write_schema_file(
+        project_path,
+        "schemas/PicoTest.md",
+        """\
+---
+title: PicoTest
+type: schema
+entity: pico_test
+schema:
+  name: string
+  status(enum, current state): [active, inactive]
+  tags(array, list of tags): string
+settings:
+  validation: warn
+---
+
+# PicoTest
+""",
+    )
+    _write_schema_file(
+        project_path,
+        "pico/PicoTest1.md",
+        """\
+---
+title: PicoTest1
+type: pico_test
+permalink: pico/pico-test-1
+---
+
+# PicoTest1
+
+## Observations
+- [name] PicoTest1
+- [status] active
+- [tags] foo
+- [tags] bar
+""",
+    )
+
+    await sync_service.sync(project_path)
+
+    result = await schema_validate(
+        note_type="pico_test",
+        project=test_project.name,
+        output_format="json",
+    )
+
+    assert isinstance(result, dict)
+    note_result = result["results"][0]
+    field_statuses = {fr["field_name"]: fr["status"] for fr in note_result["field_results"]}
+    assert result["valid_count"] == 1
+    assert note_result["warnings"] == []
+    assert note_result["unmatched_observations"] == {}
+    assert field_statuses == {
+        "name": "present",
+        "status": "present",
+        "tags": "present",
+    }
+
+
@pytest.mark.asyncio
 async def test_schema_validate_by_identifier(app, test_project, sync_service):
    """Validate a specific note by identifier."""
@@ -28,7 +28,10 @@ async def test_search_text(client, test_project):

    # Search for it (use json format to inspect structured results)
    response = await search_notes(
-        project=test_project.name, query="searchable", output_format="json"
+        project=test_project.name,
+        query="searchable",
+        search_type="text",
+        output_format="json",
    )

    # Verify results - handle both success and error cases
@@ -183,7 +186,12 @@ async def test_search_pagination(client, test_project):

    # Search for it (use json format to inspect structured results)
    response = await search_notes(
-        project=test_project.name, query="searchable", page=1, page_size=1, output_format="json"
+        project=test_project.name,
+        query="searchable",
+        search_type="text",
+        page=1,
+        page_size=1,
+        output_format="json",
    )

    # Verify results - handle both success and error cases
@@ -212,7 +220,11 @@ async def test_search_with_type_filter(client, test_project):

    # Search with note type filter (use json format to inspect structured results)
    response = await search_notes(
-        project=test_project.name, query="type", note_types=["note"], output_format="json"
+        project=test_project.name,
+        query="type",
+        search_type="text",
+        note_types=["note"],
+        output_format="json",
    )

    # Verify results - handle both success and error cases
@@ -237,7 +249,11 @@ async def test_search_with_entity_type_filter(client, test_project):

    # Search with entity_types (SearchItemType) filter (use json format)
    response = await search_notes(
-        project=test_project.name, query="type", entity_types=["entity"], output_format="json"
+        project=test_project.name,
+        query="type",
+        search_type="text",
+        entity_types=["entity"],
+        output_format="json",
    )

    # Verify results - handle both success and error cases
@@ -265,6 +281,7 @@ async def test_search_with_date_filter(client, test_project):
    response = await search_notes(
        project=test_project.name,
        query="recent",
+        search_type="text",
        after_date=one_hour_ago.isoformat(),
        output_format="json",
    )
@@ -157,6 +157,7 @@ async def test_search_notes_emits_root_operation_and_project_context(
            "tool_name": "search_notes",
            "requested_project": test_project.name,
            "requested_project_id": None,
+            "search_all_projects": False,
            "search_type": "text",
            "output_format": "json",
            "page": 1,
@@ -13,6 +13,11 @@ from basic_memory.mcp.tools.utils import (
    call_put,
    get_error_message,
 )
+from basic_memory.workspace_context import (
+    WORKSPACE_SLUG_HEADER,
+    WORKSPACE_TYPE_HEADER,
+    workspace_permalink_context,
+)


@pytest.fixture
@@ -170,6 +175,26 @@ async def test_call_get_with_params(mock_response):
    assert kwargs["params"] == params


+@pytest.mark.asyncio
+async def test_call_post_adds_workspace_permalink_headers_at_request_time(mock_response):
+    client = _Client()
+    client.set_response("post", mock_response())
+
+    with workspace_permalink_context("team-paul", "organization"):
+        await call_post(
+            _client(client),
+            "http://test.com",
+            headers={"X-Existing": "value"},
+        )
+
+    assert len(client.calls) == 1
+    _, _args, kwargs = client.calls[0]
+    request_headers = kwargs["headers"]
+    assert request_headers["X-Existing"] == "value"
+    assert request_headers[WORKSPACE_SLUG_HEADER] == "team-paul"
+    assert request_headers[WORKSPACE_TYPE_HEADER] == "organization"
+
+
@pytest.mark.asyncio
 async def test_get_error_message():
    """Test the get_error_message function."""
@@ -7,6 +7,7 @@ import pytest

 from basic_memory import config as config_module
 from basic_memory.mcp.tools import write_note, read_note, delete_note
+from basic_memory.repository.relation_repository import RelationRepository
 from basic_memory.utils import normalize_newlines


@@ -309,7 +310,7 @@ async def test_write_note_with_tag_array_from_bug_report(app, test_project):


@pytest.mark.asyncio
-async def test_write_note_verbose(app, test_project):
+async def test_write_note_verbose(app, test_project, engine_factory):
    """Test creating a new note.

    Should:
@@ -326,7 +327,7 @@ async def test_write_note_verbose(app, test_project):
 # Test\nThis is a test note

 - [note] First observation
- relates to [[Knowledge]]
+- "relates to" [[Knowledge]]

 """,
        tags=["test", "documentation"],
@@ -343,6 +344,11 @@ async def test_write_note_verbose(app, test_project):
    assert "- test, documentation" in result
    assert f"[Session: Using project '{test_project.name}']" in result

+    _, session_maker = engine_factory
+    relation_repository = RelationRepository(session_maker, project_id=test_project.id)
+    relations = await relation_repository.find_by_type("relates to")
+    assert any(relation.to_name == "Knowledge" for relation in relations)
+

@pytest.mark.asyncio
 async def test_write_note_preserves_custom_metadata(app, project_config, test_project):
@@ -0,0 +1,102 @@
+"""Regression tests for workspace-qualified permalink resolution."""
+
+import pytest
+
+from basic_memory.mcp.tools.delete_note import delete_note
+from basic_memory.mcp.tools.edit_note import edit_note
+from basic_memory.mcp.tools.read_note import read_note
+from basic_memory.mcp.tools.write_note import write_note
+from basic_memory.workspace_context import workspace_permalink_context
+
+
+@pytest.mark.asyncio
+async def test_link_resolver_strictly_finds_legacy_project_permalink_from_workspace_url(
+    link_resolver,
+    test_project,
+    entity_service,
+):
+    """Workspace/project IDs should resolve legacy project-prefixed rows centrally."""
+    await write_note(
+        project=test_project.name,
+        title="Resolver Legacy Workspace Note",
+        directory="personal",
+        content="Resolver legacy content",
+    )
+
+    legacy_permalink = f"{test_project.name}/personal/resolver-legacy-workspace-note"
+
+    with workspace_permalink_context(workspace_slug="personal", workspace_type="personal"):
+        resolved = await link_resolver.resolve_link(
+            f"personal/{legacy_permalink}",
+            strict=True,
+        )
+
+    assert resolved is not None
+    assert resolved.permalink == legacy_permalink
+
+
+@pytest.mark.asyncio
+async def test_edit_note_workspace_qualified_url_edits_legacy_project_permalink(
+    app,
+    test_project,
+):
+    """IDs returned from multi-project search should be editable even for legacy rows."""
+    legacy_permalink = f"{test_project.name}/personal/edit-legacy-workspace-note"
+    qualified_permalink = f"personal/{legacy_permalink}"
+
+    await write_note(
+        project=test_project.name,
+        title="Edit Legacy Workspace Note",
+        directory="personal",
+        content="# Edit Legacy Workspace Note\n\nstatus: draft",
+    )
+
+    with workspace_permalink_context(workspace_slug="personal", workspace_type="personal"):
+        edit_result = await edit_note(
+            identifier=f"memory://{qualified_permalink}",
+            project=test_project.name,
+            operation="find_replace",
+            find_text="status: draft",
+            content="status: done",
+            output_format="json",
+        )
+
+    assert isinstance(edit_result, dict)
+    assert edit_result["fileCreated"] is False
+    assert edit_result["permalink"] == legacy_permalink
+
+    read_result = await read_note(
+        legacy_permalink,
+        project=test_project.name,
+        output_format="json",
+    )
+    assert isinstance(read_result, dict)
+    assert "status: done" in read_result["content"]
+
+
+@pytest.mark.asyncio
+async def test_delete_note_workspace_qualified_url_deletes_legacy_project_permalink(
+    app,
+    test_project,
+):
+    """IDs returned from multi-project search should be deletable even for legacy rows."""
+    legacy_permalink = f"{test_project.name}/personal/delete-legacy-workspace-note"
+    qualified_permalink = f"personal/{legacy_permalink}"
+
+    await write_note(
+        project=test_project.name,
+        title="Delete Legacy Workspace Note",
+        directory="personal",
+        content="Delete legacy content",
+    )
+
+    with workspace_permalink_context(workspace_slug="personal", workspace_type="personal"):
+        delete_result = await delete_note(
+            identifier=f"memory://{qualified_permalink}",
+            project=test_project.name,
+            output_format="json",
+        )
+
+    assert isinstance(delete_result, dict)
+    assert delete_result["deleted"] is True
+    assert delete_result["permalink"] == legacy_permalink
@@ -85,6 +85,35 @@ async def test_search_uses_dynamic_default_search_type(monkeypatch, client, test
    assert "search_type" not in captured_kwargs


+@pytest.mark.asyncio
+async def test_search_delegates_to_search_notes_without_project_iteration(
+    monkeypatch, client, test_project
+):
+    """ChatGPT search is only a compatibility wrapper around search_notes."""
+    import basic_memory.mcp.tools.chatgpt_tools as chatgpt_tools
+
+    captured_kwargs: dict = {}
+
+    async def fake_search_notes_fn(*args, **kwargs):
+        captured_kwargs.update(kwargs)
+        return {"results": []}
+
+    monkeypatch.setattr(chatgpt_tools, "search_notes", fake_search_notes_fn)
+
+    result = await chatgpt_tools.search("MCP Test Note")
+
+    content = json.loads(result[0]["text"])
+    assert content["results"] == []
+    assert content["query"] == "MCP Test Note"
+    assert captured_kwargs == {
+        "query": "MCP Test Note",
+        "page": 1,
+        "page_size": 10,
+        "output_format": "json",
+        "context": None,
+    }
+
+
@pytest.mark.asyncio
 async def test_fetch_successful_document(client, test_project):
    """Test fetch with successful document retrieval."""
@@ -127,6 +156,27 @@ async def test_fetch_document_not_found(client, test_project):
    assert content["metadata"]["error"] == "Document not found"


+@pytest.mark.asyncio
+async def test_fetch_routes_path_ids_as_memory_urls(monkeypatch, client, test_project):
+    """Workspace-qualified search ids need memory URL routing during fetch."""
+    import basic_memory.mcp.tools.chatgpt_tools as chatgpt_tools
+
+    captured: dict[str, str] = {}
+
+    async def fake_read_note(*, identifier: str, context=None):
+        captured["identifier"] = identifier
+        return "# MCP Test Note\n\nFetched from the requested workspace."
+
+    monkeypatch.setattr(chatgpt_tools, "read_note", fake_read_note)
+
+    result = await chatgpt_tools.fetch("team-paul/main/tests/mcp-test-note")
+
+    content = json.loads(result[0]["text"])
+    assert captured["identifier"] == "memory://team-paul/main/tests/mcp-test-note"
+    assert content["id"] == "team-paul/main/tests/mcp-test-note"
+    assert content["title"] == "MCP Test Note"
+
+
 def test_format_search_results_for_chatgpt():
    """Test search results formatting."""
    from basic_memory.mcp.tools.chatgpt_tools import _format_search_results_for_chatgpt
@@ -0,0 +1,368 @@
+"""Tests for optional multi-project search_notes behavior."""
+
+from contextlib import asynccontextmanager
+import importlib
+
+import pytest
+
+from basic_memory.schemas.search import SearchItemType, SearchResponse, SearchResult
+
+
+def _stub_routing_mode(monkeypatch, *, cloud: bool) -> None:
+    """Pin the three cloud-route signals search.py reads.
+
+    `_search_all_projects` only forwards project_id (external UUID) when a
+    cloud route is available. The composite mirrors get_project_client:
+    factory mode OR explicit --cloud OR has_cloud_credentials. Tests stub
+    all three so a dev box with OAuth tokens on disk can't bleed into the
+    local-mode case.
+    """
+    search_mod = importlib.import_module("basic_memory.mcp.tools.search")
+    monkeypatch.setattr(search_mod, "is_factory_mode", lambda: False)
+    monkeypatch.setattr(search_mod, "_explicit_routing", lambda: cloud)
+    monkeypatch.setattr(search_mod, "_force_local_mode", lambda: False)
+    monkeypatch.setattr(search_mod, "has_cloud_credentials", lambda config: cloud)
+
+
+@pytest.fixture
+def cloud_routing(monkeypatch):
+    """Force the cloud-routing path for multi-project search tests."""
+    _stub_routing_mode(monkeypatch, cloud=True)
+
+
+@pytest.fixture
+def local_routing(monkeypatch):
+    """Force the local-routing path for multi-project search tests."""
+    _stub_routing_mode(monkeypatch, cloud=False)
+
+
+@pytest.mark.asyncio
+async def test_search_notes_search_all_projects_qualifies_result_permalinks(
+    monkeypatch, cloud_routing
+):
+    """Multi-project search belongs to search_notes and keeps result ids routable."""
+    clients_mod = importlib.import_module("basic_memory.mcp.clients")
+    search_mod = importlib.import_module("basic_memory.mcp.tools.search")
+
+    project_refs = [
+        {
+            "project": "personal/main",
+            "project_id": "11111111-1111-1111-1111-111111111111",
+        },
+        {
+            "project": "team-paul/main",
+            "project_id": "22222222-2222-2222-2222-222222222222",
+        },
+    ]
+    searched_projects: list[tuple[str | None, str | None]] = []
+
+    async def fake_load_search_project_refs(context=None):
+        return project_refs
+
+    class StubProject:
+        def __init__(self, name: str | None, external_id: str | None):
+            self.name = name or "main"
+            self.external_id = external_id or "local-main"
+
+    @asynccontextmanager
+    async def fake_get_project_client(project=None, context=None, project_id=None):
+        searched_projects.append((project, project_id))
+        yield object(), StubProject(project, project_id)
+
+    async def fake_resolve_project_and_path(client, identifier, project=None, context=None):
+        return StubProject(project, None), identifier, False
+
+    class MockSearchClient:
+        def __init__(self, client, project_id):
+            self.project_id = project_id
+
+        async def search(self, payload, page, page_size):
+            if self.project_id == "11111111-1111-1111-1111-111111111111":
+                title = "Personal MCP Test Note"
+                score = 0.5
+            else:
+                title = "Team MCP Test Note"
+                score = 0.9
+            return SearchResponse(
+                results=[
+                    SearchResult(
+                        title=title,
+                        permalink="main/tests/mcp-test-note",
+                        content="MCP content",
+                        type=SearchItemType.ENTITY,
+                        score=score,
+                        file_path="/main/tests/mcp-test-note.md",
+                    )
+                ],
+                current_page=page,
+                page_size=page_size,
+                total=1,
+            )
+
+    monkeypatch.setattr(search_mod, "_load_search_project_refs", fake_load_search_project_refs)
+    monkeypatch.setattr(search_mod, "get_project_client", fake_get_project_client)
+    monkeypatch.setattr(search_mod, "resolve_project_and_path", fake_resolve_project_and_path)
+    monkeypatch.setattr(clients_mod, "SearchClient", MockSearchClient)
+
+    result = await search_mod.search_notes(
+        query="MCP Test Note",
+        search_all_projects=True,
+        output_format="json",
+    )
+
+    assert isinstance(result, dict)
+    assert searched_projects == [
+        ("personal/main", "11111111-1111-1111-1111-111111111111"),
+        ("team-paul/main", "22222222-2222-2222-2222-222222222222"),
+    ]
+    assert [item["permalink"] for item in result["results"]] == [
+        "team-paul/main/tests/mcp-test-note",
+        "personal/main/tests/mcp-test-note",
+    ]
+
+
+@pytest.mark.asyncio
+async def test_search_notes_multi_project_search_is_opt_in(monkeypatch):
+    """Default search_notes calls stay scoped to the resolved project."""
+    clients_mod = importlib.import_module("basic_memory.mcp.clients")
+    search_mod = importlib.import_module("basic_memory.mcp.tools.search")
+
+    searched_projects: list[tuple[str | None, str | None]] = []
+
+    async def fake_load_search_project_refs(context=None):
+        raise AssertionError("project discovery should only run when search_all_projects=True")
+
+    class StubProject:
+        name = "main"
+        external_id = "local-main"
+
+    @asynccontextmanager
+    async def fake_get_project_client(project=None, context=None, project_id=None):
+        searched_projects.append((project, project_id))
+        yield object(), StubProject()
+
+    async def fake_resolve_project_and_path(client, identifier, project=None, context=None):
+        return StubProject(), identifier, False
+
+    class MockSearchClient:
+        def __init__(self, *args, **kwargs):
+            pass
+
+        async def search(self, payload, page, page_size):
+            return SearchResponse(results=[], current_page=page, page_size=page_size)
+
+    monkeypatch.setattr(search_mod, "_load_search_project_refs", fake_load_search_project_refs)
+    monkeypatch.setattr(search_mod, "get_project_client", fake_get_project_client)
+    monkeypatch.setattr(search_mod, "resolve_project_and_path", fake_resolve_project_and_path)
+    monkeypatch.setattr(clients_mod, "SearchClient", MockSearchClient)
+
+    result = await search_mod.search_notes(query="MCP Test Note", output_format="json")
+
+    assert isinstance(result, dict)
+    assert result["results"] == []
+    assert searched_projects == [(None, None)]
+
+
+@pytest.mark.asyncio
+async def test_search_notes_search_all_projects_with_no_refs_returns_empty_all_projects(
+    monkeypatch,
+):
+    """Explicit all-project search must not silently fall back to one project."""
+    search_mod = importlib.import_module("basic_memory.mcp.tools.search")
+
+    async def fake_load_search_project_refs(context=None):
+        return []
+
+    @asynccontextmanager
+    async def fail_get_project_client(*args, **kwargs):
+        raise AssertionError("search_all_projects=True should not fall back to scoped search")
+        yield
+
+    monkeypatch.setattr(search_mod, "_load_search_project_refs", fake_load_search_project_refs)
+    monkeypatch.setattr(search_mod, "get_project_client", fail_get_project_client)
+
+    result = await search_mod.search_notes(
+        query="MCP Test Note",
+        search_all_projects=True,
+        output_format="json",
+    )
+
+    assert isinstance(result, dict)
+    assert result == {
+        "results": [],
+        "current_page": 1,
+        "page_size": 10,
+        "total": 0,
+        "has_more": False,
+    }
+
+
+@pytest.mark.asyncio
+async def test_search_notes_search_all_projects_continues_after_project_failure(
+    monkeypatch, cloud_routing
+):
+    """One failing project should not discard successful all-project search results."""
+    clients_mod = importlib.import_module("basic_memory.mcp.clients")
+    search_mod = importlib.import_module("basic_memory.mcp.tools.search")
+
+    project_refs = [
+        {
+            "project": "personal/main",
+            "project_id": "11111111-1111-1111-1111-111111111111",
+        },
+        {
+            "project": "team-paul/main",
+            "project_id": "22222222-2222-2222-2222-222222222222",
+        },
+    ]
+    warnings: list[str] = []
+
+    async def fake_load_search_project_refs(context=None):
+        return project_refs
+
+    class StubProject:
+        def __init__(self, name: str | None, external_id: str | None):
+            self.name = name or "main"
+            self.external_id = external_id or "local-main"
+
+    @asynccontextmanager
+    async def fake_get_project_client(project=None, context=None, project_id=None):
+        yield object(), StubProject(project, project_id)
+
+    async def fake_resolve_project_and_path(client, identifier, project=None, context=None):
+        return StubProject(project, None), identifier, False
+
+    class FakeLogger:
+        def debug(self, *args, **kwargs):
+            pass
+
+        def error(self, *args, **kwargs):
+            pass
+
+        def warning(self, message, *args, **kwargs):
+            warnings.append(str(message))
+
+    class MockSearchClient:
+        def __init__(self, client, project_id):
+            self.project_id = project_id
+
+        async def search(self, payload, page, page_size):
+            if self.project_id == "22222222-2222-2222-2222-222222222222":
+                raise RuntimeError("team index unavailable")
+            return SearchResponse(
+                results=[
+                    SearchResult(
+                        title="Personal MCP Test Note",
+                        permalink="main/tests/mcp-test-note",
+                        content="MCP content",
+                        type=SearchItemType.ENTITY,
+                        score=0.5,
+                        file_path="/main/tests/mcp-test-note.md",
+                    )
+                ],
+                current_page=page,
+                page_size=page_size,
+                total=1,
+            )
+
+    monkeypatch.setattr(search_mod, "_load_search_project_refs", fake_load_search_project_refs)
+    monkeypatch.setattr(search_mod, "get_project_client", fake_get_project_client)
+    monkeypatch.setattr(search_mod, "resolve_project_and_path", fake_resolve_project_and_path)
+    monkeypatch.setattr(search_mod, "logger", FakeLogger())
+    monkeypatch.setattr(clients_mod, "SearchClient", MockSearchClient)
+
+    result = await search_mod.search_notes(
+        query="MCP Test Note",
+        search_all_projects=True,
+        output_format="json",
+    )
+
+    assert isinstance(result, dict)
+    assert [item["permalink"] for item in result["results"]] == [
+        "personal/main/tests/mcp-test-note",
+    ]
+    assert result["total"] == 1
+    assert any("team-paul/main" in warning for warning in warnings)
+    assert any("team index unavailable" in warning for warning in warnings)
+
+
+@pytest.mark.asyncio
+async def test_search_notes_search_all_projects_local_omits_project_id(
+    monkeypatch, local_routing
+):
+    """Without a cloud route, fan-out must address each project by name only.
+
+    project_id (external UUID) routes through the cloud v2 API path, which
+    returns 401 on local installs because there's no JWT to present. Local
+    fan-out has to fall back to the name-routed path so each per-project
+    search actually returns results instead of silently failing.
+    """
+    clients_mod = importlib.import_module("basic_memory.mcp.clients")
+    search_mod = importlib.import_module("basic_memory.mcp.tools.search")
+
+    project_refs = [
+        {
+            "project": "alpha",
+            "project_id": "11111111-1111-1111-1111-111111111111",
+        },
+        {
+            "project": "beta",
+            "project_id": "22222222-2222-2222-2222-222222222222",
+        },
+    ]
+    searched_projects: list[tuple[str | None, str | None]] = []
+
+    async def fake_load_search_project_refs(context=None):
+        return project_refs
+
+    class StubProject:
+        def __init__(self, name: str | None, external_id: str | None):
+            self.name = name or "main"
+            self.external_id = external_id or "local-main"
+
+    @asynccontextmanager
+    async def fake_get_project_client(project=None, context=None, project_id=None):
+        searched_projects.append((project, project_id))
+        yield object(), StubProject(project, project_id)
+
+    async def fake_resolve_project_and_path(client, identifier, project=None, context=None):
+        return StubProject(project, None), identifier, False
+
+    class MockSearchClient:
+        def __init__(self, client, project_id):
+            self.project_id = project_id
+
+        async def search(self, payload, page, page_size):
+            return SearchResponse(
+                results=[
+                    SearchResult(
+                        title=f"Note in {self.project_id or 'local'}",
+                        permalink="notes/example",
+                        content="",
+                        type=SearchItemType.ENTITY,
+                        score=0.5,
+                        file_path="/notes/example.md",
+                    )
+                ],
+                current_page=page,
+                page_size=page_size,
+                total=1,
+            )
+
+    monkeypatch.setattr(search_mod, "_load_search_project_refs", fake_load_search_project_refs)
+    monkeypatch.setattr(search_mod, "get_project_client", fake_get_project_client)
+    monkeypatch.setattr(search_mod, "resolve_project_and_path", fake_resolve_project_and_path)
+    monkeypatch.setattr(clients_mod, "SearchClient", MockSearchClient)
+
+    result = await search_mod.search_notes(
+        query="anything",
+        search_all_projects=True,
+        output_format="json",
+    )
+
+    assert isinstance(result, dict)
+    assert searched_projects == [("alpha", None), ("beta", None)], (
+        "Local fan-out must omit project_id so the recursive search_notes calls "
+        "take the name-routed path."
+    )
+    assert result["total"] == 2
@@ -1050,6 +1050,25 @@ async def test_get_all_permalinks(entity_repository: EntityRepository, session_m
        assert isinstance(permalink, str)


+@pytest.mark.asyncio
+async def test_find_by_ids_for_hydration_skips_eager_load_options(
+    entity_repository: EntityRepository, sample_entity: Entity, monkeypatch: pytest.MonkeyPatch
+):
+    """Context hydration should bypass relationship loader options."""
+
+    def fail_get_load_options():
+        raise AssertionError("hydration lookup must not eager load entity relationships")
+
+    monkeypatch.setattr(entity_repository, "get_load_options", fail_get_load_options)
+
+    found = await entity_repository.find_by_ids_for_hydration([sample_entity.id])
+
+    assert len(found) == 1
+    assert found[0].id == sample_entity.id
+    assert found[0].title == sample_entity.title
+    assert found[0].external_id == sample_entity.external_id
+
+
@pytest.mark.asyncio
 async def test_get_permalink_to_file_path_map(entity_repository: EntityRepository, session_maker):
    """Test getting permalink -> file_path mapping for bulk operations."""
@@ -1114,3 +1133,150 @@ async def test_get_file_path_to_permalink_map(entity_repository: EntityRepositor
    assert len(mapping) == 2
    assert mapping["test/entity1.md"] == "test/entity1"
    assert mapping["test/entity2.md"] == "test/entity2"
+
+
+@pytest.mark.asyncio
+async def test_find_without_relations_returns_isolated_entities(
+    entity_repository: EntityRepository, session_maker, test_project: Project
+):
+    """Entities with no incoming or outgoing relations are returned as orphans."""
+    async with db.scoped_session(session_maker) as session:
+        orphan = Entity(
+            project_id=test_project.id,
+            title="Orphan",
+            note_type="test",
+            permalink="orphan/orphan",
+            file_path="orphan/orphan.md",
+            content_type="text/markdown",
+            created_at=datetime.now(timezone.utc),
+            updated_at=datetime.now(timezone.utc),
+        )
+        source = Entity(
+            project_id=test_project.id,
+            title="Source",
+            note_type="test",
+            permalink="source/source",
+            file_path="source/source.md",
+            content_type="text/markdown",
+            created_at=datetime.now(timezone.utc),
+            updated_at=datetime.now(timezone.utc),
+        )
+        target = Entity(
+            project_id=test_project.id,
+            title="Target",
+            note_type="test",
+            permalink="target/target",
+            file_path="target/target.md",
+            content_type="text/markdown",
+            created_at=datetime.now(timezone.utc),
+            updated_at=datetime.now(timezone.utc),
+        )
+        session.add_all([orphan, source, target])
+        await session.flush()
+
+        relation = Relation(
+            project_id=test_project.id,
+            from_id=source.id,
+            to_id=target.id,
+            to_name=target.title,
+            relation_type="links_to",
+        )
+        session.add(relation)
+
+    result = await entity_repository.find_without_relations()
+    titles = {entity.title for entity in result}
+
+    assert "Orphan" in titles
+    assert "Source" not in titles
+    assert "Target" not in titles
+
+
+@pytest.mark.asyncio
+async def test_find_without_relations_excludes_unresolved_outgoing_links(
+    entity_repository: EntityRepository, session_maker, test_project: Project
+):
+    """Entities with unresolved outgoing relations are still connected source nodes."""
+    async with db.scoped_session(session_maker) as session:
+        source = Entity(
+            project_id=test_project.id,
+            title="Source",
+            note_type="test",
+            permalink="source/source",
+            file_path="source/source.md",
+            content_type="text/markdown",
+            created_at=datetime.now(timezone.utc),
+            updated_at=datetime.now(timezone.utc),
+        )
+        orphan = Entity(
+            project_id=test_project.id,
+            title="Orphan",
+            note_type="test",
+            permalink="orphan/orphan",
+            file_path="orphan/orphan.md",
+            content_type="text/markdown",
+            created_at=datetime.now(timezone.utc),
+            updated_at=datetime.now(timezone.utc),
+        )
+        session.add_all([source, orphan])
+        await session.flush()
+
+        unresolved_relation = Relation(
+            project_id=test_project.id,
+            from_id=source.id,
+            to_id=None,
+            to_name="Missing Target",
+            relation_type="links_to",
+        )
+        session.add(unresolved_relation)
+
+    result = await entity_repository.find_without_relations()
+    titles = {entity.title for entity in result}
+
+    assert "Orphan" in titles
+    assert "Source" not in titles
+
+
+@pytest.mark.asyncio
+async def test_find_without_relations_respects_project_scope(
+    entity_repository: EntityRepository, session_maker, test_project: Project
+):
+    """Orphan detection only returns isolated entities for the active project."""
+    async with db.scoped_session(session_maker) as session:
+        active_orphan = Entity(
+            project_id=test_project.id,
+            title="Active Project Orphan",
+            note_type="test",
+            permalink="active/orphan",
+            file_path="active/orphan.md",
+            content_type="text/markdown",
+            created_at=datetime.now(timezone.utc),
+            updated_at=datetime.now(timezone.utc),
+        )
+        other_project = Project(name="other-project", path="/tmp/other")
+        session.add_all([active_orphan, other_project])
+        await session.flush()
+
+        other_orphan = Entity(
+            project_id=other_project.id,
+            title="Other Project Orphan",
+            note_type="test",
+            permalink="other/orphan",
+            file_path="other/orphan.md",
+            content_type="text/markdown",
+            created_at=datetime.now(timezone.utc),
+            updated_at=datetime.now(timezone.utc),
+        )
+        session.add(other_orphan)
+
+    result = await entity_repository.find_without_relations()
+    titles = {entity.title for entity in result}
+
+    assert "Active Project Orphan" in titles
+    assert "Other Project Orphan" not in titles
+
+
+@pytest.mark.asyncio
+async def test_find_without_relations_empty_project(entity_repository: EntityRepository):
+    """An empty project returns no orphans."""
+    result = await entity_repository.find_without_relations()
+    assert result == []
@@ -235,6 +235,7 @@ async def test_postgres_search_repository_tsquery_syntax_error_returns_empty(
    # Trailing boolean operator creates an invalid tsquery; repository should return []
    results = await repo.search(search_text="coffee AND")
    assert results == []
+    assert await repo.count(search_text="coffee AND") == 0


@pytest.mark.asyncio
@@ -318,6 +318,25 @@ async def test_sqlite_hybrid_search_raises_disabled_error(search_repository):
        )


+@pytest.mark.asyncio
+@pytest.mark.parametrize("retrieval_mode", [SearchRetrievalMode.VECTOR, SearchRetrievalMode.HYBRID])
+async def test_count_rejects_semantic_modes_without_running_search(monkeypatch, retrieval_mode):
+    """Semantic counts must not materialize vector or hybrid retrieval."""
+    repo = _ConcreteRepo()
+    search_calls = []
+
+    async def fail_if_search_runs(**kwargs):
+        search_calls.append(kwargs)
+        return []
+
+    monkeypatch.setattr(repo, "search", fail_if_search_runs)
+
+    with pytest.raises(ValueError, match="Exact counts are only supported for full-text search"):
+        await repo.count(search_text="semantic query", retrieval_mode=retrieval_mode)
+
+    assert search_calls == []
+
+
@pytest.mark.asyncio
 async def test_sync_entity_vectors_batch_flushes_at_configured_threshold(monkeypatch):
    """Batch sync should flush queued jobs at semantic_embedding_sync_batch_size boundaries."""
@@ -7,6 +7,7 @@ from basic_memory.schema.parser import (
    parse_picoschema,
    parse_schema_note,
    _parse_field_key,
+    _parse_field_key_parts,
    _parse_type_and_description,
    _parse_enum_string,
    _is_entity_ref_type,
@@ -43,18 +44,50 @@ class TestParseFieldKey:
        assert required is False
        assert is_array is True

+    def test_array_with_description_in_modifier(self):
+        name, required, is_array, is_enum, is_object = _parse_field_key("tags(array, list of tags)")
+        assert name == "tags"
+        assert required is True
+        assert is_array is True
+        assert is_enum is False
+        assert is_object is False
+
+    def test_optional_array_with_description_in_modifier(self):
+        name, required, is_array, is_enum, is_object = _parse_field_key(
+            "tags?(array, list of tags)"
+        )
+        assert name == "tags"
+        assert required is False
+        assert is_array is True
+
    def test_enum(self):
        name, required, is_array, is_enum, is_object = _parse_field_key("status?(enum)")
        assert name == "status"
        assert required is False
        assert is_enum is True

+    def test_enum_with_description_in_modifier(self):
+        name, required, is_array, is_enum, is_object = _parse_field_key(
+            "status(enum, current state)"
+        )
+        assert name == "status"
+        assert required is True
+        assert is_enum is True
+
    def test_object(self):
        name, required, is_array, is_enum, is_object = _parse_field_key("metadata?(object)")
        assert name == "metadata"
        assert required is False
        assert is_object is True

+    def test_object_with_description_in_modifier(self):
+        name, required, is_array, is_enum, is_object = _parse_field_key(
+            "metadata?(object, nested metadata)"
+        )
+        assert name == "metadata"
+        assert required is False
+        assert is_object is True
+
    def test_required_enum(self):
        name, required, is_array, is_enum, is_object = _parse_field_key("status(enum)")
        assert name == "status"
@@ -62,6 +95,68 @@ class TestParseFieldKey:
        assert is_enum is True


+class TestParseFieldKeyParts:
+    def test_modifier_description_returned(self):
+        assert _parse_field_key_parts("tags(array, list of tags)") == (
+            "tags",
+            True,
+            True,
+            False,
+            False,
+            "list of tags",
+        )
+
+    def test_optional_enum_description_returned(self):
+        assert _parse_field_key_parts("status?(enum, current state)") == (
+            "status",
+            False,
+            False,
+            True,
+            False,
+            "current state",
+        )
+
+    def test_no_modifier_description_is_none(self):
+        assert _parse_field_key_parts("name") == (
+            "name",
+            True,
+            False,
+            False,
+            False,
+            None,
+        )
+
+    def test_description_can_contain_parentheses(self):
+        assert _parse_field_key_parts("tags(array, labels (freeform))") == (
+            "tags",
+            True,
+            True,
+            False,
+            False,
+            "labels (freeform)",
+        )
+
+    def test_field_name_can_contain_parentheses_before_modifier(self):
+        assert _parse_field_key_parts("risk(score)(array)") == (
+            "risk(score)",
+            True,
+            True,
+            False,
+            False,
+            None,
+        )
+
+    def test_optional_field_name_can_contain_parentheses_before_modifier(self):
+        assert _parse_field_key_parts("risk(score)?(array, score buckets)") == (
+            "risk(score)",
+            False,
+            True,
+            False,
+            False,
+            "score buckets",
+        )
+
+
 # --- _parse_type_and_description ---


@@ -152,6 +247,19 @@ class TestParsePicoschema:
        assert fields[0].is_array is True
        assert fields[0].required is False

+    def test_array_field_with_description_in_modifier(self):
+        fields = parse_picoschema({"tags(array, list of tags)": "string"})
+        assert fields[0].name == "tags"
+        assert fields[0].type == "string"
+        assert fields[0].is_array is True
+        assert fields[0].description == "list of tags"
+
+    def test_parenthesized_field_name_with_array_modifier(self):
+        fields = parse_picoschema({"risk(score)(array)": "string"})
+        assert fields[0].name == "risk(score)"
+        assert fields[0].type == "string"
+        assert fields[0].is_array is True
+
    def test_entity_ref_field(self):
        fields = parse_picoschema({"works_at?": "Organization, employer"})
        assert fields[0].name == "works_at"
@@ -165,6 +273,15 @@ class TestParsePicoschema:
        assert fields[0].is_enum is True
        assert fields[0].enum_values == ["active", "inactive"]

+    def test_enum_field_with_description_in_modifier(self):
+        fields = parse_picoschema({"status(enum, current state)": ["active", "inactive"]})
+        assert fields[0].name == "status"
+        assert fields[0].type == "enum"
+        assert fields[0].required is True
+        assert fields[0].is_enum is True
+        assert fields[0].enum_values == ["active", "inactive"]
+        assert fields[0].description == "current state"
+
    def test_enum_field_with_string(self):
        fields = parse_picoschema({"status?(enum)": "active"})
        assert fields[0].is_enum is True
@@ -204,6 +321,20 @@ class TestParsePicoschema:
        assert fields[0].children[0].name == "street"
        assert fields[0].children[1].name == "city"

+    def test_object_field_with_description_in_modifier(self):
+        fields = parse_picoschema(
+            {
+                "address?(object, mailing address)": {
+                    "street": "string",
+                }
+            }
+        )
+        assert fields[0].name == "address"
+        assert fields[0].type == "object"
+        assert fields[0].required is False
+        assert fields[0].description == "mailing address"
+        assert fields[0].children[0].name == "street"
+
    def test_dict_value_treated_as_object(self):
        """A dict value without explicit (object) is still treated as an object."""
        fields = parse_picoschema(
@@ -315,6 +446,31 @@ class TestParseSchemaNote:
        assert status_field.is_enum is True
        assert status_field.enum_values == ["draft", "published"]

+    def test_settings_frontmatter_parses_modifier_descriptions(self):
+        frontmatter = {
+            "entity": "Person",
+            "schema": {"name": "string"},
+            "settings": {
+                "validation": "warn",
+                "frontmatter": {
+                    "tags?(array, note tags)": "string",
+                    "status?(enum, publication state)": ["draft", "published"],
+                },
+            },
+        }
+        result = parse_schema_note(frontmatter)
+
+        tags_field = next(f for f in result.frontmatter_fields if f.name == "tags")
+        assert tags_field.required is False
+        assert tags_field.is_array is True
+        assert tags_field.description == "note tags"
+
+        status_field = next(f for f in result.frontmatter_fields if f.name == "status")
+        assert status_field.required is False
+        assert status_field.is_enum is True
+        assert status_field.enum_values == ["draft", "published"]
+        assert status_field.description == "publication state"
+
    def test_no_settings_frontmatter_defaults_to_empty(self):
        frontmatter = {
            "entity": "Person",
@@ -127,6 +127,7 @@ def test_search_response():
            metadata={},
        ),
    ]
-    response = SearchResponse(results=results, current_page=1, page_size=1)
+    response = SearchResponse(results=results, current_page=1, page_size=1, total=2)
    assert len(response.results) == 2
    assert response.results[0].score > response.results[1].score
+    assert response.total == 2
--- a/Show More
+++ b/Show More
Author	SHA1	Message	Date
phernandez	214a54d740	chore: update version to 0.21.0 for v0.21.0 release	2026-05-16 17:15:53 -05:00
phernandez	5a90c7cedf	docs: add v0.21.0 changelog entry Promotes the Unreleased breaking-change note and adds the full v0.21.0 section covering ~80 commits since v0.20.3: workspace-routing fixes across MCP/CLI/API, recent_activity ordering and search opt-in changes, sync hardening, sqlite-vec graceful degrade, perf wins on CLI startup and sync, and the project-delete cleanup landed in #832. Signed-off-by: phernandez <paul@basicmachines.co>	2026-05-16 17:15:43 -05:00
Paul Hernandez	9e3fe26a83	fix(core): purge SQLite search_index on project delete (#832 ) Signed-off-by: phernandez <paul@basicmachines.co>	2026-05-16 16:47:24 -05:00
Paul Hernandez	47ee982041	perf(cli): defer local ASGI app import (#828 ) Signed-off-by: phernandez <paul@basicmachines.co>	2026-05-15 17:59:58 -05:00
Paul Hernandez	4d22c398c6	fix(sync): preserve bmignore rclone filters (#827 ) Signed-off-by: phernandez <paul@basicmachines.co>	2026-05-15 17:48:49 -05:00
phernandez	8ac2d975f9	update README.md Signed-off-by: phernandez <paul@basicmachines.co>	2026-05-15 17:13:34 -05:00
Paul Hernandez	34830bfad7	Update README.md update agent matrix Signed-off-by: Paul Hernandez <60959+phernandez@users.noreply.github.com>	2026-05-15 14:55:00 -05:00
Paul Hernandez	f5e0c42047	Update README.md remove sync commands from cli examples Signed-off-by: Paul Hernandez <60959+phernandez@users.noreply.github.com>	2026-05-15 14:52:27 -05:00
phernandez	3f98da8c67	update README.md Signed-off-by: phernandez <paul@basicmachines.co>	2026-05-15 14:50:35 -05:00
phernandez	14ff77d1c2	update to fastmcp 3.3.1 Signed-off-by: phernandez <paul@basicmachines.co>	2026-05-15 12:28:03 -05:00
phernandez	4e4da6128d	ci: run github actions on node 24 Signed-off-by: phernandez <paul@basicmachines.co>	2026-05-15 12:14:06 -05:00
Paul Hernandez	3bed6d8890	chore(deps): update deps and harden security (#825 ) Signed-off-by: phernandez <paul@basicmachines.co>	2026-05-15 10:45:14 -05:00
Paul Hernandez	4cba7ba01c	fix(core): parse prose wikilinks as inline links (#824 ) Signed-off-by: phernandez <paul@basicmachines.co>	2026-05-14 11:43:11 -05:00
Drew Cain	8eeec64e28	fix: `basic-memory project list` does not list projects from all workspaces (#822 ) Signed-off-by: Drew Cain <groksrc@gmail.com>	2026-05-14 09:46:02 -05:00
Paul Hernandez	c6fa185bf3	fix(mcp): route edit_note workspace-qualified permalinks (#813 ) Signed-off-by: phernandez <paul@basicmachines.co>	2026-05-11 12:56:26 -05:00
Paul Hernandez	415c2b3d6e	feat(cli): add orphan entity command (#816 ) Signed-off-by: phernandez <paul@basicmachines.co>	2026-05-11 12:13:14 -05:00
Paul Hernandez	4aa0cbdd62	fix(sync): ignore hidden paths relative to watched project (#815 ) Signed-off-by: phernandez <paul@basicmachines.co>	2026-05-11 11:14:03 -05:00
Paul Hernandez	55f314237d	fix(sync): avoid shell for scan subprocesses (#814 ) Signed-off-by: phernandez <paul@basicmachines.co>	2026-05-11 09:20:11 -05:00
Drew Cain	9862ef5411	fix(core): use updated_at for recent_activity filter and ordering (#812 ) Signed-off-by: claude[bot] <41898282+claude[bot]@users.noreply.github.com> Signed-off-by: Drew Cain <groksrc@gmail.com> Signed-off-by: phernandez <paul@basicmachines.co> Co-authored-by: claude[bot] <41898282+claude[bot]@users.noreply.github.com> Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com> Co-authored-by: phernandez <paul@basicmachines.co>	2026-05-11 09:14:06 -05:00
Paul Hernandez	df5e8d805f	fix(mcp): centralize workspace permalink routing (#808 ) Signed-off-by: phernandez <paul@basicmachines.co>	2026-05-08 16:44:57 -05:00
Paul Hernandez	831dc1ecdc	fix(mcp): make multi-project search opt-in (#807 ) Signed-off-by: phernandez <paul@basicmachines.co>	2026-05-08 12:54:20 -05:00
Paul Hernandez	26381aeed1	fix(mcp): use lightweight graph hydration lookup (#806 ) Signed-off-by: phernandez <paul@basicmachines.co>	2026-05-08 10:07:29 -05:00
Paul Hernandez	7918e5c6bf	fix(mcp): preserve workspace paths in build_context (#801 ) Signed-off-by: phernandez <paul@basicmachines.co>	2026-05-08 09:53:54 -05:00
Paul Hernandez	f312341020	fix(mcp): add workspace routing to delete_project (#803 ) Signed-off-by: phernandez <paul@basicmachines.co>	2026-05-08 09:48:51 -05:00
phernandez	e871298e95	Merge branch 'main' of github.com:basicmachines-co/basic-memory	2026-05-07 18:50:10 -05:00
phernandez	177ae21ba7	pass context to recent_activity Signed-off-by: phernandez <paul@basicmachines.co>	2026-05-07 18:50:02 -05:00
Drew Cain	3415fd1014	fix(core): parse picoschema modifier descriptions (#796 ) Signed-off-by: Drew Cain <groksrc@gmail.com> Signed-off-by: phernandez <paul@basicmachines.co> Co-authored-by: phernandez <paul@basicmachines.co>	2026-05-06 12:21:35 -05:00
Paul Hernandez	b08659e228	fix(api): accept qualified project resolver hints (#795 ) Signed-off-by: phernandez <paul@basicmachines.co>	2026-05-06 10:33:11 -05:00
Paul Hernandez	09a4b09436	feat(api): include search result totals (#791 ) Signed-off-by: phernandez <paul@basicmachines.co>	2026-05-04 14:57:04 -05:00