fix(core): preserve sqlite rollback semantics on windows

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

.claude-plugin/marketplace.json

@@ -6,14 +6,14 @@
   },
   "metadata": {
     "description": "Official Basic Memory plugins from the canonical basic-memory repository",
-    "version": "0.22.0"
+    "version": "0.22.1"
   },
   "plugins": [
     {
       "name": "basic-memory",
       "source": "./plugins/claude-code",
       "description": "The bridge between Claude's working memory and Basic Memory's durable knowledge graph \u2014 session briefings, pre-compaction checkpoints, and capture reflexes",
-      "version": "0.22.0",
+      "version": "0.22.1",
       "author": {
         "name": "Basic Machines"
       },

.claude/commands/release/release.md

@@ -28,7 +28,10 @@ You are an expert release manager for the Basic Memory project. When the user ru
 
 #### Documentation Validation
 1. **Changelog Check**
-   - CHANGELOG.md contains entry for target version
+   - CHANGELOG.md contains entry for target version **already landed on `main`**
+     (main only accepts changes via PR, so the changelog entry must go through
+     its own PR before running the release; the recipe pre-flight-checks for a
+     `## vX.Y.Z` heading)
    - Entry includes all major features and fixes
    - Breaking changes are documented
 
@@ -41,11 +44,15 @@ just release <version>
 The justfile target handles:
 - ✅ Version format validation
 - ✅ Git status and branch checks
-- ✅ Quality checks (`just check` - lint, format, type-check, tests)
+- ✅ Changelog entry check (must already be on `main`)
+- ✅ Quality checks (`just lint` + `just typecheck`)
 - ✅ Version update across all consolidated manifests via `just set-version` (Python
   package + Claude Code plugin/marketplaces + Codex plugin + Hermes + OpenClaw)
-- ✅ Automatic commit with proper message
-- ✅ Tag creation and pushing to GitHub
+- ✅ Release PR: commits the bump on a `release/vX.Y.Z` branch, opens a PR
+  (`chore(core): release vX.Y.Z`), and rebase-merges it — the `main` ruleset
+  rejects direct pushes and the repo disallows merge commits
+- ✅ Tags the rebased bump commit on `main` (found by commit subject, since
+  the rebase rewrites the SHA) and pushes the tag
 - ✅ Release workflow trigger (automatic on tag push)
 
 The GitHub Actions workflow (`.github/workflows/release.yml`) then:
@@ -89,7 +96,7 @@ After PyPI release is published, update the MCP registry:
 
 2. **Publish to MCP Registry**
    ```bash
-   cd /Users/drew/code/basic-memory
+   # from the basic-memory repo root
    mcp-publisher publish
    ```
 
@@ -109,43 +116,50 @@ After PyPI release is published, update the MCP registry:
 
 #### Website Updates
 
-**1. basicmachines.co** (`/Users/drew/code/basicmachines.co`)
-   - **Goal**: Update version number displayed on the homepage
-   - **Location**: Search for "Basic Memory v0." in the codebase to find version displays
-   - **What to update**:
-     - Hero section heading that shows "Basic Memory v{VERSION}"
-     - "What's New in v{VERSION}" section heading
-     - Feature highlights array (look for array of features with title/description)
-   - **Process**:
+**1. basicmemory.com** (sibling `basicmemory.com` repo —
+`basicmachines-co/basicmemory.com`, formerly `basicmachines.co`)
+   - **No version bump needed.** The marketing site is an Astro + React app and
+     carries **no hardcoded Basic Memory version number** anywhere in its UI
+     (`hero.tsx` and the rest of the site have no version string). The old
+     instruction to bump `src/components/sections/hero.tsx` is obsolete — that
+     file no longer holds a version. Release announcements are dated blog posts,
+     not an in-place edit.
+   - **Skip entirely for patch releases.**
+   - **Significant releases only — optional announcement post**:
      1. Pull latest from GitHub: `git pull origin main`
      2. Create release branch: `git checkout -b release/v{VERSION}`
-     3. Search codebase for current version number (e.g., "v0.16.1")
-     4. Update version numbers to new release version
-     5. Update feature highlights with 3-5 key features from this release (extract from CHANGELOG.md)
-     6. Commit changes: `git commit -m "chore: update to v{VERSION}"`
-     7. Push branch: `git push origin release/v{VERSION}`
-   - **Deploy**: Follow deployment process for basicmachines.co
+     3. Add a dated post under `src/content/blog/` modeled on an existing
+        release post (e.g. `basic-memory-v0-19-0-release.md`), summarizing 3–5
+        headline features from `CHANGELOG.md`
+     4. Commit (`git commit -s -m "..."`), push, and open a PR against
+        `basicmachines-co/basicmemory.com`
+   - **Deploy**: follow that repo's deployment process.
 
-**2. docs.basicmemory.com** (`/Users/drew/code/docs.basicmemory.com`)
-   - **Goal**: Add new release notes section to the latest-releases page
-   - **File**: `src/pages/latest-releases.mdx`
+**2. docs.basicmemory.com** (sibling `docs.basicmemory.com` repo)
+   - **Goal**: Add a What's New page for the release and bump the homepage badge
+   - **Site shape**: Nuxt/Docus content site. The changelog page
+     (`content/2.whats-new/*.changelog.md`) auto-fetches GitHub releases — no
+     manual changelog update needed. See that repo's CLAUDE.md "Version Bump
+     Checklist".
    - **What to do**:
      1. Pull latest from GitHub: `git pull origin main`
      2. Create release branch: `git checkout -b release/v{VERSION}`
-     3. Read the existing file to understand the format and structure
-     4. Read `/Users/drew/code/basic-memory/CHANGELOG.md` to get release content
-     5. Add new release section **at the top** (after MDX imports, before other releases)
-     6. Follow the existing pattern:
-        - Heading: `## [v{VERSION}](github-link) — YYYY-MM-DD`
-        - Focus statement if applicable
-        - `<Info>` block with highlights (3-5 key items)
-        - Sections for Features, Bug Fixes, Breaking Changes, etc.
-        - Link to full changelog at the end
-        - Separator `---` between releases
-     7. Commit changes: `git commit -m "docs: add v{VERSION} release notes"`
-     8. Push branch: `git push origin release/v{VERSION}`
-   - **Source content**: Extract and format sections from CHANGELOG.md for this version
-   - **Deploy**: Follow deployment process for docs.basicmemory.com
+     3. Read `CHANGELOG.md` in the `basic-memory` repo to get release content
+     4. **New minor/major release**: add `content/2.whats-new/1.v{VERSION}.md`
+        modeled on the previous version page (frontmatter title/description,
+        headline feature first, then sections, then an Upgrading note) and
+        renumber the existing what's-new pages down one slot (URLs don't
+        change — Nuxt strips the numeric prefixes)
+     5. **Patch release**: append a short note to the current version's page
+        instead of creating a new one
+     6. Update the homepage version badge in `content/index.md` (the
+        `v0.XX →` button text and its `to: /whats-new/v{VERSION}` link)
+     7. If the release adds user-facing features, update the relevant guide
+        and reference pages (`content/3.cloud/`, `content/9.reference/`)
+     8. Commit: `git commit -s -m "docs: add v{VERSION} release notes"`
+     9. Push branch and open a PR; merge after the release is tagged
+   - **Deploy**: push to main auto-deploys to development; production requires
+     manual workflow dispatch via GitHub Actions
 
 **4. Announce Release**
    - Post to Discord community if significant changes

AGENTS.md

@@ -300,7 +300,9 @@ See SPEC-16 for full context manager refactor details.
 
 ### Release Process
 
-Releases are driven by `just release` / `just beta` — never by a bare `git tag`. The recipes bump version metadata, run pre-flight checks, commit, tag, and push. GitHub Actions then publishes to PyPI and updates the Homebrew formula.
+Releases are driven by `just release` / `just beta` — never by a bare `git tag`. The recipes bump version metadata, run pre-flight checks, land the bump on `main` through a release PR, tag, and push the tag. GitHub Actions then publishes to PyPI and updates the Homebrew formula.
+
+**Main requires PRs.** The `main` ruleset rejects direct pushes ("Changes must be made through a pull request") and the repo disallows merge commits, so the recipes push a `release/vX.Y.Z` branch, open a PR titled `chore(core): release vX.Y.Z`, rebase-merge it with `gh pr merge --rebase`, then tag the rebased bump commit on `main` (located by its commit subject, since rebasing rewrites the SHA) and push the tag. The CHANGELOG entry for the version must already be on `main` — land it via a normal PR before running the recipe (it pre-flight-checks for a `## vX.Y.Z` heading).
 
 **Stable release:**
 
@@ -308,7 +310,7 @@ Releases are driven by `just release` / `just beta` — never by a bare `git tag
 just release v0.21.3
 ```
 
-The recipe runs `just lint` + `just typecheck`, then updates every release manifest through `scripts/update_versions.py`: `src/basic_memory/__init__.py`, `server.json`, the root Claude marketplace, the Claude Code plugin manifest and local marketplace, the Hermes `plugin.yaml`, and the OpenClaw `package.json`. It commits as `chore: update version to X.Y.Z for vX.Y.Z release`, creates the `vX.Y.Z` tag, and pushes both the commit and the tag to `origin/main`. After the tag lands, the `Release` workflow builds the Python package, publishes to PyPI, creates the GitHub release with auto-generated notes, publishes the OpenClaw npm package, and updates the Homebrew formula. The recipe finishes by printing the post-release tasks the workflow doesn't cover.
+The recipe runs `just lint` + `just typecheck`, then updates every release manifest through `scripts/update_versions.py`: `src/basic_memory/__init__.py`, `server.json`, the root Claude marketplace, the Claude Code plugin manifest and local marketplace, the Hermes `plugin.yaml`, and the OpenClaw `package.json`. It commits as `chore: update version to X.Y.Z for vX.Y.Z release` on a `release/vX.Y.Z` branch, lands it on `main` via a rebase-merged PR, then tags the rebased commit and pushes the tag. After the tag lands, the `Release` workflow builds the Python package, publishes to PyPI, creates the GitHub release with auto-generated notes, publishes the OpenClaw npm package, and updates the Homebrew formula. The recipe finishes by printing the post-release tasks the workflow doesn't cover.
 
 **Beta release:** `just beta v0.21.3b1` — same flow with a beta-suffixed tag. PyPI consumers install with `pip install basic-memory --pre`.
 
@@ -319,8 +321,13 @@ The recipe runs `just lint` + `just typecheck`, then updates every release manif
 **Do not tag releases by hand.** A bare `git tag vX.Y.Z` skips the in-code version bump. Package metadata is still correct (uv-dynamic-versioning derives it from the git tag) but `basic-memory --version` reports the previous release, which is what happened with v0.21.2 → v0.21.3.
 
 **Post-release tasks** the recipe surfaces but doesn't run:
-- `docs.basicmemory.com` — add notes to `src/pages/latest-releases.mdx`
-- `basicmachines.co` — bump version in `src/components/sections/hero.tsx`
+- `docs.basicmemory.com` — add a What's New page under `content/2.whats-new/` and bump the version badge in `content/index.md` (the changelog page auto-fetches GitHub releases; see that repo's CLAUDE.md version-bump checklist)
+- `basicmemory.com` — the marketing site (Astro + React, repo
+  `basicmachines-co/basicmemory.com`, formerly `basicmachines.co`) carries **no
+  hardcoded version number** in its UI, so there is nothing to bump. For a
+  significant release, optionally add a dated announcement post under
+  `src/content/blog/` (model it on an existing `basic-memory-vX-Y-Z-release.md`).
+  Skip entirely for routine patch releases.
 - MCP Registry — `mcp-publisher publish` from the repo root
 
 See `.claude/commands/release/release.md` (and `beta.md`, `release-check.md`, `changelog.md` alongside it) for the full release + post-release runbook, including the slash commands.

CHANGELOG.md

@@ -1,5 +1,49 @@
 # CHANGELOG
 
+## v0.22.1 (2026-06-12)
+
+Follow-up patch to v0.22.0. Fixes project and default-project resolution on
+fresh installs, MCP workspace routing, sync project selection, and CLI startup
+latency, plus a few MCP parity additions.
+
+### Features
+
+- Added a `workspace` parameter to `write_note` for parity with `edit_note`.
+- **#826**: Added `title` and `tags` annotations to all MCP tool decorators
+  (phase 1).
+- **#930**: `search_notes` now comma-splits `note_types`, `entity_types`, and
+  `categories`.
+- **#971**: Added the manual-pages flow — manpage seed schema, flow docs, and
+  verification fixes.
+
+### Bug Fixes
+
+- Fresh installs no longer fail when the projects table is empty: resolve now
+  points them at project setup, the first project is promoted to default when
+  the config default is missing from the database, the promoted default state
+  is returned from the project-create API, and a default can be set when none
+  is currently set. An existing database default is preserved when repairing a
+  missing config default.
+- **#949**: Sync skips projects without an absolute local path and excludes
+  orphan DB projects that are absent from config.
+- **#952 / #981**: Resolved workspace display names and tenant ids in qualified
+  project routes, closing out the manual verification findings.
+- `note_types`/`entity_types`/`categories` are normalized on the direct-call
+  path, with non-string list elements rejected.
+- Vector-search hydration keys on `(type, id)` to prevent id collisions.
+- `file_utils` requires line-anchored frontmatter fences.
+- CLI startup is faster: FastAPI and app imports are deferred out of CLI
+  startup, and rich/typer modules are preloaded before an in-place upgrade.
+- `config.json` is written atomically.
+- In-memory SQLite sessions are serialized so concurrent rollbacks cannot
+  destroy writes.
+
+### Maintenance
+
+- Release recipes route through PRs and wait for the release PR merge to land
+  before tagging; the release runbook is refreshed and stripped of
+  user-specific absolute paths.
+
 ## v0.22.0 (2026-06-11)
 
 Team-safe cloud sync. New additive `bm cloud push` and `bm cloud pull`

README.md

@@ -6,6 +6,7 @@
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 ![](https://badge.mcpx.dev?type=server 'MCP Server')
 ![](https://badge.mcpx.dev?type=dev 'MCP Dev')
+[![Ask DeepWiki](https://deepwiki.com/badge.svg)](https://deepwiki.com/basicmachines-co/basic-memory)
 
 ## Skip the install — try Basic Memory in the cloud
 
@@ -590,7 +591,7 @@ retention).
 | `BASIC_MEMORY_IMPORT_UPLOAD_MAX_BYTES` | `104857600` | Max uploaded import size |
 
 ```bash
-BASIC_MEMORY_LOG_LEVEL=DEBUG basic-memory sync
+BASIC_MEMORY_LOG_LEVEL=DEBUG basic-memory reindex
 tail -f ~/.basic-memory/basic-memory.log
 ```
 

docs/Docker.md

@@ -111,7 +111,7 @@ You can run Basic Memory CLI commands inside the container using `docker exec`:
 docker exec basic-memory-server basic-memory status
 
 # Sync files
-docker exec basic-memory-server basic-memory sync
+docker exec basic-memory-server basic-memory reindex
 
 # Show help
 docker exec basic-memory-server basic-memory --help
@@ -137,7 +137,7 @@ When using Docker volumes, you'll need to configure projects to point to your mo
 
 3. **Sync the new project:**
    ```bash
-   docker exec basic-memory-server basic-memory sync
+   docker exec basic-memory-server basic-memory reindex
    ```
 
 ### Example: Setting up an Obsidian Vault
@@ -157,7 +157,7 @@ docker exec basic-memory-server basic-memory project create obsidian /app/data
 docker exec basic-memory-server basic-memory project set-default obsidian
 
 # Sync to index all files
-docker exec basic-memory-server basic-memory sync
+docker exec basic-memory-server basic-memory reindex
 ```
 
 ### Environment Variables

docs/character-handling.md

@@ -184,8 +184,8 @@ finance/           (lowercase f)
 Use Basic Memory's built-in conflict detection:
 
 ```bash
-# Sync will report conflicts
-basic-memory sync
+# Index local file changes (conflicts are handled during the scan)
+basic-memory reindex
 
 # Check sync status for warnings
 basic-memory status

docs/manual-pages.md

@@ -0,0 +1,183 @@
+# Manual Pages
+
+Basic Memory's manual is written in the style of Unix man pages — and
+implemented as Basic Memory notes ([#952](https://github.com/basicmachines-co/basic-memory/issues/952)).
+Every page is a markdown note conforming to the `Manpage` schema, `SEE ALSO`
+entries are real knowledge-graph relations, and every example on every page
+was executed against a live project before the page shipped. The manual
+documents the tools; the tools verify the manual.
+
+## Where it lives
+
+The canonical manual is the **`manual` project in the Basic Memory team
+workspace** (cloud, shared). Anyone can build their own: the schema ships as
+an opt-in seed at `plugins/claude-code/schemas/manpage.md` — copy it into any
+project's folder and start writing pages against it.
+
+Layout:
+
+```
+manual/
+├── schemas/Manpage.md      # the manpage schema (type: schema)
+├── man1/                   # CLI commands        bm(1), bm-status(1), ...
+├── man3/                   # MCP tools           write-note(3), search-notes(3), ...
+├── man5/                   # file formats        bm-note(5), bm-observation(5), ...
+├── man7/                   # concepts            basic-memory(7), semantic-memory(7), ...
+├── playground/             # scratch notes for destructive examples
+└── diagrams/               # canvas visualizations of the manual graph
+```
+
+### Why "man1", "man3", "man5"?
+
+The folder names are Unix's, unchanged since 1971. The manual is divided
+into numbered **sections**, pages physically live in directories named
+after them (`/usr/share/man/man1`, `man5`, ...), and the number tells you
+what *kind* of thing is documented — not importance, not reading order:
+
+- **1** — user commands (`ls`, `grep`)
+- **2** — system calls
+- **3** — library functions / APIs (`printf(3)`)
+- **4** — devices
+- **5** — file formats and config files (`crontab(5)`, `passwd(5)`)
+- **6** — games (really)
+- **7** — miscellanea: concepts, conventions, overviews (`regex(7)`, `signal(7)`)
+- **8** — system administration
+
+That's also why man page names carry the parenthesized number —
+`crontab(1)` is the command, `crontab(5)` is the file format, same name in
+two sections. `man 5 crontab` picks the section explicitly.
+
+This manual copies that layout with the sections that have a Basic Memory
+analog:
+
+- **man1/** — `bm` CLI commands → `bm-status(1)`
+- **man3/** — MCP tools, our equivalent of the "library API" section → `write-note(3)`
+- **man5/** — file formats: note syntax, observations, relations, schemas → `bm-note(5)`
+- **man7/** — concepts → `basic-memory(7)`, `semantic-memory(7)`
+- **8** is reserved for admin/cloud operations but has no pages yet; 2, 4,
+  and 6 have no analog (no system calls, no devices, and no games — yet)
+
+When a page says `see_also [[bm-note(5)]]`, the `(5)` reads "the
+file-format page," exactly the way a Unix manual cross-references — except
+here it's a traversable relation in the graph instead of a typographic
+convention. The manual explains its own conventions in `man-pages(7)` —
+fittingly, the same page name Linux uses for this, and that almost nobody
+ever reads.
+
+## Page anatomy
+
+Pages use the classic headers where applicable: `NAME`, `SYNOPSIS`,
+`DESCRIPTION`, `PARAMETERS`, `MCP USAGE`, `CLI EQUIVALENT`, `EXAMPLES`,
+`GOTCHAS`, `SEE ALSO`. Frontmatter (validated by the schema):
+
+```yaml
+type: manpage
+section: 3                      # 1 | 3 | 5 | 7 | 8
+name: write-note                # page name without section suffix
+summary: create or overwrite a markdown note in the knowledge base
+generated: hand                 # hand | registry | typer  (regeneration ownership)
+tool: write_note                # section-3 pages: the MCP tool documented
+command: basic-memory status    # section-1 pages: the CLI command documented
+verified: 0.21.6 mcp+cli        # version + path(s) that proved the page
+```
+
+Field knowledge accumulates as observations — `[gotcha]`, `[bug]` (with issue
+links), `[pattern]` — and `SEE ALSO` entries are `see_also` relations, so the
+manual is a navigable graph, not a folder of files.
+
+## How to use it
+
+Man-style reads (any MCP client or the CLI):
+
+```bash
+# read a page
+bm tool read-note "man3/write-note-3" --project manual
+
+# apropos — find pages by section, tool, or text
+bm tool search-notes --project manual          # then filter, or via MCP:
+#   search_notes(project="manual", metadata_filters={"type": "manpage", "section": 3})
+#   search_notes(project="manual", metadata_filters={"type": "manpage", "tool": "write_note"})
+
+# traverse SEE ALSO from any page
+#   build_context(url="man3/write-note-3", project="manual")
+```
+
+A future `bm man <topic>` command is thin sugar over exactly these calls.
+
+And for the real thing — `man bm` in an actual terminal:
+
+```bash
+bm man install        # copies bundled groff pages to ~/.local/share/man
+man bm                # the overview page, rendered by man(1)
+man basic-memory      # same page via its alias
+```
+
+`bm man install` warns with a one-line `MANPATH` fix if the install root
+isn't searched by your `man`. Agents with shell access can use `man bm` as
+an offline quick reference; the full per-tool detail stays in the manual
+project's section-3 pages.
+
+## The verification discipline
+
+Two rules make the manual trustworthy:
+
+1. **Examples must have run.** An `EXAMPLES` (or `MCP USAGE` / `CLI
+   EQUIVALENT`) block contains only commands that actually executed against
+   the manual project. Destructive operations (`delete_note`, `move_note`,
+   destructive `edit_note`) run only against `playground/` notes — never
+   against pages. The `verified:` field records the version and which path
+   proved the page: `mcp` (live service), `cli` (dev checkout), or both.
+
+2. **The schema is the linter.** Validate the whole manual any time:
+
+   ```bash
+   bm tool schema-validate manpage --project manual
+   # → {"total_notes": 38, "valid_count": 38, "warning_count": 0, ...}
+   ```
+
+   `bm orphans --project manual` confirms every page is connected to the
+   graph, and `schema_diff`/`schema_infer` report drift between the schema
+   and how pages are actually written.
+
+Because verification exercises real tool calls against the live service,
+building the manual doubles as an end-to-end smoke test. The initial build
+found six bugs in one pass (#954–#959) — including the verification rule
+catching a test that asserted a bug as expected output (#958).
+
+## Adding or updating a page
+
+1. Run the commands you intend to document; keep the actual output.
+2. Write the page with `write_note`, passing frontmatter through the
+   `metadata` parameter (nested YAML in content frontmatter is unreliable on
+   some clients):
+
+   ```
+   write_note(title="my-tool(3)", directory="man3", project="manual",
+              note_type="manpage",
+              metadata={"section": 3, "name": "my-tool",
+                        "summary": "...", "generated": "hand",
+                        "tool": "my_tool", "verified": "<version> mcp"})
+   ```
+
+3. Link related pages in `SEE ALSO` with `see_also [[other-page(3)]]`.
+   Forward references to pages that don't exist yet are fine — they resolve
+   automatically when the target is written.
+4. Validate: `bm tool schema-validate manpage --project manual`.
+
+For mechanical updates to generated sections, prefer `edit_note` with
+`replace_section` / `insert_after_section` so curated content (EXAMPLES,
+GOTCHAS, SEE ALSO, observations) survives — that ownership split is what the
+`generated:` field declares.
+
+## Roadmap
+
+- **Registry generator** — section-3 SYNOPSIS/PARAMETERS generated from the
+  MCP tool registry (docstrings + pydantic schemas), section-1 from Typer
+  help; the hand-written corpus is the template spec. Regenerate-and-diff in
+  CI becomes the drift gate.
+- **`bm man <topic>`** — CLI sugar over `read_note` + metadata search.
+  (`bm man install` + a hand-written `bm.1` already ship — the first slice
+  of [#610](https://github.com/basicmachines-co/basic-memory/issues/610);
+  the generator will produce per-command pages from the same extraction.)
+- **Docs site** — the notes remain canonical for sections 5 and 7, code is
+  canonical for 1 and 3; both render to the hosted docs site.

integrations/hermes/__init__.py

@@ -38,7 +38,7 @@ from typing import Any, Callable
 from agent.memory_provider import MemoryProvider
 from tools.registry import tool_error
 
-__version__ = "0.22.0"
+__version__ = "0.22.1"
 
 logger = logging.getLogger("hermes.memory.basic-memory")
 

integrations/hermes/plugin.yaml

@@ -1,5 +1,5 @@
 name: basic-memory
-version: 0.22.0
+version: 0.22.1
 description: "Basic Memory — persistent knowledge graph backed by the basic-memory MCP server"
 pip_dependencies:
   - mcp

integrations/openclaw/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@basicmemory/openclaw-basic-memory",
-  "version": "0.22.0",
+  "version": "0.22.1",
   "type": "module",
   "main": "./dist/index.js",
   "types": "./dist/index.d.ts",

justfile

@@ -383,17 +383,31 @@ release version:
         echo "❌ Tag {{version}} already exists"
         exit 1
     fi
-    
+
+    # Changelog must already be on main (land it via a normal PR first)
+    if ! grep -q "^## {{version}} " CHANGELOG.md; then
+        echo "❌ CHANGELOG.md has no entry for {{version}}. Land one via PR first."
+        exit 1
+    fi
+
     # Run quality checks
     echo "🔍 Running lint  checks..."
     just lint
     just typecheck
-    
+
     # Update all package manifests to the one Basic Memory product version.
     echo "📝 Updating consolidated package versions..."
     just set-version "{{version}}"
 
-    # Commit version update
+    # Trigger: main's ruleset rejects direct pushes ("Changes must be made
+    # through a pull request").
+    # Why: the version bump must land on main before the tag is cut, so it
+    # rides a release PR that is rebase-merged (the repo disallows merge
+    # commits).
+    # Outcome: the bump commit gets a new SHA on main; the tag is created on
+    # that rebased commit, found by its commit subject.
+    COMMIT_SUBJECT="chore: update version to $VERSION_NUM for {{version}} release"
+    git checkout -b "release/{{version}}"
     git add \
         src/basic_memory/__init__.py \
         server.json \
@@ -404,23 +418,58 @@ release version:
         integrations/hermes/plugin.yaml \
         integrations/hermes/__init__.py \
         integrations/openclaw/package.json
-    git commit -s -m "chore: update version to $VERSION_NUM for {{version}} release"
-    
-    # Create and push tag
-    echo "🏷️  Creating tag {{version}}..."
-    git tag "{{version}}"
-    
-    echo "📤 Pushing to GitHub..."
-    git push origin main
+    git commit -s -m "$COMMIT_SUBJECT"
+
+    echo "📤 Opening release PR..."
+    git push -u origin "release/{{version}}"
+    gh pr create --title "chore(core): release {{version}}" \
+        --body "Version bump for {{version}}. See CHANGELOG.md for release notes."
+
+    # Trigger: the PR may not be mergeable synchronously (merge gates,
+    # required checks added later, or GitHub still computing mergeability).
+    # Why: the tag must point at the bump commit on main, so the recipe
+    # cannot tag until the merge has actually landed.
+    # Outcome: try a direct rebase-merge, fall back to queueing auto-merge,
+    # then poll main for the rebased bump commit before tagging.
+    if ! gh pr merge "release/{{version}}" --rebase --delete-branch; then
+        echo "⚠️  Direct merge did not complete (merge gates pending?). Queueing auto-merge..."
+        gh pr merge "release/{{version}}" --rebase --delete-branch --auto
+    fi
+
+    echo "⏳ Waiting for the bump commit to land on main..."
+    TAG_COMMIT=""
+    for _ in $(seq 1 60); do
+        git fetch origin main --quiet
+        TAG_COMMIT=$(git log FETCH_HEAD --fixed-strings --grep "$COMMIT_SUBJECT" --format='%H' -1)
+        [[ -n "$TAG_COMMIT" ]] && break
+        sleep 5
+    done
+    if [[ -z "$TAG_COMMIT" ]]; then
+        echo "❌ Bump commit not on main after 5 minutes (merge still pending?)."
+        echo "   Once the release PR merges, finish the release manually:"
+        echo "   git fetch origin main"
+        echo "   git tag {{version}} \$(git log FETCH_HEAD --fixed-strings --grep \"$COMMIT_SUBJECT\" --format='%H' -1)"
+        echo "   git push origin {{version}}"
+        exit 1
+    fi
+
+    git checkout main
+    git pull --ff-only origin main
+    git branch -D "release/{{version}}" 2>/dev/null || true
+
+    echo "🏷️  Creating tag {{version}} at $TAG_COMMIT..."
+    git tag "{{version}}" "$TAG_COMMIT"
     git push origin "{{version}}"
-    
+
     echo "✅ Release {{version}} created successfully!"
     echo "📦 GitHub Actions will build and publish to PyPI"
     echo "🔗 Monitor at: https://github.com/basicmachines-co/basic-memory/actions"
     echo ""
     echo "📝 REMINDER: Post-release tasks:"
-    echo "   1. docs.basicmemory.com - Add release notes to src/pages/latest-releases.mdx"
-    echo "   2. basicmachines.co - Update version in src/components/sections/hero.tsx"
+    echo "   1. docs.basicmemory.com - Add a What's New page under content/2.whats-new/"
+    echo "      and bump the badge in content/index.md (see that repo's CLAUDE.md)"
+    echo "   2. basicmemory.com - No version number in the site UI; for a significant"
+    echo "      release optionally add a post under src/content/blog/. Skip for patches."
     echo "   3. MCP Registry - Run: mcp-publisher publish"
     echo "   See: .claude/commands/release/release.md for detailed instructions"
 
@@ -467,7 +516,15 @@ beta version:
     echo "📝 Updating consolidated package versions..."
     just set-version "{{version}}"
 
-    # Commit version update
+    # Trigger: main's ruleset rejects direct pushes ("Changes must be made
+    # through a pull request").
+    # Why: the version bump must land on main before the tag is cut, so it
+    # rides a release PR that is rebase-merged (the repo disallows merge
+    # commits).
+    # Outcome: the bump commit gets a new SHA on main; the tag is created on
+    # that rebased commit, found by its commit subject.
+    COMMIT_SUBJECT="chore: update version to $VERSION_NUM for {{version}} beta release"
+    git checkout -b "release/{{version}}"
     git add \
         src/basic_memory/__init__.py \
         server.json \
@@ -478,24 +535,59 @@ beta version:
         integrations/hermes/plugin.yaml \
         integrations/hermes/__init__.py \
         integrations/openclaw/package.json
-    git commit -s -m "chore: update version to $VERSION_NUM for {{version}} beta release"
-    
-    # Create and push tag
-    echo "🏷️  Creating tag {{version}}..."
-    git tag "{{version}}"
-    
-    echo "📤 Pushing to GitHub..."
-    git push origin main
+    git commit -s -m "$COMMIT_SUBJECT"
+
+    echo "📤 Opening release PR..."
+    git push -u origin "release/{{version}}"
+    gh pr create --title "chore(core): release {{version}}" \
+        --body "Version bump for {{version}} beta."
+
+    # Trigger: the PR may not be mergeable synchronously (merge gates,
+    # required checks added later, or GitHub still computing mergeability).
+    # Why: the tag must point at the bump commit on main, so the recipe
+    # cannot tag until the merge has actually landed.
+    # Outcome: try a direct rebase-merge, fall back to queueing auto-merge,
+    # then poll main for the rebased bump commit before tagging.
+    if ! gh pr merge "release/{{version}}" --rebase --delete-branch; then
+        echo "⚠️  Direct merge did not complete (merge gates pending?). Queueing auto-merge..."
+        gh pr merge "release/{{version}}" --rebase --delete-branch --auto
+    fi
+
+    echo "⏳ Waiting for the bump commit to land on main..."
+    TAG_COMMIT=""
+    for _ in $(seq 1 60); do
+        git fetch origin main --quiet
+        TAG_COMMIT=$(git log FETCH_HEAD --fixed-strings --grep "$COMMIT_SUBJECT" --format='%H' -1)
+        [[ -n "$TAG_COMMIT" ]] && break
+        sleep 5
+    done
+    if [[ -z "$TAG_COMMIT" ]]; then
+        echo "❌ Bump commit not on main after 5 minutes (merge still pending?)."
+        echo "   Once the release PR merges, finish the release manually:"
+        echo "   git fetch origin main"
+        echo "   git tag {{version}} \$(git log FETCH_HEAD --fixed-strings --grep \"$COMMIT_SUBJECT\" --format='%H' -1)"
+        echo "   git push origin {{version}}"
+        exit 1
+    fi
+
+    git checkout main
+    git pull --ff-only origin main
+    git branch -D "release/{{version}}" 2>/dev/null || true
+
+    echo "🏷️  Creating tag {{version}} at $TAG_COMMIT..."
+    git tag "{{version}}" "$TAG_COMMIT"
     git push origin "{{version}}"
-    
+
     echo "✅ Beta release {{version}} created successfully!"
     echo "📦 GitHub Actions will build and publish to PyPI as pre-release"
     echo "🔗 Monitor at: https://github.com/basicmachines-co/basic-memory/actions"
     echo "📥 Install with: uv tool install basic-memory --pre"
     echo ""
     echo "📝 REMINDER: For stable releases, update documentation sites:"
-    echo "   1. docs.basicmemory.com - Add release notes to src/pages/latest-releases.mdx"
-    echo "   2. basicmachines.co - Update version in src/components/sections/hero.tsx"
+    echo "   1. docs.basicmemory.com - Add a What's New page under content/2.whats-new/"
+    echo "      and bump the badge in content/index.md (see that repo's CLAUDE.md)"
+    echo "   2. basicmemory.com - No version number in the site UI; for a significant"
+    echo "      release optionally add a post under src/content/blog/. Skip for patches."
     echo "   See: .claude/commands/release/release.md for detailed instructions"
 
 # List all available recipes

plugins/claude-code/.claude-plugin/marketplace.json

@@ -6,14 +6,14 @@
   },
   "metadata": {
     "description": "Official plugins from Basic Machines for knowledge management and AI-assisted development",
-    "version": "0.22.0"
+    "version": "0.22.1"
   },
   "plugins": [
     {
       "name": "basic-memory",
       "source": "./",
       "description": "The bridge between Claude's working memory and Basic Memory's durable knowledge graph \u2014 session briefings, pre-compaction checkpoints, and capture reflexes",
-      "version": "0.22.0",
+      "version": "0.22.1",
       "author": {
         "name": "Basic Machines"
       },

plugins/claude-code/.claude-plugin/plugin.json

@@ -1,7 +1,7 @@
 {
   "name": "basic-memory",
   "description": "The bridge between Claude's working memory and Basic Memory's durable knowledge graph \u2014 session briefings, pre-compaction checkpoints, and capture reflexes",
-  "version": "0.22.0",
+  "version": "0.22.1",
   "author": {
     "name": "Basic Machines"
   },

plugins/claude-code/schemas/manpage.md

@@ -0,0 +1,55 @@
+---
+title: Manpage
+type: schema
+entity: Manpage
+version: 1
+schema:
+  gotcha?(array): string, sharp edges and surprising behavior learned from live verification
+  example?(array): string, worked examples beyond the generated synopsis
+  pattern?(array): string, recommended idioms and usage patterns
+  bug?(array): string, known defects affecting this surface, with issue links
+  see_also?(array): Entity, related manual pages — the SEE ALSO graph
+settings:
+  validation: warn
+  frontmatter:
+    section(enum, Unix manual section number): [1, 3, 5, 7, 8]
+    name: string, page name without section suffix (e.g. write-note)
+    summary: string, one-line NAME description
+    generated?(enum, who owns the mechanical sections): [registry, typer, hand]
+    tool?: string, MCP tool this page documents (section 3 pages)
+    command?: string, CLI command this page documents (section 1 pages)
+    verified?: string, version and path that verified this page (e.g. 0.21.6 mcp+cli)
+    since?: string, version this surface first appeared
+---
+
+# Manpage
+
+A **ManpageNote** is one page of a Unix-style manual implemented as Basic
+Memory notes (issue #952): commands in section 1, MCP tools in section 3,
+file formats in section 5, concepts in section 7, admin in section 8. The
+manual becomes a knowledge graph — `SEE ALSO` entries are typed relations,
+and pages are found by structured recall:
+`search_notes(metadata_filters={"type": "manpage", "section": 3})`.
+
+This schema is an opt-in seed for documentation projects; the canonical
+manual lives in the Basic Memory team workspace `manual` project.
+
+## What makes a good ManpageNote
+
+- **NAME / SYNOPSIS / DESCRIPTION** — classic man-page structure, with
+  PARAMETERS, MCP USAGE, CLI EQUIVALENT, EXAMPLES, GOTCHAS, SEE ALSO where
+  applicable.
+- **Verified examples** — EXAMPLES contain only commands that actually ran;
+  the `verified` field records the version and path (mcp, cli, or both).
+- **generated** — declares regeneration ownership: `registry` (from the MCP
+  tool registry) and `typer` (from CLI help) pages get mechanical sections
+  rewritten; curated sections (EXAMPLES, GOTCHAS, SEE ALSO, observations)
+  are never overwritten.
+- **gotcha / bug observations** — field knowledge accumulates on pages
+  without being clobbered by regeneration; bugs link their tracking issues.
+
+## Frontmatter
+
+`type: manpage` plus `section` makes the manual queryable like `man -k`:
+by section, by `tool`, by `command`, or by missing/stale `verified` stamps.
+Validation is `warn`, never blocking.

plugins/codex/.codex-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "codex",
-  "version": "0.22.0",
+  "version": "0.22.1",
   "description": "A Codex-native bridge to Basic Memory for durable engineering context, decisions, and resumable checkpoints.",
   "author": {
     "name": "Basic Machines",

server.json

@@ -6,12 +6,12 @@
     "url": "https://github.com/basicmachines-co/basic-memory.git",
     "source": "github"
   },
-  "version": "0.22.0",
+  "version": "0.22.1",
   "packages": [
     {
       "registryType": "pypi",
       "identifier": "basic-memory",
-      "version": "0.22.0",
+      "version": "0.22.1",
       "runtimeHint": "uvx",
       "runtimeArguments": [
         {

src/basic_memory/__init__.py

@@ -1,7 +1,7 @@
 """basic-memory - Local-first knowledge management combining Zettelkasten with knowledge graphs"""
 
 # Package version - updated by release automation
-__version__ = "0.22.0"
+__version__ = "0.22.1"
 
 # API version for FastAPI - independent of package version
 __api_version__ = "v0"

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

@@ -17,6 +17,7 @@ from fastapi import APIRouter, HTTPException, Response, Path
 from loguru import logger
 
 import logfire
+from basic_memory import db
 from basic_memory.ignore_utils import (
     IGNORED_PATH_REJECTION_DETAIL,
     load_gitignore_patterns,
@@ -34,6 +35,8 @@ from basic_memory.deps import (
     ProjectExternalIdPathDep,
     SyncServiceV2ExternalDep,
     TaskSchedulerDep,
+    SessionDep,
+    SessionMakerDep,
 )
 from basic_memory.schemas import DeleteEntitiesResponse
 from basic_memory.schemas.base import Entity
@@ -81,6 +84,7 @@ async def get_graph(
     project_id: ProjectExternalIdPathDep,
     entity_repository: EntityRepositoryV2ExternalDep,
     relation_repository: RelationRepositoryV2ExternalDep,
+    session: SessionDep,
 ) -> GraphResponse:
     """Return all entities and resolved relations for knowledge graph visualization.
 
@@ -96,7 +100,7 @@ async def get_graph(
         logger.info("API v2 request: get_graph")
 
         # Fetch all entities for this project
-        entities = await entity_repository.find_all(use_load_options=False)
+        entities = await entity_repository.find_all(session, use_load_options=False)
         nodes = [
             GraphNode(
                 external_id=entity.external_id,
@@ -108,7 +112,7 @@ async def get_graph(
         ]
 
         # Fetch all resolved relations (to_id is not null) with eager-loaded entities
-        relations = await relation_repository.find_all()
+        relations = await relation_repository.find_all(session)
         edges = [
             GraphEdge(
                 from_id=relation.from_entity.external_id,
@@ -130,6 +134,7 @@ async def get_graph(
 async def get_orphan_entities(
     project_id: ProjectExternalIdPathDep,
     entity_repository: EntityRepositoryV2ExternalDep,
+    session: SessionDep,
 ) -> OrphanEntitiesResponse:
     """Return entities that have no incoming or outgoing relations."""
     with logfire.span(
@@ -140,7 +145,7 @@ async def get_orphan_entities(
     ):
         logger.info("API v2 request: get_orphan_entities")
 
-        entities = await entity_repository.find_without_relations()
+        entities = await entity_repository.find_without_relations(session)
         nodes = [
             GraphNode(
                 external_id=entity.external_id,
@@ -165,6 +170,7 @@ async def resolve_identifier(
     link_resolver: LinkResolverV2ExternalDep,
     entity_repository: EntityRepositoryV2ExternalDep,
     project_repository: ProjectRepositoryDep,
+    session: SessionDep,
 ) -> EntityResolveResponse:
     """Resolve a string identifier (external_id, permalink, title, or path) to entity info.
 
@@ -203,12 +209,15 @@ async def resolve_identifier(
     ):
         logger.info(f"API v2 request: resolve_identifier for '{data.identifier}'")
 
-        entity = await entity_repository.get_by_external_id(data.identifier)
+        entity = await entity_repository.get_by_external_id(session, data.identifier)
         resolution_method = "external_id" if entity else "search"
 
         if not entity:
             entity = await link_resolver.resolve_link(
-                data.identifier, source_path=data.source_path, strict=data.strict
+                data.identifier,
+                source_path=data.source_path,
+                strict=data.strict,
+                session=session,
             )
             if entity:
                 if entity.permalink == data.identifier:
@@ -223,7 +232,7 @@ async def resolve_identifier(
         if not entity:
             raise HTTPException(status_code=404, detail=f"Entity not found: '{data.identifier}'")
 
-        owner_project = await project_repository.get_by_id(entity.project_id)
+        owner_project = await project_repository.get_by_id(session, entity.project_id)
         if not owner_project:  # pragma: no cover
             raise HTTPException(
                 status_code=500,
@@ -304,6 +313,7 @@ async def sync_file(
     project_config: ProjectConfigV2ExternalDep,
     search_service: SearchServiceV2ExternalDep,
     app_config: AppConfigDep,
+    session_maker: SessionMakerDep,
 ) -> EntityResponseV2:
     """Index a single markdown file that exists on disk but is not indexed yet.
 
@@ -406,7 +416,8 @@ async def sync_file(
         # Trigger: the file may already have a DB row (e.g. modified on disk after indexing)
         # Why: the indexer needs to know whether to insert or update the entity
         # Outcome: new is computed from the database instead of assumed by the caller
-        existing = await sync_service.entity_repository.get_by_file_path(file_path)
+        async with db.scoped_session(session_maker) as session:
+            existing = await sync_service.entity_repository.get_by_file_path(session, file_path)
         synced = await sync_service.sync_one_markdown_file(
             file_path, new=existing is None, index_search=True
         )
@@ -435,6 +446,7 @@ async def sync_file(
 async def get_entity_by_id(
     project_id: ProjectExternalIdPathDep,
     entity_repository: EntityRepositoryV2ExternalDep,
+    session: SessionDep,
     entity_id: str = Path(..., description="Entity external ID (UUID)"),
 ) -> EntityResponseV2:
     """Get an entity by its external ID (UUID).
@@ -459,7 +471,7 @@ async def get_entity_by_id(
     ):
         logger.info(f"API v2 request: get_entity_by_id entity_id={entity_id}")
 
-        entity = await entity_repository.get_by_external_id(entity_id)
+        entity = await entity_repository.get_by_external_id(session, entity_id)
         if not entity:
             raise HTTPException(
                 status_code=404, detail=f"Entity with external_id '{entity_id}' not found"
@@ -536,6 +548,7 @@ async def update_entity_by_id(
     entity_repository: EntityRepositoryV2ExternalDep,
     task_scheduler: TaskSchedulerDep,
     app_config: AppConfigDep,
+    session_maker: SessionMakerDep,
     entity_id: str = Path(..., description="Entity external ID (UUID)"),
 ) -> EntityResponseV2:
     """Update an entity by external ID.
@@ -557,7 +570,8 @@ async def update_entity_by_id(
     ):
         logger.info(f"API v2 request: update_entity_by_id entity_id={entity_id}")
 
-        existing = await entity_repository.get_by_external_id(entity_id)
+        async with db.scoped_session(session_maker) as session:
+            existing = await entity_repository.get_by_external_id(session, entity_id)
         created = existing is None
 
         if existing:
@@ -568,10 +582,12 @@ async def update_entity_by_id(
             write_result = await entity_service.create_entity_with_content(data)
             entity = write_result.entity
             if entity.external_id != entity_id:
-                entity = await entity_repository.update(
-                    entity.id,
-                    {"external_id": entity_id},
-                )
+                async with db.scoped_session(session_maker) as session:
+                    entity = await entity_repository.update(
+                        session,
+                        entity.id,
+                        {"external_id": entity_id},
+                    )
                 # external_id fixup only changes the DB row. The file content is unchanged,
                 # so the markdown captured during the write remains valid downstream.
                 if not entity:
@@ -607,6 +623,7 @@ async def edit_entity_by_id(
     entity_repository: EntityRepositoryV2ExternalDep,
     task_scheduler: TaskSchedulerDep,
     app_config: AppConfigDep,
+    session_maker: SessionMakerDep,
     entity_id: str = Path(..., description="Entity external ID (UUID)"),
 ) -> EntityResponseV2:
     """Edit an existing entity by external ID using operations like append, prepend, etc.
@@ -631,7 +648,8 @@ async def edit_entity_by_id(
             f"API v2 request: edit_entity_by_id entity_id={entity_id}, operation='{data.operation}'"
         )
 
-        entity = await entity_repository.get_by_external_id(entity_id)
+        async with db.scoped_session(session_maker) as session:
+            entity = await entity_repository.get_by_external_id(session, entity_id)
         if not entity:  # pragma: no cover
             raise HTTPException(
                 status_code=404, detail=f"Entity with external_id '{entity_id}' not found"
@@ -678,6 +696,7 @@ async def delete_entity_by_id(
     project_id: ProjectExternalIdPathDep,
     entity_service: EntityServiceV2ExternalDep,
     entity_repository: EntityRepositoryV2ExternalDep,
+    session_maker: SessionMakerDep,
     entity_id: str = Path(..., description="Entity external ID (UUID)"),
 ) -> DeleteEntitiesResponse:
     """Delete an entity by external ID.
@@ -698,7 +717,8 @@ async def delete_entity_by_id(
     ):
         logger.info(f"API v2 request: delete_entity_by_id entity_id={entity_id}")
 
-        entity = await entity_repository.get_by_external_id(entity_id)
+        async with db.scoped_session(session_maker) as session:
+            entity = await entity_repository.get_by_external_id(session, entity_id)
         if entity is None:
             logger.info(f"API v2 response: external_id={entity_id} not found, deleted=False")
             return DeleteEntitiesResponse(deleted=False)
@@ -724,6 +744,7 @@ async def move_entity(
     app_config: AppConfigDep,
     search_service: SearchServiceV2ExternalDep,
     task_scheduler: TaskSchedulerDep,
+    session_maker: SessionMakerDep,
     entity_id: str = Path(..., description="Entity external ID (UUID)"),
 ) -> EntityResponseV2:
     """Move an entity to a new file location.
@@ -751,7 +772,8 @@ async def move_entity(
 
         try:
             # First, get the entity by external_id to verify it exists
-            entity = await entity_repository.get_by_external_id(entity_id)
+            async with db.scoped_session(session_maker) as session:
+                entity = await entity_repository.get_by_external_id(session, entity_id)
             if not entity:  # pragma: no cover
                 raise HTTPException(
                     status_code=404, detail=f"Entity with external_id '{entity_id}' not found"
@@ -766,9 +788,11 @@ async def move_entity(
             )
 
             # Reindex at new location
-            reindexed_entity = await entity_service.link_resolver.resolve_link(
-                data.destination_path
-            )
+            async with db.scoped_session(session_maker) as session:
+                reindexed_entity = await entity_service.link_resolver.resolve_link(
+                    data.destination_path,
+                    session=session,
+                )
             if reindexed_entity:
                 await search_service.index_entity(reindexed_entity)
                 _schedule_vector_sync_if_enabled(
@@ -805,6 +829,7 @@ async def move_directory(
     app_config: AppConfigDep,
     search_service: SearchServiceV2ExternalDep,
     task_scheduler: TaskSchedulerDep,
+    session_maker: SessionMakerDep,
 ) -> DirectoryMoveResult:
     """Move all entities in a directory to a new location.
 
@@ -840,7 +865,10 @@ async def move_directory(
 
             # Reindex moved entities
             for file_path in result.moved_files:
-                entity = await entity_service.link_resolver.resolve_link(file_path)
+                async with db.scoped_session(session_maker) as session:
+                    entity = await entity_service.link_resolver.resolve_link(
+                        file_path, session=session
+                    )
                 if entity:
                     await search_service.index_entity(entity)
                     _schedule_vector_sync_if_enabled(

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

@@ -10,7 +10,12 @@ from fastapi import APIRouter, Query, Path
 from loguru import logger
 
 import logfire
-from basic_memory.deps import ContextServiceV2ExternalDep, EntityRepositoryV2ExternalDep
+from basic_memory import db
+from basic_memory.deps import (
+    ContextServiceV2ExternalDep,
+    EntityRepositoryV2ExternalDep,
+    SessionMakerDep,
+)
 from basic_memory.schemas.base import TimeFrame, parse_timeframe
 from basic_memory.schemas.memory import (
     GraphContext,
@@ -27,6 +32,7 @@ router = APIRouter(tags=["memory"])
 async def recent(
     context_service: ContextServiceV2ExternalDep,
     entity_repository: EntityRepositoryV2ExternalDep,
+    session_maker: SessionMakerDep,
     project_id: str = Path(..., description="Project external UUID"),
     type: Annotated[list[SearchItemType] | None, Query()] = None,
     depth: int = 1,
@@ -95,9 +101,14 @@ async def recent(
             phase="shape_response",
             result_count=len(context.results),
         ):
-            recent_context = await to_graph_context(
-                context, entity_repository=entity_repository, page=page, page_size=page_size
-            )
+            async with db.scoped_session(session_maker) as session:
+                recent_context = await to_graph_context(
+                    context,
+                    entity_repository=entity_repository,
+                    session=session,
+                    page=page,
+                    page_size=page_size,
+                )
         logger.debug(f"V2 Recent context: {recent_context.model_dump_json()}")
         return recent_context
 
@@ -109,6 +120,7 @@ async def recent(
 async def get_memory_context(
     context_service: ContextServiceV2ExternalDep,
     entity_repository: EntityRepositoryV2ExternalDep,
+    session_maker: SessionMakerDep,
     uri: str,
     project_id: str = Path(..., description="Project external UUID"),
     depth: int = 1,
@@ -177,6 +189,11 @@ async def get_memory_context(
             phase="shape_response",
             result_count=len(context.results),
         ):
-            return await to_graph_context(
-                context, entity_repository=entity_repository, page=page, page_size=page_size
-            )
+            async with db.scoped_session(session_maker) as session:
+                return await to_graph_context(
+                    context,
+                    entity_repository=entity_repository,
+                    session=session,
+                    page=page,
+                    page_size=page_size,
+                )

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

@@ -16,6 +16,7 @@ from typing import Literal, Optional
 from fastapi import APIRouter, HTTPException, Body, Query, Path
 from loguru import logger
 
+from basic_memory import db
 from basic_memory.deps import (
     ProjectServiceDep,
     ProjectRepositoryDep,
@@ -23,6 +24,8 @@ from basic_memory.deps import (
     SyncServiceV2ExternalDep,
     TaskSchedulerDep,
     ProjectExternalIdPathDep,
+    SessionDep,
+    SessionMakerDep,
 )
 from basic_memory.schemas import SyncReportResponse
 from basic_memory.models import Project
@@ -54,21 +57,22 @@ def _split_qualified_project_identifier(identifier: str) -> tuple[str | None, st
 
 
 async def _resolve_project_identifier_candidate(
+    session: SessionDep,
     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)
+    project = await project_repository.get_by_external_id(session, identifier)
     if project:
         return project, "external_id"
 
-    project = await project_repository.get_by_permalink(identifier_permalink)
+    project = await project_repository.get_by_permalink(session, identifier_permalink)
     if project:
         return project, "permalink"
 
-    project = await project_repository.get_by_name_case_insensitive(identifier)
+    project = await project_repository.get_by_name_case_insensitive(session, identifier)
     if project:
         return project, "name"  # pragma: no cover
 
@@ -76,11 +80,13 @@ async def _resolve_project_identifier_candidate(
 
 
 async def _resolve_project_identifier(
+    session: SessionDep,
     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(
+        session,
         project_repository,
         identifier,
     )
@@ -96,6 +102,7 @@ async def _resolve_project_identifier(
     #   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(
+        session,
         project_repository,
         project_identifier,
     )
@@ -193,7 +200,7 @@ async def add_project(
         return ProjectStatusResponse(  # pyright: ignore [reportCallIssue]
             message=f"Project '{new_project.name}' added successfully",
             status="success",
-            default=project_data.set_default,
+            default=new_project.is_default or False,
             new_project=ProjectItem(
                 id=new_project.id,
                 external_id=new_project.external_id,
@@ -277,6 +284,7 @@ async def get_project_status(
 @router.post("/resolve", response_model=ProjectResolveResponse)
 async def resolve_project_identifier(
     data: ProjectResolveRequest,
+    session: SessionDep,
     project_repository: ProjectRepositoryDep,
 ) -> ProjectResolveResponse:
     """Resolve a project identifier (name, permalink, or external_id) to project info.
@@ -315,12 +323,26 @@ async def resolve_project_identifier(
     logger.info(f"API v2 request: resolve_project_identifier for '{data.identifier}'")
 
     project, resolution_method = await _resolve_project_identifier(
+        session,
         project_repository,
         data.identifier,
     )
 
     if not project:
-        raise HTTPException(status_code=404, detail=f"Project not found: '{data.identifier}'")
+        detail = f"Project not found: '{data.identifier}'"
+        # Trigger: resolution missed and the projects table is empty.
+        # Why: a fresh install bootstraps config.json's default project before any
+        #      reconciliation has created database rows (the one-shot CLI never runs
+        #      the server lifespan), so the first read fails on the configured
+        #      default and the bare not-found message reads as a broken install
+        #      rather than a missing first-run step (#974 follow-up).
+        # Outcome: the error names the setup command instead.
+        if not await project_repository.find_all(session, limit=1, use_load_options=False):
+            detail = (
+                f"{detail}. No projects are set up yet — run "
+                "'basic-memory project add <name> <path>' to create one."
+            )
+        raise HTTPException(status_code=404, detail=detail)
 
     return ProjectResolveResponse(
         external_id=project.external_id,
@@ -336,6 +358,7 @@ async def resolve_project_identifier(
 
 @router.get("/{project_id}", response_model=ProjectItem)
 async def get_project_by_id(
+    session: SessionDep,
     project_repository: ProjectRepositoryDep,
     project_id: str = Path(..., description="Project external ID (UUID)"),
 ) -> ProjectItem:
@@ -358,7 +381,7 @@ async def get_project_by_id(
     """
     logger.info(f"API v2 request: get_project_by_id for project_id={project_id}")
 
-    project = await project_repository.get_by_external_id(project_id)
+    project = await project_repository.get_by_external_id(session, project_id)
     if not project:
         raise HTTPException(
             status_code=404, detail=f"Project with external_id '{project_id}' not found"
@@ -376,12 +399,14 @@ async def get_project_by_id(
 @router.get("/{project_id}/info", response_model=ProjectInfoResponse)
 async def get_project_info_by_id(
     project_service: ProjectServiceDep,
+    session_maker: SessionMakerDep,
     project_repository: ProjectRepositoryDep,
     project_id: str = Path(..., description="Project external ID (UUID)"),
 ) -> ProjectInfoResponse:
     """Get detailed project information by external ID."""
     logger.info(f"API v2 request: get_project_info_by_id for project_id={project_id}")
-    project = await project_repository.get_by_external_id(project_id)
+    async with db.scoped_session(session_maker) as session:
+        project = await project_repository.get_by_external_id(session, project_id)
     if not project:
         raise HTTPException(
             status_code=404, detail=f"Project with external_id '{project_id}' not found"
@@ -392,6 +417,7 @@ async def get_project_info_by_id(
 @router.patch("/{project_id}", response_model=ProjectStatusResponse)
 async def update_project_by_id(
     project_service: ProjectServiceDep,
+    session_maker: SessionMakerDep,
     project_repository: ProjectRepositoryDep,
     project_id: str = Path(..., description="Project external ID (UUID)"),
     path: Optional[str] = Body(None, description="New absolute path for the project"),
@@ -422,7 +448,8 @@ async def update_project_by_id(
             raise HTTPException(status_code=400, detail="Path must be absolute")
 
         # Get original project info for the response
-        old_project = await project_repository.get_by_external_id(project_id)
+        async with db.scoped_session(session_maker) as session:
+            old_project = await project_repository.get_by_external_id(session, project_id)
         if not old_project:
             raise HTTPException(
                 status_code=404, detail=f"Project with external_id '{project_id}' not found"
@@ -443,7 +470,8 @@ async def update_project_by_id(
             await project_service.update_project(old_project.name, is_active=is_active)
 
         # Get updated project info (use the same external_id)
-        updated_project = await project_repository.get_by_external_id(project_id)
+        async with db.scoped_session(session_maker) as session:
+            updated_project = await project_repository.get_by_external_id(session, project_id)
         if not updated_project:  # pragma: no cover
             raise HTTPException(
                 status_code=404,
@@ -470,6 +498,7 @@ async def update_project_by_id(
 @router.delete("/{project_id}", response_model=ProjectStatusResponse)
 async def delete_project_by_id(
     project_service: ProjectServiceDep,
+    session_maker: SessionMakerDep,
     project_repository: ProjectRepositoryDep,
     project_id: str = Path(..., description="Project external ID (UUID)"),
     delete_notes: bool = Query(
@@ -496,7 +525,8 @@ async def delete_project_by_id(
     )
 
     try:
-        old_project = await project_repository.get_by_external_id(project_id)
+        async with db.scoped_session(session_maker) as session:
+            old_project = await project_repository.get_by_external_id(session, project_id)
         if not old_project:
             raise HTTPException(
                 status_code=404, detail=f"Project with external_id '{project_id}' not found"
@@ -539,6 +569,7 @@ async def delete_project_by_id(
 @router.put("/{project_id}/default", response_model=ProjectStatusResponse)
 async def set_default_project_by_id(
     project_service: ProjectServiceDep,
+    session_maker: SessionMakerDep,
     project_repository: ProjectRepositoryDep,
     project_id: str = Path(..., description="Project external ID (UUID)"),
 ) -> ProjectStatusResponse:
@@ -559,15 +590,14 @@ async def set_default_project_by_id(
     logger.info(f"API v2 request: set_default_project_by_id for project_id={project_id}")
 
     try:
-        # Get the old default project from database
-        default_project = await project_repository.get_default_project()
-        if not default_project:
-            raise HTTPException(  # pragma: no cover
-                status_code=404, detail="No default project is currently set"
-            )
+        # Get the old default project from database. It may be absent during
+        # bootstrap/recovery (no default row yet); that is a valid state, not an
+        # error, so we only echo it back when one exists.
+        async with db.scoped_session(session_maker) as session:
+            default_project = await project_repository.get_default_project(session)
 
-        # Get the new default project by external_id
-        new_default_project = await project_repository.get_by_external_id(project_id)
+            # Get the new default project by external_id
+            new_default_project = await project_repository.get_by_external_id(session, project_id)
         if not new_default_project:
             raise HTTPException(
                 status_code=404, detail=f"Project with external_id '{project_id}' not found"
@@ -576,17 +606,27 @@ async def set_default_project_by_id(
         # Set as default using project name (service layer still uses names internally)
         await project_service.set_default_project(new_default_project.name)
 
-        return ProjectStatusResponse(
-            message=f"Project '{new_default_project.name}' set as default successfully",
-            status="success",
-            default=True,
-            old_project=ProjectItem(
+        # Trigger: a previous default existed
+        # Why: ProjectStatusResponse.old_project is Optional; the no-default
+        #   bootstrap case must succeed with old_project=None
+        # Outcome: response echoes the prior default only when there was one
+        old_project = (
+            ProjectItem(
                 id=default_project.id,
                 external_id=default_project.external_id,
                 name=default_project.name,
                 path=default_project.path,
                 is_default=False,
-            ),
+            )
+            if default_project
+            else None
+        )
+
+        return ProjectStatusResponse(
+            message=f"Project '{new_default_project.name}' set as default successfully",
+            status="success",
+            default=True,
+            old_project=old_project,
             new_project=ProjectItem(
                 id=new_default_project.id,
                 external_id=new_default_project.external_id,

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

@@ -10,6 +10,7 @@ from typing import Any
 from fastapi import APIRouter, HTTPException, status, Path
 from loguru import logger
 
+from basic_memory import db
 from basic_memory.api.v2.utils import to_graph_context, to_search_results
 from basic_memory.api.template_loader import template_loader
 from basic_memory.schemas.base import parse_timeframe
@@ -18,6 +19,7 @@ from basic_memory.deps import (
     EntityRepositoryV2ExternalDep,
     SearchServiceV2ExternalDep,
     EntityServiceV2ExternalDep,
+    SessionMakerDep,
 )
 from basic_memory.schemas.prompt import (
     ContinueConversationRequest,
@@ -36,6 +38,7 @@ async def continue_conversation(
     entity_service: EntityServiceV2ExternalDep,
     context_service: ContextServiceV2ExternalDep,
     entity_repository: EntityRepositoryV2ExternalDep,
+    session_maker: SessionMakerDep,
     request: ContinueConversationRequest,
     project_id: str = Path(..., description="Project external UUID"),
 ) -> PromptResponse:
@@ -82,9 +85,10 @@ async def continue_conversation(
                 )
 
                 # Process results into the schema format
-                graph_context = await to_graph_context(
-                    context_result, entity_repository=entity_repository
-                )
+                async with db.scoped_session(session_maker) as session:
+                    graph_context = await to_graph_context(
+                        context_result, entity_repository=entity_repository, session=session
+                    )
 
                 # Add results to our collection (limit to top results for each permalink)
                 if graph_context.results:
@@ -109,7 +113,10 @@ async def continue_conversation(
             max_related=request.related_items_limit,
             include_observations=True,
         )
-        recent_context = await to_graph_context(context_result, entity_repository=entity_repository)
+        async with db.scoped_session(session_maker) as session:
+            recent_context = await to_graph_context(
+                context_result, entity_repository=entity_repository, session=session
+            )
 
         hierarchical_results = recent_context.results[:5]  # Limit to top 5 recent items
 

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

@@ -16,11 +16,14 @@ from fastapi import APIRouter, HTTPException, Response, Path
 from loguru import logger
 
 import logfire
+from basic_memory import db
 from basic_memory.deps import (
     ProjectConfigV2ExternalDep,
     FileServiceV2ExternalDep,
     EntityRepositoryV2ExternalDep,
     SearchServiceV2ExternalDep,
+    SessionDep,
+    SessionMakerDep,
 )
 from basic_memory.models.knowledge import Entity as EntityModel
 from basic_memory.schemas.v2.resource import (
@@ -38,6 +41,7 @@ async def get_resource_content(
     config: ProjectConfigV2ExternalDep,
     entity_repository: EntityRepositoryV2ExternalDep,
     file_service: FileServiceV2ExternalDep,
+    session: SessionDep,
     project_id: str = Path(..., description="Project external UUID"),
     entity_id: str = Path(..., description="Entity external UUID"),
 ) -> Response:
@@ -70,7 +74,7 @@ async def get_resource_content(
             action="get_content",
             phase="load_entity",
         ):
-            entity = await entity_repository.get_by_external_id(entity_id)
+            entity = await entity_repository.get_by_external_id(session, entity_id)
         if not entity:
             raise HTTPException(status_code=404, detail=f"Entity {entity_id} not found")
 
@@ -121,6 +125,7 @@ async def create_resource(
     file_service: FileServiceV2ExternalDep,
     entity_repository: EntityRepositoryV2ExternalDep,
     search_service: SearchServiceV2ExternalDep,
+    session_maker: SessionMakerDep,
     project_id: str = Path(..., description="Project external UUID"),
 ) -> ResourceResponse:
     """Create a new resource file.
@@ -158,13 +163,14 @@ async def create_resource(
                     "Path must be relative and stay within project boundaries.",
                 )
 
-            existing_entity = await entity_repository.get_by_file_path(data.file_path)
-            if existing_entity:
-                raise HTTPException(
-                    status_code=409,
-                    detail=f"Resource already exists at {data.file_path} with entity_id {existing_entity.external_id}. "
-                    f"Use PUT /resource/{existing_entity.external_id} to update it.",
-                )
+            async with db.scoped_session(session_maker) as session:
+                existing_entity = await entity_repository.get_by_file_path(session, data.file_path)
+                if existing_entity:
+                    raise HTTPException(
+                        status_code=409,
+                        detail=f"Resource already exists at {data.file_path} with entity_id {existing_entity.external_id}. "
+                        f"Use PUT /resource/{existing_entity.external_id} to update it.",
+                    )
 
             with logfire.span(
                 "api.resource.create.write_file",
@@ -203,7 +209,8 @@ async def create_resource(
                 action="create",
                 phase="upsert_entity",
             ):
-                entity = await entity_repository.add(entity)
+                async with db.scoped_session(session_maker) as session:
+                    entity = await entity_repository.add(session, entity)
 
             with logfire.span(
                 "api.resource.create.search_index",
@@ -236,6 +243,7 @@ async def update_resource(
     file_service: FileServiceV2ExternalDep,
     entity_repository: EntityRepositoryV2ExternalDep,
     search_service: SearchServiceV2ExternalDep,
+    session_maker: SessionMakerDep,
     project_id: str = Path(..., description="Project external UUID"),
     entity_id: str = Path(..., description="Entity external UUID"),
 ) -> ResourceResponse:
@@ -265,7 +273,8 @@ async def update_resource(
         action="update",
     ):
         try:
-            entity = await entity_repository.get_by_external_id(entity_id)
+            async with db.scoped_session(session_maker) as session:
+                entity = await entity_repository.get_by_external_id(session, entity_id)
             if not entity:
                 raise HTTPException(status_code=404, detail=f"Entity {entity_id} not found")
 
@@ -315,17 +324,19 @@ async def update_resource(
                 action="update",
                 phase="update_entity",
             ):
-                updated_entity = await entity_repository.update(
-                    entity.id,
-                    {
-                        "title": file_name,
-                        "note_type": note_type,
-                        "content_type": content_type,
-                        "file_path": target_file_path,
-                        "checksum": checksum,
-                        "updated_at": file_metadata.modified_at,
-                    },
-                )
+                async with db.scoped_session(session_maker) as session:
+                    updated_entity = await entity_repository.update(
+                        session,
+                        entity.id,
+                        {
+                            "title": file_name,
+                            "note_type": note_type,
+                            "content_type": content_type,
+                            "file_path": target_file_path,
+                            "checksum": checksum,
+                            "updated_at": file_metadata.modified_at,
+                        },
+                    )
             if updated_entity is None:
                 raise HTTPException(status_code=404, detail=f"Entity {entity_id} not found")
 

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

@@ -13,11 +13,13 @@ from pathlib import Path as FilePath
 import frontmatter
 from fastapi import APIRouter, Path, Query
 from loguru import logger
+from sqlalchemy.ext.asyncio import AsyncSession
 
 from basic_memory.deps import (
     EntityRepositoryV2ExternalDep,
     FileServiceV2ExternalDep,
     LinkResolverV2ExternalDep,
+    SessionDep,
 )
 from basic_memory.models.knowledge import Entity
 from basic_memory.schemas.schema import (
@@ -131,6 +133,7 @@ async def validate_schema(
     entity_repository: EntityRepositoryV2ExternalDep,
     file_service: FileServiceV2ExternalDep,
     link_resolver: LinkResolverV2ExternalDep,
+    session: SessionDep,
     project_id: str = Path(..., description="Project external UUID"),
     note_type: str | None = Query(None, description="Note type to validate"),
     identifier: str | None = Query(None, description="Specific note identifier"),
@@ -150,7 +153,7 @@ async def validate_schema(
     if identifier:
         # Resolve identifier flexibly (permalink, title, path, fuzzy)
         # to match how read_note and other tools resolve identifiers
-        entity = await link_resolver.resolve_link(identifier)
+        entity = await link_resolver.resolve_link(identifier, session=session)
         if not entity:
             return ValidationReport(note_type=note_type, total_notes=0, total_entities=0)
 
@@ -159,6 +162,7 @@ async def validate_schema(
 
         async def search_fn(query: str) -> list[dict]:
             entities = await _find_schema_entities(
+                session,
                 entity_repository,
                 query,
                 allow_reference_match=isinstance(schema_ref, str) and query == schema_ref,
@@ -187,7 +191,7 @@ async def validate_schema(
         )
 
     # --- Batch validation by note type ---
-    entities = await _find_by_note_type(entity_repository, note_type) if note_type else []
+    entities = await _find_by_note_type(session, entity_repository, note_type) if note_type else []
 
     for entity in entities:
         frontmatter = _entity_frontmatter(entity)
@@ -195,6 +199,7 @@ async def validate_schema(
 
         async def search_fn(query: str) -> list[dict]:
             entities = await _find_schema_entities(
+                session,
                 entity_repository,
                 query,
                 allow_reference_match=isinstance(schema_ref, str) and query == schema_ref,
@@ -230,6 +235,7 @@ async def validate_schema(
 @router.post("/schema/infer", response_model=InferenceReport)
 async def infer_schema_endpoint(
     entity_repository: EntityRepositoryV2ExternalDep,
+    session: SessionDep,
     project_id: str = Path(..., description="Project external UUID"),
     note_type: str = Query(..., description="Note type to analyze"),
     threshold: float = Query(0.25, description="Minimum frequency for optional fields"),
@@ -239,7 +245,7 @@ async def infer_schema_endpoint(
     Examines observation categories and relation types across all notes
     of the given type. Returns frequency analysis and suggested Picoschema.
     """
-    entities = await _find_by_note_type(entity_repository, note_type)
+    entities = await _find_by_note_type(session, entity_repository, note_type)
     notes_data = [_entity_to_note_data(entity) for entity in entities]
 
     result = infer_schema(note_type, notes_data, optional_threshold=threshold)
@@ -274,6 +280,7 @@ async def infer_schema_endpoint(
 async def diff_schema_endpoint(
     entity_repository: EntityRepositoryV2ExternalDep,
     file_service: FileServiceV2ExternalDep,
+    session: SessionDep,
     note_type: str = Path(..., description="Note type to check for drift"),
     project_id: str = Path(..., description="Project external UUID"),
 ):
@@ -285,7 +292,7 @@ async def diff_schema_endpoint(
     """
 
     async def search_fn(query: str) -> list[dict]:
-        entities = await _find_schema_entities(entity_repository, query)
+        entities = await _find_schema_entities(session, entity_repository, query)
         return [await _schema_frontmatter_from_file(file_service, e) for e in entities]
 
     # Resolve schema by note type
@@ -296,7 +303,7 @@ async def diff_schema_endpoint(
         return DriftReport(note_type=note_type, schema_found=False)
 
     # Collect all notes of this type
-    entities = await _find_by_note_type(entity_repository, note_type)
+    entities = await _find_by_note_type(session, entity_repository, note_type)
     notes_data = [_entity_to_note_data(entity) for entity in entities]
 
     result = diff_schema(schema_def, notes_data)
@@ -331,16 +338,18 @@ async def diff_schema_endpoint(
 
 
 async def _find_by_note_type(
+    session: AsyncSession,
     entity_repository: EntityRepositoryV2ExternalDep,
     note_type: str,
 ) -> list[Entity]:
     """Find all entities of a given type using the repository's select pattern."""
     query = entity_repository.select().where(Entity.note_type == note_type)
-    result = await entity_repository.execute_query(query)
+    result = await entity_repository.execute_query(session, query)
     return list(result.scalars().all())
 
 
 async def _find_schema_entities(
+    session: AsyncSession,
     entity_repository: EntityRepositoryV2ExternalDep,
     target_note_type: str,
     *,
@@ -355,7 +364,7 @@ async def _find_schema_entities(
        exact reference matching by title/permalink (explicit schema references)
     """
     query = entity_repository.select().where(Entity.note_type == "schema")
-    result = await entity_repository.execute_query(query)
+    result = await entity_repository.execute_query(session, query)
     entities = list(result.scalars().all())
 
     normalized_target = generate_permalink(target_note_type)

src/basic_memory/api/v2/utils.py

@@ -1,6 +1,7 @@
 from typing import Any, Protocol, Optional, List, Sequence
 
 import logfire
+from sqlalchemy.ext.asyncio import AsyncSession
 from basic_memory.repository.search_repository import SearchIndexRow
 from basic_memory.schemas.memory import (
     EntitySummary,
@@ -19,7 +20,11 @@ from basic_memory.services.context_service import (
 
 class EntityBatchLookup(Protocol):
     async def find_by_ids_for_hydration(
-        self, ids: List[int], *, include_cross_project: bool = False
+        self,
+        session: AsyncSession,
+        ids: List[int],
+        *,
+        include_cross_project: bool = False,
     ) -> Sequence[Any]: ...
 
 
@@ -42,6 +47,7 @@ def _search_item_type(value: str | SearchItemType) -> SearchItemType:
 async def to_graph_context(
     context_result: ServiceContextResult,
     entity_repository: EntityBatchLookup,
+    session: AsyncSession,
     page: Optional[int] = None,
     page_size: Optional[int] = None,
 ) -> GraphContext:
@@ -90,7 +96,7 @@ async def to_graph_context(
                 result_count=len(entity_ids_needed),
             ):
                 entities = await entity_repository.find_by_ids_for_hydration(
-                    list(entity_ids_needed), include_cross_project=True
+                    session, list(entity_ids_needed), include_cross_project=True
                 )
             for e in entities:
                 entity_title_lookup[e.id] = e.title
@@ -147,6 +153,7 @@ async def to_graph_context(
                         from_entity_id=item.from_id,
                         from_entity_external_id=from_ext_id,
                         to_entity=to_title,
+                        to_name=item.to_name,
                         to_entity_id=item.to_id,
                         to_entity_external_id=to_ext_id,
                         created_at=item.created_at,

src/basic_memory/cli/app.py

@@ -83,8 +83,11 @@ def app_callback(
     # Skip for 'mcp' command - it has its own lifespan that handles initialization
     # Skip for API-using commands (status, sync, etc.) - they handle initialization via deps.py
     # Skip for 'reset' command - it manages its own database lifecycle
+    # Skip for 'man' - it only copies packaged files; a broken local database
+    # must not block installing the offline docs
     skip_init_commands = {
         "doctor",
+        "man",
         "mcp",
         "status",
         "sync",

src/basic_memory/cli/auto_update.py

@@ -168,6 +168,20 @@ def _manual_update_hint(source: InstallSource) -> str:
     )
 
 
+def _preload_lazy_console_modules() -> None:
+    """Import modules the post-upgrade output path defers until print time.
+
+    Trigger: an in-place upgrade is about to replace this installation on disk.
+    Why: rich and typer defer some imports until print/excepthook time; once
+    `brew upgrade` / `uv tool upgrade` removes the running version's files,
+    those imports raise ModuleNotFoundError and the final status message
+    crashes the exiting process.
+    Outcome: import the deferred modules now, while the files still exist.
+    """
+    import rich._emoji_codes  # noqa: F401
+    import typer.rich_utils  # noqa: F401
+
+
 def _save_last_checked_timestamp(config_manager: ConfigManager, checked_at: datetime) -> None:
     """Persist the timestamp for the most recent attempted update check."""
     config = config_manager.load_config()
@@ -288,6 +302,7 @@ def run_auto_update(
             else BREW_UPGRADE_TIMEOUT_SECONDS
         )
 
+        _preload_lazy_console_modules()
         install_result = _run_subprocess(
             command,
             timeout_seconds=timeout,

src/basic_memory/cli/commands/__init__.py

@@ -4,6 +4,7 @@ from . import ci, status, db, doctor, import_memory_json, mcp, import_claude_con
 from . import (
     import_claude_projects,
     import_chatgpt,
+    man,
     tool,
     project,
     format,
@@ -29,4 +30,5 @@ __all__ = [
     "schema",
     "update",
     "workspace",
+    "man",
 ]

src/basic_memory/cli/commands/ci.py

@@ -34,8 +34,10 @@ from basic_memory.ci.project_updates import (
 from basic_memory.cli.app import app
 from basic_memory.cli.commands.command_utils import run_with_cleanup
 from basic_memory.cli.commands.routing import force_routing, validate_routing_flags
-from basic_memory.mcp.tools import search_notes as mcp_search_notes
-from basic_memory.mcp.tools import write_note as mcp_write_note
+
+# MCP tool functions are imported inside the async helpers below: importing
+# basic_memory.mcp.tools loads the entire tool stack (fastmcp, mcp SDK,
+# SQLAlchemy), which would slow every CLI invocation, including --help (#886).
 
 
 console = Console()
@@ -252,6 +254,10 @@ async def seed_project_update_schemas(
     refresh: bool = False,
 ) -> list[str]:
     """Seed Auto BM schema notes without overwriting customized schemas."""
+    # Deferred: loading the MCP tool stack at module import slows CLI startup (#886).
+    from basic_memory.mcp.tools import search_notes as mcp_search_notes
+    from basic_memory.mcp.tools import write_note as mcp_write_note
+
     seeded: list[str] = []
     routed_project = _routed_project(project=project, project_id=project_id, workspace=workspace)
     for spec in schema_seed_specs():
@@ -295,6 +301,10 @@ async def publish_project_update_note(
     note: ProjectUpdateNote,
 ) -> dict[str, Any]:
     """Search by idempotency key and then upsert the deterministic note path."""
+    # Deferred: loading the MCP tool stack at module import slows CLI startup (#886).
+    from basic_memory.mcp.tools import search_notes as mcp_search_notes
+    from basic_memory.mcp.tools import write_note as mcp_write_note
+
     routed_project = _routed_project(
         project=config.project,
         project_id=config.project_id,

src/basic_memory/cli/commands/command_utils.py

@@ -3,12 +3,10 @@
 import asyncio
 from typing import Optional, TypeVar, Coroutine, Any
 
-from mcp.server.fastmcp.exceptions import ToolError
 import typer
 
 from rich.console import Console
 
-from basic_memory import db
 from basic_memory.config import ConfigManager
 from basic_memory.mcp.async_client import get_client
 from basic_memory.mcp.clients import ProjectClient
@@ -31,6 +29,9 @@ def run_with_cleanup(coro: Coroutine[Any, Any, T]) -> T:
     Returns:
         The result of the coroutine
     """
+    # Deferred: basic_memory.db pulls SQLAlchemy + Alembic, which must not load
+    # at CLI import time — only when a command actually runs (#886).
+    from basic_memory import db
 
     async def _with_cleanup() -> T:
         try:
@@ -53,6 +54,8 @@ async def run_sync(
         force_full: If True, force a full scan bypassing watermark optimization
         run_in_background: If True, return immediately; if False, wait for completion
     """
+    # Deferred: ToolError lives in the mcp SDK, which must not load at CLI startup (#886).
+    from mcp.server.fastmcp.exceptions import ToolError
 
     # Resolve default project so get_client() can route per-project
     project = project or ConfigManager().default_project
@@ -86,6 +89,9 @@ async def run_sync(
 
 async def get_project_info(project: str):
     """Get project information via API endpoint."""
+    # Deferred: ToolError lives in the mcp SDK, which must not load at CLI startup (#886).
+    from mcp.server.fastmcp.exceptions import ToolError
+
     try:
         async with get_client(project_name=project) as client:
             project_item = await get_active_project(client, project, None)

src/basic_memory/cli/commands/db.py

@@ -1,24 +1,27 @@
 """Database management commands."""
 
+# PEP 563 lazy annotations let signatures reference IndexProgress without importing
+# the indexing stack at module load; reset/reindex import their heavy database and
+# sync dependencies at call time so CLI startup stays fast (#886).
+from __future__ import annotations
+
 import os
 from dataclasses import dataclass
 from pathlib import Path, PurePosixPath, PureWindowsPath
+from typing import TYPE_CHECKING
 
 import psutil
 import typer
 from loguru import logger
 from rich.console import Console
 from rich.progress import Progress, SpinnerColumn, TextColumn, BarColumn, TaskProgressColumn
-from sqlalchemy.exc import OperationalError
 
-from basic_memory import db
 from basic_memory.cli.app import app
 from basic_memory.cli.commands.command_utils import run_with_cleanup
 from basic_memory.config import ConfigManager, ProjectMode
-from basic_memory.indexing import IndexProgress
-from basic_memory.repository import ProjectRepository
-from basic_memory.services.initialization import reconcile_projects_with_config
-from basic_memory.sync.sync_service import get_sync_service
+
+if TYPE_CHECKING:
+    from basic_memory.indexing import IndexProgress
 
 console = Console()
 
@@ -159,6 +162,13 @@ async def _reindex_projects(app_config):
     This ensures all database operations use the same event loop,
     and proper cleanup happens when the function completes.
     """
+    # Deferred: SQLAlchemy, repositories, and the sync stack load only when a
+    # reindex actually runs, not on every CLI start (#886).
+    from basic_memory import db
+    from basic_memory.repository import ProjectRepository
+    from basic_memory.services.initialization import reconcile_projects_with_config
+    from basic_memory.sync.sync_service import get_sync_service
+
     try:
         await reconcile_projects_with_config(app_config)
 
@@ -167,8 +177,9 @@ async def _reindex_projects(app_config):
             db_path=app_config.database_path,
             db_type=db.DatabaseType.FILESYSTEM,
         )
-        project_repository = ProjectRepository(session_maker)
-        projects = await project_repository.get_active_projects()
+        project_repository = ProjectRepository()
+        async with db.scoped_session(session_maker) as session:
+            projects = await project_repository.get_active_projects(session)
 
         for project in projects:
             console.print(f"  Indexing [cyan]{project.name}[/cyan]...")
@@ -197,6 +208,12 @@ def reset(
     ),
 ):  # pragma: no cover
     """Reset database (drop all tables and recreate)."""
+    # Deferred: SQLAlchemy and the db module load only when a reset actually
+    # runs, not on every CLI start (#886).
+    from sqlalchemy.exc import OperationalError
+
+    from basic_memory import db
+
     console.print(
         "[yellow]Note:[/yellow] This only deletes the index database. "
         "Your markdown note files will not be affected.\n"
@@ -320,10 +337,15 @@ async def _reindex(
     project: str | None,
 ):
     """Run reindex operations."""
-    from basic_memory.repository import EntityRepository
+    # Deferred: SQLAlchemy, repositories, and the sync stack load only when a
+    # reindex actually runs, not on every CLI start (#886).
+    from basic_memory import db
+    from basic_memory.repository import EntityRepository, ProjectRepository
     from basic_memory.repository.search_repository import create_search_repository
+    from basic_memory.services.initialization import reconcile_projects_with_config
     from basic_memory.services.search_service import SearchService
     from basic_memory.services.file_service import FileService
+    from basic_memory.sync.sync_service import get_sync_service
     from basic_memory.markdown.markdown_processor import MarkdownProcessor
     from basic_memory.markdown.entity_parser import EntityParser
 
@@ -334,8 +356,9 @@ async def _reindex(
             db_path=app_config.database_path,
             db_type=db.DatabaseType.FILESYSTEM,
         )
-        project_repository = ProjectRepository(session_maker)
-        projects = await project_repository.get_active_projects()
+        project_repository = ProjectRepository()
+        async with db.scoped_session(session_maker) as session:
+            projects = await project_repository.get_active_projects(session)
 
         if project:
             projects = [p for p in projects if p.name == project]
@@ -397,7 +420,7 @@ async def _reindex(
                 console.print(
                     f"  Building vector embeddings ([cyan]{embedding_mode_label}[/cyan])..."
                 )
-                entity_repository = EntityRepository(session_maker, project_id=proj.id)
+                entity_repository = EntityRepository(project_id=proj.id)
                 search_repository = create_search_repository(
                     session_maker, project_id=proj.id, app_config=app_config
                 )
@@ -405,7 +428,12 @@ async def _reindex(
                 entity_parser = EntityParser(project_path)
                 markdown_processor = MarkdownProcessor(entity_parser, app_config=app_config)
                 file_service = FileService(project_path, markdown_processor, app_config=app_config)
-                search_service = SearchService(search_repository, entity_repository, file_service)
+                search_service = SearchService(
+                    search_repository,
+                    entity_repository,
+                    file_service,
+                    session_maker=session_maker,
+                )
 
                 with Progress(
                     SpinnerColumn(),

src/basic_memory/cli/commands/doctor.py

@@ -7,16 +7,12 @@ import uuid
 from pathlib import Path
 
 from loguru import logger
-from mcp.server.fastmcp.exceptions import ToolError
 from rich.console import Console
 import typer
 
 from basic_memory.cli.app import app
 from basic_memory.cli.commands.command_utils import run_with_cleanup
 from basic_memory.cli.commands.routing import force_routing, validate_routing_flags
-from basic_memory.markdown.entity_parser import EntityParser
-from basic_memory.markdown.markdown_processor import MarkdownProcessor
-from basic_memory.markdown.schemas import EntityFrontmatter, EntityMarkdown
 from basic_memory.mcp.async_client import get_client
 from basic_memory.mcp.clients import KnowledgeClient, ProjectClient, SearchClient
 from basic_memory.schemas.base import Entity
@@ -27,8 +23,72 @@ from basic_memory.schemas import SyncReportResponse
 console = Console()
 
 
+def _is_default_project_delete_error(error: Exception) -> bool:
+    """Return True only for the API guard that blocks deleting the default project."""
+    error_text = str(error)
+    return "Cannot delete default project" in error_text
+
+
+async def _delete_doctor_project_locally(project_name: str, project_id: str) -> None:
+    """Remove the generated doctor project when the public API guard blocks cleanup."""
+    from basic_memory import db
+    from basic_memory.config import ConfigManager
+    from basic_memory.repository import ProjectRepository
+
+    config_manager = ConfigManager()
+    repository = ProjectRepository()
+    _, session_maker = await db.get_or_create_db(
+        db_path=config_manager.config.database_path,
+        db_type=db.DatabaseType.FILESYSTEM,
+    )
+
+    async with db.scoped_session(session_maker) as session:
+        project = await repository.get_by_external_id(session, project_id)
+        if project is None:
+            raise ValueError(f"Doctor cleanup project '{project_id}' not found")
+        if project.name != project_name:
+            raise ValueError(
+                f"Doctor cleanup expected project '{project_name}', found '{project.name}'"
+            )
+        await repository.delete(session, project.id)
+
+    config = config_manager.load_config()
+    if project_name in config.projects:
+        del config.projects[project_name]
+        if config.default_project == project_name:
+            config.default_project = next(iter(config.projects), None)
+        config_manager.save_config(config)
+
+
+async def _delete_doctor_project(
+    project_client: ProjectClient, project_name: str, project_id: str
+) -> None:
+    """Delete the generated doctor project without weakening the public API guard."""
+    # Deferred: ToolError lives in the mcp SDK, which must not load at CLI startup (#886).
+    from mcp.server.fastmcp.exceptions import ToolError
+
+    try:
+        await project_client.delete_project(project_id)
+    except ToolError as exc:
+        if not _is_default_project_delete_error(exc):
+            raise
+
+        # Trigger: fresh local configs can promote the generated doctor project
+        # to default because the placeholder default has no DB row.
+        # Why: the project is disposable doctor-owned state, while the public API
+        # must keep rejecting default-project deletion for normal callers.
+        # Outcome: cleanup removes only the exact doctor project it created.
+        await _delete_doctor_project_locally(project_name, project_id)
+
+
 async def run_doctor() -> None:
     """Run local consistency checks for file <-> database flows."""
+    # Deferred: the markdown parsing stack is only needed while the checks run,
+    # and importing it at module level slows every CLI invocation (#886).
+    from basic_memory.markdown.entity_parser import EntityParser
+    from basic_memory.markdown.markdown_processor import MarkdownProcessor
+    from basic_memory.markdown.schemas import EntityFrontmatter, EntityMarkdown
+
     console.print("[blue]Running Basic Memory doctor checks...[/blue]")
 
     project_name = f"doctor-{uuid.uuid4().hex[:8]}"
@@ -127,7 +187,7 @@ async def run_doctor() -> None:
 
             finally:
                 if project_id:
-                    await project_client.delete_project(project_id)
+                    await _delete_doctor_project(project_client, project_name, project_id)
 
     console.print("[green]Doctor checks passed.[/green]")
 
@@ -140,6 +200,9 @@ def doctor(
     cloud: bool = typer.Option(False, "--cloud", help="Force cloud API routing"),
 ) -> None:
     """Run local consistency checks to verify file/database sync."""
+    # Deferred: ToolError lives in the mcp SDK, which must not load at CLI startup (#886).
+    from mcp.server.fastmcp.exceptions import ToolError
+
     try:
         validate_routing_flags(local, cloud)
         # Doctor runs local filesystem checks — always default to local routing

src/basic_memory/cli/commands/import_chatgpt.py

@@ -1,25 +1,34 @@
 """Import command for ChatGPT conversations."""
 
+# PEP 563 lazy annotations keep heavy importer types out of module import (#886).
+from __future__ import annotations
+
 import json
 from pathlib import Path
-from typing import Annotated, Tuple
+from typing import TYPE_CHECKING, Annotated, Tuple
 
 import typer
 from basic_memory.cli.app import import_app
 from basic_memory.cli.commands.command_utils import run_with_cleanup
 from basic_memory.config import ConfigManager, get_project_config
-from basic_memory.importers import ChatGPTImporter
-from basic_memory.markdown import EntityParser, MarkdownProcessor
-from basic_memory.services.file_service import FileService
 from loguru import logger
 from rich.console import Console
 from rich.panel import Panel
 
+if TYPE_CHECKING:
+    from basic_memory.markdown import MarkdownProcessor
+    from basic_memory.services.file_service import FileService
+
 console = Console()
 
 
 async def get_importer_dependencies() -> Tuple[MarkdownProcessor, FileService]:
     """Get MarkdownProcessor and FileService instances for importers."""
+    # Deferred: the markdown/file-service stack pulls SQLAlchemy and must load
+    # only when an import actually runs, not on every CLI start (#886).
+    from basic_memory.markdown import EntityParser, MarkdownProcessor
+    from basic_memory.services.file_service import FileService
+
     config = get_project_config()
     app_config = ConfigManager().config
     entity_parser = EntityParser(config.home)
@@ -60,6 +69,9 @@ def import_chatgpt(
         console.print(f"\nImporting chats from {conversations_json}...writing to {base_path}")
 
         # Create importer and run import
+        # Deferred: importer stack loads at import-command run time only (#886).
+        from basic_memory.importers import ChatGPTImporter
+
         importer = ChatGPTImporter(
             config.home, markdown_processor, file_service, project_name=config.name
         )

src/basic_memory/cli/commands/import_claude_conversations.py

@@ -1,25 +1,34 @@
 """Import command for basic-memory CLI to import chat data from conversations2.json format."""
 
+# PEP 563 lazy annotations keep heavy importer types out of module import (#886).
+from __future__ import annotations
+
 import json
 from pathlib import Path
-from typing import Annotated, Tuple
+from typing import TYPE_CHECKING, Annotated, Tuple
 
 import typer
 from basic_memory.cli.app import claude_app
 from basic_memory.cli.commands.command_utils import run_with_cleanup
 from basic_memory.config import ConfigManager, get_project_config
-from basic_memory.importers.claude_conversations_importer import ClaudeConversationsImporter
-from basic_memory.markdown import EntityParser, MarkdownProcessor
-from basic_memory.services.file_service import FileService
 from loguru import logger
 from rich.console import Console
 from rich.panel import Panel
 
+if TYPE_CHECKING:
+    from basic_memory.markdown import MarkdownProcessor
+    from basic_memory.services.file_service import FileService
+
 console = Console()
 
 
 async def get_importer_dependencies() -> Tuple[MarkdownProcessor, FileService]:
     """Get MarkdownProcessor and FileService instances for importers."""
+    # Deferred: the markdown/file-service stack pulls SQLAlchemy and must load
+    # only when an import actually runs, not on every CLI start (#886).
+    from basic_memory.markdown import EntityParser, MarkdownProcessor
+    from basic_memory.services.file_service import FileService
+
     config = get_project_config()
     app_config = ConfigManager().config
     entity_parser = EntityParser(config.home)
@@ -57,6 +66,9 @@ def import_claude(
         markdown_processor, file_service = run_with_cleanup(get_importer_dependencies())
 
         # Create the importer
+        # Deferred: importer stack loads at import-command run time only (#886).
+        from basic_memory.importers.claude_conversations_importer import ClaudeConversationsImporter
+
         importer = ClaudeConversationsImporter(
             config.home, markdown_processor, file_service, project_name=config.name
         )

src/basic_memory/cli/commands/import_claude_projects.py

@@ -1,25 +1,34 @@
 """Import command for basic-memory CLI to import project data from Claude.ai."""
 
+# PEP 563 lazy annotations keep heavy importer types out of module import (#886).
+from __future__ import annotations
+
 import json
 from pathlib import Path
-from typing import Annotated, Tuple
+from typing import TYPE_CHECKING, Annotated, Tuple
 
 import typer
 from basic_memory.cli.app import claude_app
 from basic_memory.cli.commands.command_utils import run_with_cleanup
 from basic_memory.config import ConfigManager, get_project_config
-from basic_memory.importers.claude_projects_importer import ClaudeProjectsImporter
-from basic_memory.markdown import EntityParser, MarkdownProcessor
-from basic_memory.services.file_service import FileService
 from loguru import logger
 from rich.console import Console
 from rich.panel import Panel
 
+if TYPE_CHECKING:
+    from basic_memory.markdown import MarkdownProcessor
+    from basic_memory.services.file_service import FileService
+
 console = Console()
 
 
 async def get_importer_dependencies() -> Tuple[MarkdownProcessor, FileService]:
     """Get MarkdownProcessor and FileService instances for importers."""
+    # Deferred: the markdown/file-service stack pulls SQLAlchemy and must load
+    # only when an import actually runs, not on every CLI start (#886).
+    from basic_memory.markdown import EntityParser, MarkdownProcessor
+    from basic_memory.services.file_service import FileService
+
     config = get_project_config()
     app_config = ConfigManager().config
     entity_parser = EntityParser(config.home)
@@ -56,6 +65,9 @@ def import_projects(
         markdown_processor, file_service = run_with_cleanup(get_importer_dependencies())
 
         # Create the importer
+        # Deferred: importer stack loads at import-command run time only (#886).
+        from basic_memory.importers.claude_projects_importer import ClaudeProjectsImporter
+
         importer = ClaudeProjectsImporter(
             config.home, markdown_processor, file_service, project_name=config.name
         )

src/basic_memory/cli/commands/import_memory_json.py

@@ -1,25 +1,34 @@
 """Import command for basic-memory CLI to import from JSON memory format."""
 
+# PEP 563 lazy annotations keep heavy importer types out of module import (#886).
+from __future__ import annotations
+
 import json
 from pathlib import Path
-from typing import Annotated, Tuple
+from typing import TYPE_CHECKING, Annotated, Tuple
 
 import typer
 from basic_memory.cli.app import import_app
 from basic_memory.cli.commands.command_utils import run_with_cleanup
 from basic_memory.config import ConfigManager, get_project_config
-from basic_memory.importers.memory_json_importer import MemoryJsonImporter
-from basic_memory.markdown import EntityParser, MarkdownProcessor
-from basic_memory.services.file_service import FileService
 from loguru import logger
 from rich.console import Console
 from rich.panel import Panel
 
+if TYPE_CHECKING:
+    from basic_memory.markdown import MarkdownProcessor
+    from basic_memory.services.file_service import FileService
+
 console = Console()
 
 
 async def get_importer_dependencies() -> Tuple[MarkdownProcessor, FileService]:
     """Get MarkdownProcessor and FileService instances for importers."""
+    # Deferred: the markdown/file-service stack pulls SQLAlchemy and must load
+    # only when an import actually runs, not on every CLI start (#886).
+    from basic_memory.markdown import EntityParser, MarkdownProcessor
+    from basic_memory.services.file_service import FileService
+
     config = get_project_config()
     app_config = ConfigManager().config
     entity_parser = EntityParser(config.home)
@@ -55,6 +64,9 @@ def memory_json(
         markdown_processor, file_service = run_with_cleanup(get_importer_dependencies())
 
         # Create the importer
+        # Deferred: importer stack loads at import-command run time only (#886).
+        from basic_memory.importers.memory_json_importer import MemoryJsonImporter
+
         importer = MemoryJsonImporter(
             config.home, markdown_processor, file_service, project_name=config.name
         )

src/basic_memory/cli/commands/man.py

@@ -0,0 +1,76 @@
+"""Install the bundled man pages so `man bm` works."""
+
+import shutil
+import subprocess
+from pathlib import Path
+from typing import Annotated, Optional
+
+import typer
+from rich.console import Console
+
+from basic_memory.cli.app import app
+
+console = Console()
+
+man_app = typer.Typer(help="Manage the bm man pages.")
+app.add_typer(man_app, name="man")
+
+# Bundled groff sources ship inside the package (src/basic_memory/man).
+_MAN_SOURCE_DIR = Path(__file__).parent.parent.parent / "man"
+
+
+def _default_man_root() -> Path:
+    # Why ~/.local/share/man: manpath(1) derives man directories from PATH
+    # entries on both man-db (Linux) and BSD man (macOS), so ~/.local/bin on
+    # PATH — the pipx/uv tool layout — makes this root searchable without any
+    # MANPATH configuration.
+    return Path.home() / ".local" / "share" / "man"
+
+
+def _man_root_on_manpath(man_root: Path) -> Optional[bool]:
+    """Best-effort check whether man(1) will search man_root; None if unknown."""
+    try:
+        result = subprocess.run(["manpath"], capture_output=True, text=True, timeout=5)
+    except (FileNotFoundError, subprocess.TimeoutExpired):
+        return None
+    if result.returncode != 0:
+        return None
+    paths = [entry.rstrip("/") for entry in result.stdout.strip().split(":") if entry]
+    return str(man_root).rstrip("/") in paths
+
+
+@man_app.command()
+def install(
+    directory: Annotated[
+        Optional[Path],
+        typer.Option(
+            "--dir",
+            help="Man root to install into (default: ~/.local/share/man)",
+        ),
+    ] = None,
+) -> None:
+    """Install the bm man pages, then try `man bm`."""
+    man_root = (directory or _default_man_root()).expanduser()
+    man1 = man_root / "man1"
+    man1.mkdir(parents=True, exist_ok=True)
+
+    pages = sorted(_MAN_SOURCE_DIR.glob("*.1"))
+    if not pages:  # pragma: no cover - broken packaging, not a runtime state
+        console.print("[red]No bundled man pages found — broken installation[/red]")
+        raise typer.Exit(1)
+
+    for page in pages:
+        shutil.copyfile(page, man1 / page.name)
+        console.print(f"installed {man1 / page.name}")
+
+    # Trigger: the chosen root is provably absent from manpath output.
+    # Why: a silent install into an unsearched directory looks like success
+    #   but `man bm` still fails; say so and hand over the one-line fix.
+    # Outcome: actionable hint; unknown (None) stays quiet to avoid false alarms.
+    if _man_root_on_manpath(man_root) is False:
+        console.print(
+            f"\n[yellow]{man_root} is not on your manpath.[/yellow] Add it with:\n"
+            f'  export MANPATH="{man_root}:$MANPATH"'
+        )
+
+    console.print("\nTry: [bold]man bm[/bold]")

src/basic_memory/cli/commands/orphans.py

@@ -5,7 +5,6 @@ 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
 
@@ -50,6 +49,9 @@ def orphans(
     """
     from basic_memory.cli.commands.command_utils import run_with_cleanup
 
+    # Deferred: ToolError lives in the mcp SDK, which must not load at CLI startup (#886).
+    from mcp.server.fastmcp.exceptions import ToolError
+
     try:
         validate_routing_flags(local, cloud)
         with force_routing(local=local, cloud=cloud):

src/basic_memory/cli/commands/project.py

@@ -1050,12 +1050,13 @@ async def _detach_local_project_row(app_config: BasicMemoryConfig, name: str) ->
         db_type=db.DatabaseType.FILESYSTEM,
     )
     try:
-        repo = ProjectRepository(session_maker)
-        existing = await repo.get_by_name(name)
-        if existing is None:
-            return False
-        await repo.delete(existing.id)
-        return True
+        repo = ProjectRepository()
+        async with db.scoped_session(session_maker) as session:
+            existing = await repo.get_by_name(session, name)
+            if existing is None:
+                return False
+            await repo.delete(session, existing.id)
+            return True
     finally:
         # CLI-only: safe to tear down the global DB singleton here since
         # set-cloud/set-local never run inside a long-lived MCP/API server.
@@ -1082,20 +1083,22 @@ async def _attach_local_project_row(app_config: BasicMemoryConfig, name: str, pa
         db_type=db.DatabaseType.FILESYSTEM,
     )
     try:
-        repo = ProjectRepository(session_maker)
-        existing = await repo.get_by_name(name)
-        if existing is None:
-            await repo.create(
-                {
-                    "name": name,
-                    "path": path,
-                    "permalink": generate_permalink(name),
-                    "is_active": True,
-                }
-            )
-            return
-        if existing.path != path:
-            await repo.update_path(existing.id, path)
+        repo = ProjectRepository()
+        async with db.scoped_session(session_maker) as session:
+            existing = await repo.get_by_name(session, name)
+            if existing is None:
+                await repo.create(
+                    session,
+                    {
+                        "name": name,
+                        "path": path,
+                        "permalink": generate_permalink(name),
+                        "is_active": True,
+                    },
+                )
+                return
+            if existing.path != path:
+                await repo.update_path(session, existing.id, path)
     finally:
         # CLI-only: safe to tear down the global DB singleton here since
         # set-cloud/set-local never run inside a long-lived MCP/API server.

src/basic_memory/cli/commands/schema.py

@@ -20,9 +20,10 @@ from basic_memory.cli.app import app
 from basic_memory.cli.commands.command_utils import run_with_cleanup
 from basic_memory.cli.commands.routing import force_routing, validate_routing_flags
 from basic_memory.config import ConfigManager
-from basic_memory.mcp.tools import schema_diff as mcp_schema_diff
-from basic_memory.mcp.tools import schema_infer as mcp_schema_infer
-from basic_memory.mcp.tools import schema_validate as mcp_schema_validate
+
+# MCP tool functions are imported inside each command: importing
+# basic_memory.mcp.tools loads the entire tool stack (fastmcp, mcp SDK,
+# SQLAlchemy), which would slow every CLI invocation, including --help (#886).
 
 console = Console()
 
@@ -189,6 +190,9 @@ def validate(
     Use --local to force local routing when cloud mode is enabled.
     Use --cloud to force cloud routing when cloud mode is disabled.
     """
+    # Deferred: loading the MCP tool stack at module import slows CLI startup (#886).
+    from basic_memory.mcp.tools import schema_validate as mcp_schema_validate
+
     try:
         validate_routing_flags(local, cloud)
         project_name = _resolve_project_name(project)
@@ -272,6 +276,9 @@ def infer(
     Use --local to force local routing when cloud mode is enabled.
     Use --cloud to force cloud routing when cloud mode is disabled.
     """
+    # Deferred: loading the MCP tool stack at module import slows CLI startup (#886).
+    from basic_memory.mcp.tools import schema_infer as mcp_schema_infer
+
     try:
         validate_routing_flags(local, cloud)
         project_name = _resolve_project_name(project)
@@ -352,6 +359,9 @@ def diff(
     Use --local to force local routing when cloud mode is enabled.
     Use --cloud to force cloud routing when cloud mode is disabled.
     """
+    # Deferred: loading the MCP tool stack at module import slows CLI startup (#886).
+    from basic_memory.mcp.tools import schema_diff as mcp_schema_diff
+
     try:
         validate_routing_flags(local, cloud)
         project_name = _resolve_project_name(project)

src/basic_memory/cli/commands/status.py

@@ -5,7 +5,6 @@ import json
 import time
 from typing import Annotated, Dict, Optional, Set
 
-from mcp.server.fastmcp.exceptions import ToolError
 import typer
 from loguru import logger
 from rich.console import Console
@@ -190,9 +189,16 @@ async def run_status(
             if sync_report.total == 0:
                 return project_item.name, sync_report
             if time.monotonic() >= deadline:
+                # Why the hint: indexing is done by the sync coordinator, which
+                # only runs inside a live server (bm mcp / hosted API). In a
+                # CLI-only session nothing will ever drain the pending count,
+                # so this wait cannot succeed — point at the command that
+                # actually indexes (#959).
                 raise StatusTimeout(
                     f"Timed out after {timeout:g}s waiting for '{project_item.name}' "
-                    f"to finish indexing ({sync_report.total} pending change(s) remaining)."
+                    f"to finish indexing ({sync_report.total} pending change(s) remaining). "
+                    f"If no Basic Memory server is running, pending changes are never "
+                    f"indexed — run 'bm reindex --project {project_item.name}' instead."
                 )
             await asyncio.sleep(poll_interval)
 
@@ -224,6 +230,9 @@ def status(
     """
     from basic_memory.cli.commands.command_utils import run_with_cleanup
 
+    # Deferred: ToolError lives in the mcp SDK, which must not load at CLI startup (#886).
+    from mcp.server.fastmcp.exceptions import ToolError
+
     # Trigger: --wait with a negative --timeout
     # Why: a negative deadline times out on the very first poll, producing a confusing
     #      "Timed out after -5s" message instead of flagging the bad input. Raised

src/basic_memory/cli/commands/tool.py

@@ -14,18 +14,10 @@ from loguru import logger
 from basic_memory.cli.app import app
 from basic_memory.cli.commands.command_utils import run_with_cleanup
 from basic_memory.cli.commands.routing import force_routing, validate_routing_flags
-from basic_memory.mcp.tools import build_context as mcp_build_context
-from basic_memory.mcp.tools import delete_note as mcp_delete_note
-from basic_memory.mcp.tools import edit_note as mcp_edit_note
-from basic_memory.mcp.tools import list_memory_projects as mcp_list_projects
-from basic_memory.mcp.tools import list_workspaces as mcp_list_workspaces
-from basic_memory.mcp.tools import read_note as mcp_read_note
-from basic_memory.mcp.tools import recent_activity as mcp_recent_activity
-from basic_memory.mcp.tools import schema_diff as mcp_schema_diff
-from basic_memory.mcp.tools import schema_infer as mcp_schema_infer
-from basic_memory.mcp.tools import schema_validate as mcp_schema_validate
-from basic_memory.mcp.tools import search_notes as mcp_search
-from basic_memory.mcp.tools import write_note as mcp_write_note
+
+# MCP tool functions are imported inside each command: importing
+# basic_memory.mcp.tools loads the entire tool stack (fastmcp, mcp SDK,
+# SQLAlchemy), which would slow every CLI invocation, including --help (#886).
 
 tool_app = typer.Typer()
 app.add_typer(tool_app, name="tool", help="Access to MCP tools via CLI")
@@ -120,6 +112,9 @@ def write_note(
     bm tool write-note --title "My Note" --folder "notes" --overwrite
     bm tool write-note --title "My Note" --folder "notes" --local
     """
+    # Deferred: loading the MCP tool stack at module import slows CLI startup (#886).
+    from basic_memory.mcp.tools import write_note as mcp_write_note
+
     try:
         validate_routing_flags(local, cloud)
 
@@ -206,6 +201,9 @@ def read_note(
     bm tool read-note my-note
     bm tool read-note my-note --include-frontmatter
     """
+    # Deferred: loading the MCP tool stack at module import slows CLI startup (#886).
+    from basic_memory.mcp.tools import read_note as mcp_read_note
+
     try:
         validate_routing_flags(local, cloud)
 
@@ -272,6 +270,9 @@ def delete_note(
     bm tool delete-note notes/old-draft
     bm tool delete-note docs/archive --is-directory
     """
+    # Deferred: loading the MCP tool stack at module import slows CLI startup (#886).
+    from basic_memory.mcp.tools import delete_note as mcp_delete_note
+
     try:
         validate_routing_flags(local, cloud)
 
@@ -346,6 +347,9 @@ def edit_note(
     bm tool edit-note my-note --operation find_replace --find-text "old" --content "new"
     bm tool edit-note my-note --operation replace_section --section "## Notes" --content "updated"
     """
+    # Deferred: loading the MCP tool stack at module import slows CLI startup (#886).
+    from basic_memory.mcp.tools import edit_note as mcp_edit_note
+
     try:
         validate_routing_flags(local, cloud)
 
@@ -413,6 +417,9 @@ def build_context(
     bm tool build-context memory://specs/search
     bm tool build-context specs/search --depth 2 --timeframe 30d
     """
+    # Deferred: loading the MCP tool stack at module import slows CLI startup (#886).
+    from basic_memory.mcp.tools import build_context as mcp_build_context
+
     try:
         validate_routing_flags(local, cloud)
 
@@ -476,6 +483,9 @@ def recent_activity(
     bm tool recent-activity --timeframe 30d --page-size 20
     bm tool recent-activity --type entity --type observation
     """
+    # Deferred: loading the MCP tool stack at module import slows CLI startup (#886).
+    from basic_memory.mcp.tools import recent_activity as mcp_recent_activity
+
     try:
         validate_routing_flags(local, cloud)
 
@@ -582,6 +592,9 @@ def search_notes(
     bm tool search-notes --meta status=draft
     bm tool search-notes "auth" --entity-type observation --category requirement
     """
+    # Deferred: loading the MCP tool stack at module import slows CLI startup (#886).
+    from basic_memory.mcp.tools import search_notes as mcp_search
+
     try:
         validate_routing_flags(local, cloud)
 
@@ -687,6 +700,9 @@ def list_projects(
     bm tool list-projects
     bm tool list-projects --local
     """
+    # Deferred: loading the MCP tool stack at module import slows CLI startup (#886).
+    from basic_memory.mcp.tools import list_memory_projects as mcp_list_projects
+
     try:
         validate_routing_flags(local, cloud)
 
@@ -720,6 +736,9 @@ def list_workspaces(
     bm tool list-workspaces
     bm tool list-workspaces --cloud
     """
+    # Deferred: loading the MCP tool stack at module import slows CLI startup (#886).
+    from basic_memory.mcp.tools import list_workspaces as mcp_list_workspaces
+
     try:
         validate_routing_flags(local, cloud)
 
@@ -772,6 +791,9 @@ def schema_validate(
     bm tool schema-validate people/ada-lovelace.md
     bm tool schema-validate --project research
     """
+    # Deferred: loading the MCP tool stack at module import slows CLI startup (#886).
+    from basic_memory.mcp.tools import schema_validate as mcp_schema_validate
+
     try:
         validate_routing_flags(local, cloud)
 
@@ -840,6 +862,9 @@ def schema_infer(
     bm tool schema-infer meeting --threshold 0.5
     bm tool schema-infer person --project research
     """
+    # Deferred: loading the MCP tool stack at module import slows CLI startup (#886).
+    from basic_memory.mcp.tools import schema_infer as mcp_schema_infer
+
     try:
         validate_routing_flags(local, cloud)
 
@@ -896,6 +921,9 @@ def schema_diff(
     bm tool schema-diff person
     bm tool schema-diff person --project research
     """
+    # Deferred: loading the MCP tool stack at module import slows CLI startup (#886).
+    from basic_memory.mcp.tools import schema_diff as mcp_schema_diff
+
     try:
         validate_routing_flags(local, cloud)
 

src/basic_memory/cli/main.py

@@ -24,6 +24,7 @@ if not _version_only_invocation(sys.argv[1:]):
         import_claude_conversations,
         import_claude_projects,
         import_memory_json,
+        man,
         mcp,
         orphans,
         project,

src/basic_memory/config.py

@@ -4,6 +4,7 @@ import importlib.util
 import json
 import os
 import shutil
+import threading
 from dataclasses import dataclass
 from datetime import datetime
 from enum import Enum
@@ -657,6 +658,26 @@ class BasicMemoryConfig(BaseSettings):
         entry = self.projects.get(project_name)
         return entry.mode if entry else ProjectMode.CLOUD
 
+    def is_locally_syncable(self, project_name: str, project_path: str) -> bool:
+        """Whether a project should be synced/watched on the local filesystem.
+
+        Both conditions are required (issue #949):
+
+          * The project is present in config. Config is the source of truth, so a
+            stale database row that was removed from config — but whose deletion
+            has not yet been reconciled, or whose reconciliation failed — must
+            not be synced even though it still has a real directory on disk.
+          * Its path is absolute. An empty or relative path resolves against the
+            process cwd, so syncing it would adopt whatever directory the server
+            was launched from as the project root and mutate unrelated files.
+
+        Cloud-only projects (empty/slug path) and cloud projects with a real
+        local bisync copy (absolute path) are handled correctly by these two
+        conditions, so no separate mode check is needed.
+        """
+        entry = self.projects.get(project_name)
+        return entry is not None and Path(project_path).is_absolute()
+
     def set_project_mode(self, project_name: str, mode: ProjectMode) -> None:
         """Set the routing mode for a project.
 
@@ -1099,8 +1120,21 @@ def save_basic_memory_config(file_path: Path, config: BasicMemoryConfig) -> None
         _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)
+        # Trigger: long-lived readers (MCP stdio server config reload, background
+        # auto-update threads) re-read config.json whenever its mtime changes,
+        # concurrently with CLI commands saving it.
+        # Why: writing the destination in place truncates it first, so a concurrent
+        # reader can observe empty/partial JSON and load_config() exits the process.
+        # Outcome: write a sibling temp file (unique per process/thread so parallel
+        # savers cannot interleave) and publish atomically via os.replace — readers
+        # always see either the old or the new complete document. (#940)
+        tmp_path = file_path.parent / f"{file_path.name}.{os.getpid()}.{threading.get_ident()}.tmp"
+        try:
+            tmp_path.write_text(json.dumps(config_dict, indent=2))
+            _secure_config_file(tmp_path)
+            os.replace(tmp_path, file_path)
+        finally:
+            tmp_path.unlink(missing_ok=True)
     except Exception as e:  # pragma: no cover
         logger.error(f"Failed to save config: {e}")
 

src/basic_memory/db.py

@@ -19,7 +19,7 @@ from sqlalchemy.ext.asyncio import (
     AsyncEngine,
     async_scoped_session,
 )
-from sqlalchemy.pool import NullPool
+from sqlalchemy.pool import AsyncAdaptedQueuePool, NullPool
 
 from basic_memory.repository.postgres_search_repository import PostgresSearchRepository
 from basic_memory.repository.sqlite_search_repository import SQLiteSearchRepository
@@ -206,29 +206,40 @@ def _create_sqlite_engine(db_url: str, db_type: DatabaseType) -> AsyncEngine:
         Configured async engine for SQLite
     """
     # Configure connection args with Windows-specific settings
-    connect_args: dict[str, bool | float | None] = {"check_same_thread": False}
+    connect_args: dict[str, bool | float] = {"check_same_thread": False}
 
     # Add Windows-specific parameters to improve reliability
     if os.name == "nt":  # Windows
         connect_args.update(
             {
                 "timeout": 30.0,  # Increase timeout to 30 seconds for Windows
-                "isolation_level": None,  # Use autocommit mode
             }
         )
+
+    if db_type == DatabaseType.MEMORY:
+        # Trigger: an in-memory SQLite URL would default to StaticPool, which hands the
+        # same DBAPI connection to every concurrently checked-out session.
+        # Why: concurrent asyncio tasks then share one transaction scope — a rollback
+        # issued by one session (scoped_session exception handling or the pool's
+        # reset-on-return) silently destroys another session's uncommitted writes (#940).
+        # Outcome: a single-connection blocking queue pool keeps the in-memory database
+        # alive for the engine's lifetime while serializing sessions at transaction
+        # granularity, restoring the isolation the repositories assume.
+        engine = create_async_engine(
+            db_url,
+            connect_args=connect_args,
+            poolclass=AsyncAdaptedQueuePool,
+            pool_size=1,
+            max_overflow=0,
+        )
+    elif os.name == "nt":
         # Use NullPool for Windows filesystem databases to avoid connection pooling issues
-        # Important: Do NOT use NullPool for in-memory databases as it will destroy the database
-        # between connections
-        if db_type == DatabaseType.FILESYSTEM:
-            engine = create_async_engine(
-                db_url,
-                connect_args=connect_args,
-                poolclass=NullPool,  # Disable connection pooling on Windows
-                echo=False,
-            )
-        else:
-            # In-memory databases need connection pooling to maintain state
-            engine = create_async_engine(db_url, connect_args=connect_args)
+        engine = create_async_engine(
+            db_url,
+            connect_args=connect_args,
+            poolclass=NullPool,  # Disable connection pooling on Windows
+            echo=False,
+        )
     else:
         engine = create_async_engine(db_url, connect_args=connect_args)
 

src/basic_memory/deps/__init__.py

@@ -25,6 +25,8 @@ from basic_memory.deps.db import (
     EngineFactoryDep,
     get_session_maker,
     SessionMakerDep,
+    get_session,
+    SessionDep,
 )
 
 from basic_memory.deps.projects import (
@@ -169,6 +171,8 @@ __all__ = [
     "EngineFactoryDep",
     "get_session_maker",
     "SessionMakerDep",
+    "get_session",
+    "SessionDep",
     # Projects
     "get_project_repository",
     "ProjectRepositoryDep",

src/basic_memory/deps/db.py

@@ -5,6 +5,7 @@ This module provides database-related dependencies:
 - Session dependencies for request handling
 """
 
+from collections.abc import AsyncGenerator
 from typing import Annotated
 
 from fastapi import Depends, Request
@@ -54,3 +55,12 @@ async def get_session_maker(engine_factory: EngineFactoryDep) -> async_sessionma
 
 
 SessionMakerDep = Annotated[async_sessionmaker, Depends(get_session_maker)]
+
+
+async def get_session(session_maker: SessionMakerDep) -> AsyncGenerator[AsyncSession, None]:
+    """Yield a request-scoped SQLAlchemy session."""
+    async with db.scoped_session(session_maker) as session:
+        yield session
+
+
+SessionDep = Annotated[AsyncSession, Depends(get_session)]

src/basic_memory/deps/projects.py

@@ -12,6 +12,7 @@ from typing import Annotated
 
 from fastapi import Depends, HTTPException, Path, status
 
+from basic_memory import db
 from basic_memory.config import ProjectConfig
 from basic_memory.deps.db import SessionMakerDep
 from basic_memory.repository.project_repository import ProjectRepository
@@ -21,11 +22,9 @@ from basic_memory.utils import generate_permalink
 # --- Project Repository ---
 
 
-async def get_project_repository(
-    session_maker: SessionMakerDep,
-) -> ProjectRepository:
+async def get_project_repository() -> ProjectRepository:
     """Get the project repository."""
-    return ProjectRepository(session_maker)
+    return ProjectRepository()
 
 
 ProjectRepositoryDep = Annotated[ProjectRepository, Depends(get_project_repository)]
@@ -41,6 +40,7 @@ ProjectPathDep = Annotated[str, Path()]
 
 
 async def get_project_id(
+    session_maker: SessionMakerDep,
     project_repository: ProjectRepositoryDep,
     project: ProjectPathDep,
 ) -> int:
@@ -61,14 +61,17 @@ async def get_project_id(
     """
     # Convert project name to permalink for lookup
     project_permalink = generate_permalink(str(project))
-    project_obj = await project_repository.get_by_permalink(project_permalink)
-    if project_obj:
-        return project_obj.id
+    async with db.scoped_session(session_maker) as session:
+        project_obj = await project_repository.get_by_permalink(session, project_permalink)
+        if project_obj:
+            return project_obj.id
 
-    # Try by name if permalink lookup fails
-    project_obj = await project_repository.get_by_name(str(project))  # pragma: no cover
-    if project_obj:  # pragma: no cover
-        return project_obj.id
+        # Try by name if permalink lookup fails
+        project_obj = await project_repository.get_by_name(
+            session, str(project)
+        )  # pragma: no cover
+        if project_obj:  # pragma: no cover
+            return project_obj.id
 
     # Not found
     raise HTTPException(  # pragma: no cover
@@ -83,7 +86,9 @@ ProjectIdDep = Annotated[int, Depends(get_project_id)]
 
 
 async def get_project_config(
-    project: ProjectPathDep, project_repository: ProjectRepositoryDep
+    session_maker: SessionMakerDep,
+    project: ProjectPathDep,
+    project_repository: ProjectRepositoryDep,
 ) -> ProjectConfig:  # pragma: no cover
     """Get the current project referenced from request state.
 
@@ -99,9 +104,10 @@ async def get_project_config(
     """
     # Convert project name to permalink for lookup
     project_permalink = generate_permalink(str(project))
-    project_obj = await project_repository.get_by_permalink(project_permalink)
-    if project_obj:
-        return ProjectConfig(name=project_obj.name, home=pathlib.Path(project_obj.path))
+    async with db.scoped_session(session_maker) as session:
+        project_obj = await project_repository.get_by_permalink(session, project_permalink)
+        if project_obj:
+            return ProjectConfig(name=project_obj.name, home=pathlib.Path(project_obj.path))
 
     # Not found
     raise HTTPException(  # pragma: no cover
@@ -116,6 +122,7 @@ ProjectConfigDep = Annotated[ProjectConfig, Depends(get_project_config)]
 
 
 async def validate_project_id(
+    session_maker: SessionMakerDep,
     project_id: int,
     project_repository: ProjectRepositoryDep,
 ) -> int:
@@ -134,12 +141,13 @@ async def validate_project_id(
     Raises:
         HTTPException: If project with that ID is not found
     """
-    project_obj = await project_repository.get_by_id(project_id)
-    if not project_obj:
-        raise HTTPException(
-            status_code=status.HTTP_404_NOT_FOUND,
-            detail=f"Project with ID {project_id} not found.",
-        )
+    async with db.scoped_session(session_maker) as session:
+        project_obj = await project_repository.get_by_id(session, project_id)
+        if not project_obj:
+            raise HTTPException(
+                status_code=status.HTTP_404_NOT_FOUND,
+                detail=f"Project with ID {project_id} not found.",
+            )
     return project_id
 
 
@@ -147,7 +155,9 @@ ProjectIdPathDep = Annotated[int, Depends(validate_project_id)]
 
 
 async def get_project_config_v2(
-    project_id: ProjectIdPathDep, project_repository: ProjectRepositoryDep
+    session_maker: SessionMakerDep,
+    project_id: ProjectIdPathDep,
+    project_repository: ProjectRepositoryDep,
 ) -> ProjectConfig:  # pragma: no cover
     """Get the project config for v2 API (uses integer project_id from path).
 
@@ -161,9 +171,10 @@ async def get_project_config_v2(
     Raises:
         HTTPException: If project is not found
     """
-    project_obj = await project_repository.get_by_id(project_id)
-    if project_obj:
-        return ProjectConfig(name=project_obj.name, home=pathlib.Path(project_obj.path))
+    async with db.scoped_session(session_maker) as session:
+        project_obj = await project_repository.get_by_id(session, project_id)
+        if project_obj:
+            return ProjectConfig(name=project_obj.name, home=pathlib.Path(project_obj.path))
 
     # Not found (this should not happen since ProjectIdPathDep already validates existence)
     raise HTTPException(  # pragma: no cover
@@ -178,6 +189,7 @@ ProjectConfigV2Dep = Annotated[ProjectConfig, Depends(get_project_config_v2)]
 
 
 async def validate_project_external_id(
+    session_maker: SessionMakerDep,
     project_id: str,
     project_repository: ProjectRepositoryDep,
 ) -> int:
@@ -196,12 +208,13 @@ async def validate_project_external_id(
     Raises:
         HTTPException: If project with that external_id is not found
     """
-    project_obj = await project_repository.get_by_external_id(project_id)
-    if not project_obj:
-        raise HTTPException(
-            status_code=status.HTTP_404_NOT_FOUND,
-            detail=f"Project with external_id '{project_id}' not found.",
-        )
+    async with db.scoped_session(session_maker) as session:
+        project_obj = await project_repository.get_by_external_id(session, project_id)
+        if not project_obj:
+            raise HTTPException(
+                status_code=status.HTTP_404_NOT_FOUND,
+                detail=f"Project with external_id '{project_id}' not found.",
+            )
     return project_obj.id
 
 
@@ -209,7 +222,9 @@ ProjectExternalIdPathDep = Annotated[int, Depends(validate_project_external_id)]
 
 
 async def get_project_config_v2_external(
-    project_id: ProjectExternalIdPathDep, project_repository: ProjectRepositoryDep
+    session_maker: SessionMakerDep,
+    project_id: ProjectExternalIdPathDep,
+    project_repository: ProjectRepositoryDep,
 ) -> ProjectConfig:  # pragma: no cover
     """Get the project config for v2 API (uses external_id UUID from path).
 
@@ -223,9 +238,10 @@ async def get_project_config_v2_external(
     Raises:
         HTTPException: If project is not found
     """
-    project_obj = await project_repository.get_by_id(project_id)
-    if project_obj:
-        return ProjectConfig(name=project_obj.name, home=pathlib.Path(project_obj.path))
+    async with db.scoped_session(session_maker) as session:
+        project_obj = await project_repository.get_by_id(session, project_id)
+        if project_obj:
+            return ProjectConfig(name=project_obj.name, home=pathlib.Path(project_obj.path))
 
     # Not found (this should not happen since ProjectExternalIdPathDep already validates)
     raise HTTPException(  # pragma: no cover

src/basic_memory/deps/repositories.py

@@ -30,33 +30,30 @@ from basic_memory.repository.search_repository import SearchRepository, create_s
 
 
 async def get_entity_repository(
-    session_maker: SessionMakerDep,
     project_id: ProjectIdDep,
 ) -> EntityRepository:
     """Create an EntityRepository instance for the current project."""
-    return EntityRepository(session_maker, project_id=project_id)
+    return EntityRepository(project_id=project_id)
 
 
 EntityRepositoryDep = Annotated[EntityRepository, Depends(get_entity_repository)]
 
 
 async def get_entity_repository_v2(  # pragma: no cover
-    session_maker: SessionMakerDep,
     project_id: ProjectIdPathDep,
 ) -> EntityRepository:
     """Create an EntityRepository instance for v2 API (uses integer project_id from path)."""
-    return EntityRepository(session_maker, project_id=project_id)
+    return EntityRepository(project_id=project_id)
 
 
 EntityRepositoryV2Dep = Annotated[EntityRepository, Depends(get_entity_repository_v2)]
 
 
 async def get_entity_repository_v2_external(
-    session_maker: SessionMakerDep,
     project_id: ProjectExternalIdPathDep,
 ) -> EntityRepository:
     """Create an EntityRepository instance for v2 API (uses external_id from path)."""
-    return EntityRepository(session_maker, project_id=project_id)
+    return EntityRepository(project_id=project_id)
 
 
 EntityRepositoryV2ExternalDep = Annotated[
@@ -68,22 +65,20 @@ EntityRepositoryV2ExternalDep = Annotated[
 
 
 async def get_observation_repository(
-    session_maker: SessionMakerDep,
     project_id: ProjectIdDep,
 ) -> ObservationRepository:
     """Create an ObservationRepository instance for the current project."""
-    return ObservationRepository(session_maker, project_id=project_id)
+    return ObservationRepository(project_id=project_id)
 
 
 ObservationRepositoryDep = Annotated[ObservationRepository, Depends(get_observation_repository)]
 
 
 async def get_observation_repository_v2(  # pragma: no cover
-    session_maker: SessionMakerDep,
     project_id: ProjectIdPathDep,
 ) -> ObservationRepository:
     """Create an ObservationRepository instance for v2 API."""
-    return ObservationRepository(session_maker, project_id=project_id)
+    return ObservationRepository(project_id=project_id)
 
 
 ObservationRepositoryV2Dep = Annotated[
@@ -92,11 +87,10 @@ ObservationRepositoryV2Dep = Annotated[
 
 
 async def get_observation_repository_v2_external(
-    session_maker: SessionMakerDep,
     project_id: ProjectExternalIdPathDep,
 ) -> ObservationRepository:
     """Create an ObservationRepository instance for v2 API (uses external_id)."""
-    return ObservationRepository(session_maker, project_id=project_id)
+    return ObservationRepository(project_id=project_id)
 
 
 ObservationRepositoryV2ExternalDep = Annotated[
@@ -108,33 +102,30 @@ ObservationRepositoryV2ExternalDep = Annotated[
 
 
 async def get_relation_repository(
-    session_maker: SessionMakerDep,
     project_id: ProjectIdDep,
 ) -> RelationRepository:
     """Create a RelationRepository instance for the current project."""
-    return RelationRepository(session_maker, project_id=project_id)
+    return RelationRepository(project_id=project_id)
 
 
 RelationRepositoryDep = Annotated[RelationRepository, Depends(get_relation_repository)]
 
 
 async def get_relation_repository_v2(  # pragma: no cover
-    session_maker: SessionMakerDep,
     project_id: ProjectIdPathDep,
 ) -> RelationRepository:
     """Create a RelationRepository instance for v2 API."""
-    return RelationRepository(session_maker, project_id=project_id)
+    return RelationRepository(project_id=project_id)
 
 
 RelationRepositoryV2Dep = Annotated[RelationRepository, Depends(get_relation_repository_v2)]
 
 
 async def get_relation_repository_v2_external(
-    session_maker: SessionMakerDep,
     project_id: ProjectExternalIdPathDep,
 ) -> RelationRepository:
     """Create a RelationRepository instance for v2 API (uses external_id)."""
-    return RelationRepository(session_maker, project_id=project_id)
+    return RelationRepository(project_id=project_id)
 
 
 RelationRepositoryV2ExternalDep = Annotated[

src/basic_memory/deps/services.py

@@ -16,6 +16,7 @@ from fastapi import Depends
 from loguru import logger
 
 from basic_memory.deps.config import AppConfigDep
+from basic_memory.deps.db import SessionMakerDep
 from basic_memory.deps.projects import (
     ProjectConfigDep,
     ProjectConfigV2Dep,
@@ -159,9 +160,10 @@ async def get_search_service(
     search_repository: SearchRepositoryDep,
     entity_repository: EntityRepositoryDep,
     file_service: FileServiceDep,
+    session_maker: SessionMakerDep,
 ) -> SearchService:
     """Create SearchService with dependencies."""
-    return SearchService(search_repository, entity_repository, file_service)
+    return SearchService(search_repository, entity_repository, file_service, session_maker)
 
 
 SearchServiceDep = Annotated[SearchService, Depends(get_search_service)]
@@ -171,9 +173,10 @@ async def get_search_service_v2(  # pragma: no cover
     search_repository: SearchRepositoryV2Dep,
     entity_repository: EntityRepositoryV2Dep,
     file_service: FileServiceV2Dep,
+    session_maker: SessionMakerDep,
 ) -> SearchService:
     """Create SearchService for v2 API."""
-    return SearchService(search_repository, entity_repository, file_service)
+    return SearchService(search_repository, entity_repository, file_service, session_maker)
 
 
 SearchServiceV2Dep = Annotated[SearchService, Depends(get_search_service_v2)]
@@ -183,9 +186,10 @@ async def get_search_service_v2_external(
     search_repository: SearchRepositoryV2ExternalDep,
     entity_repository: EntityRepositoryV2ExternalDep,
     file_service: FileServiceV2ExternalDep,
+    session_maker: SessionMakerDep,
 ) -> SearchService:
     """Create SearchService for v2 API (uses external_id)."""
-    return SearchService(search_repository, entity_repository, file_service)
+    return SearchService(search_repository, entity_repository, file_service, session_maker)
 
 
 SearchServiceV2ExternalDep = Annotated[SearchService, Depends(get_search_service_v2_external)]
@@ -195,27 +199,45 @@ SearchServiceV2ExternalDep = Annotated[SearchService, Depends(get_search_service
 
 
 async def get_link_resolver(
-    entity_repository: EntityRepositoryDep, search_service: SearchServiceDep
+    entity_repository: EntityRepositoryDep,
+    search_service: SearchServiceDep,
+    session_maker: SessionMakerDep,
 ) -> LinkResolver:
-    return LinkResolver(entity_repository=entity_repository, search_service=search_service)
+    return LinkResolver(
+        entity_repository=entity_repository,
+        search_service=search_service,
+        session_maker=session_maker,
+    )
 
 
 LinkResolverDep = Annotated[LinkResolver, Depends(get_link_resolver)]
 
 
 async def get_link_resolver_v2(  # pragma: no cover
-    entity_repository: EntityRepositoryV2Dep, search_service: SearchServiceV2Dep
+    entity_repository: EntityRepositoryV2Dep,
+    search_service: SearchServiceV2Dep,
+    session_maker: SessionMakerDep,
 ) -> LinkResolver:
-    return LinkResolver(entity_repository=entity_repository, search_service=search_service)
+    return LinkResolver(
+        entity_repository=entity_repository,
+        search_service=search_service,
+        session_maker=session_maker,
+    )
 
 
 LinkResolverV2Dep = Annotated[LinkResolver, Depends(get_link_resolver_v2)]
 
 
 async def get_link_resolver_v2_external(
-    entity_repository: EntityRepositoryV2ExternalDep, search_service: SearchServiceV2ExternalDep
+    entity_repository: EntityRepositoryV2ExternalDep,
+    search_service: SearchServiceV2ExternalDep,
+    session_maker: SessionMakerDep,
 ) -> LinkResolver:
-    return LinkResolver(entity_repository=entity_repository, search_service=search_service)
+    return LinkResolver(
+        entity_repository=entity_repository,
+        search_service=search_service,
+        session_maker=session_maker,
+    )
 
 
 LinkResolverV2ExternalDep = Annotated[LinkResolver, Depends(get_link_resolver_v2_external)]
@@ -232,6 +254,7 @@ async def get_entity_service(
     file_service: FileServiceDep,
     link_resolver: LinkResolverDep,
     search_service: SearchServiceDep,
+    session_maker: SessionMakerDep,
     app_config: AppConfigDep,
 ) -> EntityService:
     """Create EntityService with repository."""
@@ -242,6 +265,7 @@ async def get_entity_service(
         entity_parser=entity_parser,
         file_service=file_service,
         link_resolver=link_resolver,
+        session_maker=session_maker,
         search_service=search_service,
         app_config=app_config,
     )
@@ -258,6 +282,7 @@ async def get_entity_service_v2(  # pragma: no cover
     file_service: FileServiceV2Dep,
     link_resolver: LinkResolverV2Dep,
     search_service: SearchServiceV2Dep,
+    session_maker: SessionMakerDep,
     app_config: AppConfigDep,
 ) -> EntityService:
     """Create EntityService for v2 API."""
@@ -268,6 +293,7 @@ async def get_entity_service_v2(  # pragma: no cover
         entity_parser=entity_parser,
         file_service=file_service,
         link_resolver=link_resolver,
+        session_maker=session_maker,
         search_service=search_service,
         app_config=app_config,
     )
@@ -284,6 +310,7 @@ async def get_entity_service_v2_external(
     file_service: FileServiceV2ExternalDep,
     link_resolver: LinkResolverV2ExternalDep,
     search_service: SearchServiceV2ExternalDep,
+    session_maker: SessionMakerDep,
     app_config: AppConfigDep,
 ) -> EntityService:
     """Create EntityService for v2 API (uses external_id)."""
@@ -294,6 +321,7 @@ async def get_entity_service_v2_external(
         entity_parser=entity_parser,
         file_service=file_service,
         link_resolver=link_resolver,
+        session_maker=session_maker,
         search_service=search_service,
         app_config=app_config,
     )
@@ -310,12 +338,14 @@ async def get_context_service(
     entity_repository: EntityRepositoryDep,
     observation_repository: ObservationRepositoryDep,
     link_resolver: LinkResolverDep,
+    session_maker: SessionMakerDep,
 ) -> ContextService:
     return ContextService(
         search_repository=search_repository,
         entity_repository=entity_repository,
         observation_repository=observation_repository,
         link_resolver=link_resolver,
+        session_maker=session_maker,
     )
 
 
@@ -327,6 +357,7 @@ async def get_context_service_v2(  # pragma: no cover
     entity_repository: EntityRepositoryV2Dep,
     observation_repository: ObservationRepositoryV2Dep,
     link_resolver: LinkResolverV2Dep,
+    session_maker: SessionMakerDep,
 ) -> ContextService:
     """Create ContextService for v2 API."""
     return ContextService(
@@ -334,6 +365,7 @@ async def get_context_service_v2(  # pragma: no cover
         entity_repository=entity_repository,
         observation_repository=observation_repository,
         link_resolver=link_resolver,
+        session_maker=session_maker,
     )
 
 
@@ -345,6 +377,7 @@ async def get_context_service_v2_external(
     entity_repository: EntityRepositoryV2ExternalDep,
     observation_repository: ObservationRepositoryV2ExternalDep,
     link_resolver: LinkResolverV2ExternalDep,
+    session_maker: SessionMakerDep,
 ) -> ContextService:
     """Create ContextService for v2 API (uses external_id)."""
     return ContextService(
@@ -352,6 +385,7 @@ async def get_context_service_v2_external(
         entity_repository=entity_repository,
         observation_repository=observation_repository,
         link_resolver=link_resolver,
+        session_maker=session_maker,
     )
 
 
@@ -370,6 +404,7 @@ async def get_sync_service(
     project_repository: ProjectRepositoryDep,
     search_service: SearchServiceDep,
     file_service: FileServiceDep,
+    session_maker: SessionMakerDep,
 ) -> SyncService:  # pragma: no cover
     return SyncService(
         app_config=app_config,
@@ -380,6 +415,7 @@ async def get_sync_service(
         project_repository=project_repository,
         search_service=search_service,
         file_service=file_service,
+        session_maker=session_maker,
     )
 
 
@@ -395,6 +431,7 @@ async def get_sync_service_v2(
     project_repository: ProjectRepositoryDep,
     search_service: SearchServiceV2Dep,
     file_service: FileServiceV2Dep,
+    session_maker: SessionMakerDep,
 ) -> SyncService:  # pragma: no cover
     """Create SyncService for v2 API."""
     return SyncService(
@@ -406,6 +443,7 @@ async def get_sync_service_v2(
         project_repository=project_repository,
         search_service=search_service,
         file_service=file_service,
+        session_maker=session_maker,
     )
 
 
@@ -421,6 +459,7 @@ async def get_sync_service_v2_external(
     project_repository: ProjectRepositoryDep,
     search_service: SearchServiceV2ExternalDep,
     file_service: FileServiceV2ExternalDep,
+    session_maker: SessionMakerDep,
 ) -> SyncService:  # pragma: no cover
     """Create SyncService for v2 API (uses external_id)."""
     return SyncService(
@@ -432,6 +471,7 @@ async def get_sync_service_v2_external(
         project_repository=project_repository,
         search_service=search_service,
         file_service=file_service,
+        session_maker=session_maker,
     )
 
 
@@ -535,6 +575,7 @@ TaskSchedulerDep = Annotated[TaskScheduler, Depends(get_task_scheduler)]
 
 async def get_project_service(
     project_repository: ProjectRepositoryDep,
+    session_maker: SessionMakerDep,
     app_config: AppConfigDep,
 ) -> ProjectService:
     """Create ProjectService with repository and a system-level FileService for directory operations."""
@@ -543,7 +584,9 @@ async def get_project_service(
     entity_parser = EntityParser(Path.home())
     markdown_processor = MarkdownProcessor(entity_parser, app_config=app_config)
     file_service = FileService(Path.home(), markdown_processor, app_config=app_config)
-    return ProjectService(repository=project_repository, file_service=file_service)
+    return ProjectService(
+        repository=project_repository, session_maker=session_maker, file_service=file_service
+    )
 
 
 ProjectServiceDep = Annotated[ProjectService, Depends(get_project_service)]
@@ -554,10 +597,12 @@ ProjectServiceDep = Annotated[ProjectService, Depends(get_project_service)]
 
 async def get_directory_service(
     entity_repository: EntityRepositoryDep,
+    session_maker: SessionMakerDep,
 ) -> DirectoryService:
     """Create DirectoryService with dependencies."""
     return DirectoryService(
         entity_repository=entity_repository,
+        session_maker=session_maker,
     )
 
 
@@ -566,10 +611,12 @@ DirectoryServiceDep = Annotated[DirectoryService, Depends(get_directory_service)
 
 async def get_directory_service_v2(  # pragma: no cover
     entity_repository: EntityRepositoryV2Dep,
+    session_maker: SessionMakerDep,
 ) -> DirectoryService:
     """Create DirectoryService for v2 API (uses integer project_id from path)."""
     return DirectoryService(
         entity_repository=entity_repository,
+        session_maker=session_maker,
     )
 
 
@@ -578,10 +625,12 @@ DirectoryServiceV2Dep = Annotated[DirectoryService, Depends(get_directory_servic
 
 async def get_directory_service_v2_external(
     entity_repository: EntityRepositoryV2ExternalDep,
+    session_maker: SessionMakerDep,
 ) -> DirectoryService:
     """Create DirectoryService for v2 API (uses external_id from path)."""
     return DirectoryService(
         entity_repository=entity_repository,
+        session_maker=session_maker,
     )
 
 

src/basic_memory/file_utils.py

@@ -302,26 +302,76 @@ async def format_file(
         return None
 
 
+# A frontmatter fence is a line containing exactly `---`, optionally followed by
+# trailing horizontal whitespace. Anchoring to a full line (rather than a bare
+# substring/`startswith`) prevents single-line content like
+# `---\nstatus: active\n---\nBody` — where `\n` is a literal backslash-n, not a
+# newline — from being misread as frontmatter. See issue #972.
+_FENCE_RE = re.compile(r"^---[ \t]*$")
+
+
+def _split_frontmatter(content: str) -> Optional[tuple[str, str]]:
+    """Split content into (yaml_block, body) when it opens with a line-anchored fence.
+
+    The opening fence must be the very first line and the closing fence must be a
+    later line, each matching exactly `---` (with optional trailing whitespace).
+
+    Returns:
+        A `(yaml_block, body)` tuple when a complete fenced block is present, or
+        ``None`` when the content does not open with a frontmatter fence.
+
+    Raises:
+        ParseError: If the content opens with a fence but has no closing fence.
+    """
+    lines = content.splitlines(keepends=True)
+
+    # Skip leading blank lines: a document may begin with whitespace before the
+    # opening fence (e.g. a heredoc/dedented string starting with a newline). This
+    # does NOT relax line-anchoring — the opening fence must still be the first
+    # non-blank line, all on its own, so a single-line `---\\nstatus...` (literal
+    # backslash-n) is still rejected. See issue #972.
+    start = 0
+    while start < len(lines) and lines[start].strip() == "":
+        start += 1
+
+    if start >= len(lines) or not _FENCE_RE.match(lines[start].rstrip("\r\n")):
+        return None
+
+    # Find the closing fence on its own line somewhere after the opening fence.
+    for index in range(start + 1, len(lines)):
+        if _FENCE_RE.match(lines[index].rstrip("\r\n")):
+            yaml_block = "".join(lines[start + 1 : index])
+            body = "".join(lines[index + 1 :])
+            return yaml_block, body
+
+    raise ParseError("Invalid frontmatter format")
+
+
 def has_frontmatter(content: str) -> bool:
     """
     Check if content contains valid YAML frontmatter.
 
+    Frontmatter requires `---` fences on their own lines; an inline `---` (such as
+    a single-line string that merely starts with the characters `---`) is not
+    frontmatter.
+
     Args:
         content: Content to check
 
     Returns:
-        True if content has valid frontmatter markers (---), False otherwise
+        True if content has line-anchored frontmatter fences, False otherwise
     """
     if not content:
         return False
 
     # Strip BOM before checking for frontmatter markers
-    content = strip_bom(content).strip()
-    if not content.startswith("---"):
+    content = strip_bom(content)
+    try:
+        return _split_frontmatter(content) is not None
+    except ParseError:
+        # An opening fence with no closing fence is not usable frontmatter.
         return False
 
-    return "---" in content[3:]
-
 
 def parse_frontmatter(content: str) -> Dict[str, Any]:
     """
@@ -339,17 +389,14 @@ def parse_frontmatter(content: str) -> Dict[str, Any]:
     try:
         # Strip BOM before parsing frontmatter
         content = strip_bom(content)
-        if not content.strip().startswith("---"):
+        split = _split_frontmatter(content)
+        if split is None:
             raise ParseError("Content has no frontmatter")
-
-        # Split on first two occurrences of ---
-        parts = content.split("---", 2)
-        if len(parts) < 3:
-            raise ParseError("Invalid frontmatter format")
+        yaml_block, _ = split
 
         # Parse YAML
         try:
-            frontmatter = yaml.safe_load(parts[1])
+            frontmatter = yaml.safe_load(yaml_block)
             # Handle empty frontmatter (None from yaml.safe_load)
             if frontmatter is None:
                 return {}
@@ -381,18 +428,17 @@ def remove_frontmatter(content: str) -> str:
         ParseError: If content starts with frontmatter marker but is malformed
     """
     # Strip BOM before processing
-    content = strip_bom(content).strip()
+    content = strip_bom(content)
 
-    # Return as-is if no frontmatter marker
-    if not content.startswith("---"):
-        return content
+    split = _split_frontmatter(content)
+    # Trigger: content does not open with a line-anchored fence
+    # Why: inline `---` is ordinary content, not frontmatter (issue #972)
+    # Outcome: return the content untouched (stripped to preserve prior behavior)
+    if split is None:
+        return content.strip()
 
-    # Split on first two occurrences of ---
-    parts = content.split("---", 2)
-    if len(parts) < 3:
-        raise ParseError("Invalid frontmatter format")
-
-    return parts[2].strip()
+    _, body = split
+    return body.strip()
 
 
 def dump_frontmatter(post: frontmatter.Post) -> str:

src/basic_memory/indexing/batch_indexer.py

@@ -3,15 +3,18 @@
 from __future__ import annotations
 
 import asyncio
+from contextlib import asynccontextmanager
 from dataclasses import dataclass
 from datetime import datetime
 from pathlib import Path
-from typing import Awaitable, Callable, Mapping, TypeVar
+from typing import AsyncIterator, Awaitable, Callable, Mapping, TypeVar
 
 from loguru import logger
 from sqlalchemy.exc import IntegrityError
+from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker
 
 import logfire
+from basic_memory import db
 from basic_memory.config import BasicMemoryConfig
 from basic_memory.file_utils import compute_checksum, has_frontmatter, remove_frontmatter
 from basic_memory.markdown.schemas import EntityMarkdown
@@ -69,6 +72,7 @@ class BatchIndexer:
         relation_repository: RelationRepository,
         search_service: SearchService,
         file_writer: IndexFileWriter,
+        session_maker: async_sessionmaker[AsyncSession],
     ) -> None:
         self.app_config = app_config
         self.entity_service = entity_service
@@ -76,6 +80,19 @@ class BatchIndexer:
         self.relation_repository = relation_repository
         self.search_service = search_service
         self.file_writer = file_writer
+        self.session_maker = session_maker
+
+    @asynccontextmanager
+    async def _session_scope(
+        self, session: AsyncSession | None = None
+    ) -> AsyncIterator[AsyncSession]:
+        """Use the caller's session or open a service-owned transaction."""
+        if session is not None:
+            yield session
+            return
+
+        async with db.scoped_session(self.session_maker) as owned_session:
+            yield owned_session
 
     async def index_files(
         self,
@@ -149,9 +166,10 @@ class BatchIndexer:
                 max_concurrent=max_concurrent,
             )
 
-        refreshed_entities = await self.entity_repository.find_by_ids(
-            [prepared.entity_id for prepared in prepared_entities.values()]
-        )
+        async with self._session_scope() as session:
+            refreshed_entities = await self.entity_repository.find_by_ids(
+                session, [prepared.entity_id for prepared in prepared_entities.values()]
+            )
         entities_by_id = {entity.id: entity for entity in refreshed_entities}
 
         refreshed, refresh_errors = await self._run_bounded(
@@ -196,12 +214,7 @@ class BatchIndexer:
             prepared = await self._prepare_markdown_file(file)
         if existing_permalink_by_path is None:
             with logfire.span("index.markdown_file.load_permalink_map", path=file.path):
-                existing_permalink_by_path = {
-                    path: permalink
-                    for path, permalink in (
-                        await self.entity_repository.get_file_path_to_permalink_map()
-                    ).items()
-                }
+                existing_permalink_by_path = await self._get_file_path_to_permalink_map()
 
         reserved_permalinks = {
             permalink
@@ -226,7 +239,8 @@ class BatchIndexer:
             path=file.path,
             entity_id=persisted.entity.id,
         ):
-            refreshed = await self.entity_repository.find_by_ids([persisted.entity.id])
+            async with self._session_scope() as session:
+                refreshed = await self.entity_repository.find_by_ids(session, [persisted.entity.id])
         if len(refreshed) != 1:  # pragma: no cover
             raise ValueError(f"Failed to reload indexed entity for {file.path}")
         entity = refreshed[0]
@@ -249,6 +263,17 @@ class BatchIndexer:
             markdown_content=prepared_entity.markdown_content,
         )
 
+    async def _get_file_path_to_permalink_map(self) -> dict[str, str | None]:
+        """Load current file-path to permalink mappings in a service-owned session."""
+        async with self._session_scope() as session:
+            permalink_by_path: dict[str, str | None] = {
+                path: permalink
+                for path, permalink in (
+                    await self.entity_repository.get_file_path_to_permalink_map(session)
+                ).items()
+            }
+            return permalink_by_path
+
     # --- Preparation ---
 
     async def _prepare_markdown_file(self, file: IndexInputFile) -> _PreparedMarkdownFile:
@@ -283,12 +308,7 @@ class BatchIndexer:
             return {}, {}
 
         if existing_permalink_by_path is None:
-            existing_permalink_by_path = {
-                path: permalink
-                for path, permalink in (
-                    await self.entity_repository.get_file_path_to_permalink_map()
-                ).items()
-            }
+            existing_permalink_by_path = await self._get_file_path_to_permalink_map()
 
         batch_paths = set(prepared_markdown)
         reserved_permalinks = {
@@ -406,7 +426,10 @@ class BatchIndexer:
 
     async def _upsert_regular_file(self, file: IndexInputFile) -> _PreparedEntity:
         checksum = await self._resolve_checksum(file)
-        existing = await self.entity_repository.get_by_file_path(file.path, load_relations=False)
+        async with self._session_scope() as session:
+            existing = await self.entity_repository.get_by_file_path(
+                session, file.path, load_relations=False
+            )
         is_new_entity = existing is None
 
         if existing is None:
@@ -424,7 +447,8 @@ class BatchIndexer:
             )
 
             try:
-                created = await self.entity_repository.add(entity)
+                async with self._session_scope() as session:
+                    created = await self.entity_repository.add(session, entity)
                 entity_id = created.id
             except IntegrityError as exc:
                 message = str(exc)
@@ -436,10 +460,12 @@ class BatchIndexer:
                         and "file_path" in message
                     )
                 ):
-                    existing = await self.entity_repository.get_by_file_path(
-                        file.path,
-                        load_relations=False,
-                    )
+                    async with self._session_scope() as session:
+                        existing = await self.entity_repository.get_by_file_path(
+                            session,
+                            file.path,
+                            load_relations=False,
+                        )
                     if existing is None:
                         raise ValueError(
                             f"Entity not found after file_path conflict: {file.path}"
@@ -450,10 +476,12 @@ class BatchIndexer:
         else:
             entity_id = existing.id
 
-        updated = await self.entity_repository.update(
-            entity_id,
-            self._entity_metadata_updates(file, checksum, include_created_at=is_new_entity),
-        )
+        async with self._session_scope() as session:
+            updated = await self.entity_repository.update(
+                session,
+                entity_id,
+                self._entity_metadata_updates(file, checksum, include_created_at=is_new_entity),
+            )
         if updated is None:
             raise ValueError(f"Failed to update file entity metadata for {file.path}")
 
@@ -476,10 +504,7 @@ class BatchIndexer:
         max_concurrent: int,
     ) -> tuple[int, int]:
         unresolved_relation_lists = await asyncio.gather(
-            *(
-                self.relation_repository.find_unresolved_relations_for_entity(entity_id)
-                for entity_id in entity_ids
-            )
+            *(self._find_unresolved_relations_for_entity(entity_id) for entity_id in entity_ids)
         )
         unresolved_relations = [
             relation for relation_list in unresolved_relation_lists for relation in relation_list
@@ -499,22 +524,26 @@ class BatchIndexer:
                     # link text, mismatching this with the sync_service forward-reference
                     # path and producing confidently-wrong graph edges. See
                     # sync_service.resolve_forward_references for the same change.
-                    resolved_entity = await self.entity_service.link_resolver.resolve_link(
-                        relation.to_name, strict=True
-                    )
+                    async with self._session_scope() as session:
+                        resolved_entity = await self.entity_service.link_resolver.resolve_link(
+                            relation.to_name, strict=True, session=session
+                        )
                     if resolved_entity is None or resolved_entity.id == relation.from_id:
                         return 0
 
                     try:
-                        await self.relation_repository.update(
-                            relation.id,
-                            {
-                                "to_id": resolved_entity.id,
-                                "to_name": resolved_entity.title,
-                            },
-                        )
+                        async with self._session_scope() as session:
+                            await self.relation_repository.update(
+                                session,
+                                relation.id,
+                                {
+                                    "to_id": resolved_entity.id,
+                                    "to_name": resolved_entity.title,
+                                },
+                            )
                     except IntegrityError:
-                        await self.relation_repository.delete(relation.id)
+                        async with self._session_scope() as session:
+                            await self.relation_repository.delete(session, relation.id)
                     return 1
                 except Exception as exc:  # pragma: no cover - defensive logging
                     logger.warning(
@@ -531,15 +560,19 @@ class BatchIndexer:
         )
 
         remaining_relation_lists = await asyncio.gather(
-            *(
-                self.relation_repository.find_unresolved_relations_for_entity(entity_id)
-                for entity_id in entity_ids
-            )
+            *(self._find_unresolved_relations_for_entity(entity_id) for entity_id in entity_ids)
         )
         remaining_unresolved = sum(len(relations) for relations in remaining_relation_lists)
 
         return sum(resolved_counts), remaining_unresolved
 
+    async def _find_unresolved_relations_for_entity(self, entity_id: int):
+        """Load unresolved relations for one entity in a service-owned session."""
+        async with self._session_scope() as session:
+            return await self.relation_repository.find_unresolved_relations_for_entity(
+                session, entity_id
+            )
+
     # --- Search refresh ---
 
     async def _refresh_search_index(
@@ -565,30 +598,36 @@ class BatchIndexer:
         resolve_relations: bool = True,
         reload_entity: bool = True,
     ) -> _PersistedMarkdownFile:
-        existing = await self.entity_repository.get_by_file_path(
-            prepared.file.path,
-            load_relations=False,
-        )
-        if is_new is None:
-            is_new = existing is None
-        entity = await self.entity_service.upsert_entity_from_markdown(
-            Path(prepared.file.path),
-            prepared.markdown,
-            is_new=is_new,
-            existing_entity=existing,
-            resolve_relations=resolve_relations,
-            reload_entity=reload_entity,
-        )
-        prepared = await self._reconcile_persisted_permalink(prepared, entity)
-        metadata_updates = self._entity_metadata_updates(prepared.file, prepared.final_checksum)
-        updated = await self.entity_repository.update_fields(
-            entity.id,
-            metadata_updates,
-        )
-        if not updated:
-            raise ValueError(f"Failed to update markdown entity metadata for {prepared.file.path}")
-        self._apply_entity_metadata_updates(entity, metadata_updates)
-        return _PersistedMarkdownFile(prepared=prepared, entity=entity)
+        async with self._session_scope() as session:
+            existing = await self.entity_repository.get_by_file_path(
+                session,
+                prepared.file.path,
+                load_relations=False,
+            )
+            if is_new is None:
+                is_new = existing is None
+            entity = await self.entity_service.upsert_entity_from_markdown(
+                Path(prepared.file.path),
+                prepared.markdown,
+                is_new=is_new,
+                existing_entity=existing,
+                resolve_relations=resolve_relations,
+                reload_entity=reload_entity,
+                session=session,
+            )
+            prepared = await self._reconcile_persisted_permalink(prepared, entity)
+            metadata_updates = self._entity_metadata_updates(prepared.file, prepared.final_checksum)
+            updated = await self.entity_repository.update_fields(
+                session,
+                entity.id,
+                metadata_updates,
+            )
+            if not updated:
+                raise ValueError(
+                    f"Failed to update markdown entity metadata for {prepared.file.path}"
+                )
+            self._apply_entity_metadata_updates(entity, metadata_updates)
+            return _PersistedMarkdownFile(prepared=prepared, entity=entity)
 
     async def _reconcile_persisted_permalink(
         self,

src/basic_memory/man/basic-memory.1

@@ -0,0 +1 @@
+.so man1/bm.1

src/basic_memory/man/bm.1

@@ -0,0 +1,134 @@
+.TH BM 1 "2026-06-11" "basic-memory" "Basic Memory Manual"
+.SH NAME
+bm \- local-first knowledge base for humans and AI agents
+.SH SYNOPSIS
+.B bm
+.I COMMAND
+.RI [ ARGS ]...
+.br
+.B basic-memory
+.I COMMAND
+.RI [ ARGS ]...
+.SH DESCRIPTION
+.B bm
+manages Basic Memory projects: plain markdown files that form a knowledge
+graph. Files are the source of truth; SQLite provides indexing and
+full-text search; the same operations are exposed to AI agents over the
+Model Context Protocol (MCP) and to humans and scripts through this CLI.
+.PP
+Notes use semantic markdown: observations
+.RB ( "\- [category] text #tag" )
+and relations
+.RB ( "\- relation_type [[Target]]" )
+become queryable graph structure. Projects route independently to the
+local API or to Basic Memory Cloud.
+.SH COMMANDS
+Knowledge operations:
+.TP
+.B bm tool
+CLI access to the MCP tools (write-note, read-note, search-notes,
+build-context, ...). These emit JSON and are the scriptable surface.
+.TP
+.B bm status
+Show sync status between files and the database.
+.TP
+.B bm reindex
+Index local file changes and rebuild search/embeddings. This is the manual
+sync trigger when no MCP server is running.
+.TP
+.B bm doctor
+Run end-to-end file/database consistency checks.
+.TP
+.B bm orphans
+List entities with no relations in the knowledge graph.
+.TP
+.B bm format
+Run configured formatters over note files.
+.PP
+Projects and schemas:
+.TP
+.B bm project
+Add, remove, list projects; set the default; flip a project between local
+and cloud routing.
+.TP
+.B bm schema
+List, validate, infer, and drift-check Picoschema note-type contracts.
+.PP
+Data and cloud:
+.TP
+.B bm import
+Import from ChatGPT, Claude, or memory.json exports. Imports write files;
+run
+.B bm reindex
+afterwards.
+.TP
+.B bm cloud
+Authenticate, sync (push/pull/sync/bisync), snapshots, and team workspace
+administration.
+.PP
+Infrastructure:
+.TP
+.B bm mcp
+Run the MCP server (hosts the live file watcher).
+.TP
+.B bm man
+Manage these man pages
+.RB ( "bm man install" ).
+.TP
+.B bm reset
+Drop and recreate the database (destructive).
+.PP
+Most commands accept
+.B \-\-project
+.I NAME
+to target a project and
+.BR \-\-local / \-\-cloud
+to override routing.
+.SH EXAMPLES
+Write and find a note from the shell:
+.PP
+.nf
+.RS
+echo "# Standup notes" | bm tool write-note \\
+    \-\-title "Standup" \-\-folder notes
+bm tool search-notes "standup"
+.RE
+.fi
+.PP
+Pick up files created outside the tools:
+.PP
+.nf
+.RS
+bm status            # shows pending changes
+bm reindex           # indexes them
+.RE
+.fi
+.SH FILES
+.TP
+.I ~/.basic-memory/config.json
+Projects, default project, per-project routing modes, cloud settings.
+.TP
+.I ~/.basic-memory/memory.db
+SQLite index (derived; safe to rebuild with bm reindex).
+.SH ENVIRONMENT
+.TP
+.B BASIC_MEMORY_FORCE_LOCAL
+Force local routing regardless of cloud mode.
+.TP
+.B BASIC_MEMORY_LOG_LEVEL
+Logging verbosity (e.g. DEBUG).
+.SH SEE ALSO
+Full manual (machine-readable, agent-traversable): the
+.I manual
+Basic Memory project \(em see docs/manual-pages.md in the repository.
+Documentation: https://docs.basicmemory.com
+.PP
+For AI agents: the complete tool reference lives in the manual project as
+section\-3 pages (write-note(3), search-notes(3), ...), queryable via
+.B search_notes
+with
+.BR "metadata_filters={\(dqtype\(dq: \(dqmanpage\(dq}" .
+.SH BUGS
+https://github.com/basicmachines-co/basic-memory/issues
+.SH AUTHORS
+Basic Machines (https://basicmachines.co)

src/basic_memory/mcp/async_client.py

@@ -5,14 +5,16 @@ from dataclasses import dataclass
 from threading import RLock
 from typing import TYPE_CHECKING, Annotated, Any, AsyncIterator, Callable, Optional
 
-from fastapi import Depends, FastAPI, Request
 from httpx import ASGITransport, AsyncClient, Timeout
 from loguru import logger
 
 import logfire
-from basic_memory.config import ConfigManager, ProjectMode
+from basic_memory.config import ConfigManager, ProjectMode, has_cloud_credentials
 
 if TYPE_CHECKING:
+    # FastAPI is only needed when a request routes through the local ASGI
+    # transport; importing it at module level costs ~0.1s on every CLI start (#886).
+    from fastapi import FastAPI
     from sqlalchemy.ext.asyncio import AsyncEngine, AsyncSession, async_sessionmaker
 
 LocalDatabaseState = tuple["AsyncEngine", "async_sessionmaker[AsyncSession]"]
@@ -28,8 +30,8 @@ class _PreparedLocalAsgiDatabase:
 
 
 _prepared_local_asgi_database_lock = RLock()
-_prepared_local_asgi_database_prepare_locks: dict[FastAPI, Lock] = {}
-_prepared_local_asgi_databases: dict[FastAPI, _PreparedLocalAsgiDatabase] = {}
+_prepared_local_asgi_database_prepare_locks: dict["FastAPI", Lock] = {}
+_prepared_local_asgi_databases: dict["FastAPI", _PreparedLocalAsgiDatabase] = {}
 
 
 def _force_local_mode() -> bool:
@@ -57,7 +59,7 @@ def _build_timeout() -> Timeout:
     )
 
 
-def _build_asgi_client(app: FastAPI, timeout: Timeout) -> AsyncClient:
+def _build_asgi_client(app: "FastAPI", timeout: Timeout) -> AsyncClient:
     """Create a local ASGI client for an already-prepared FastAPI app."""
     from basic_memory.workspace_context import workspace_permalink_headers
 
@@ -71,7 +73,7 @@ def _build_asgi_client(app: FastAPI, timeout: Timeout) -> AsyncClient:
     )
 
 
-def _get_prepared_local_asgi_database_prepare_lock(app: FastAPI) -> Lock:
+def _get_prepared_local_asgi_database_prepare_lock(app: "FastAPI") -> Lock:
     """Get the async lock that serializes first-time DB preparation for an app."""
     with _prepared_local_asgi_database_lock:
         prepare_lock = _prepared_local_asgi_database_prepare_locks.get(app)
@@ -82,8 +84,10 @@ def _get_prepared_local_asgi_database_prepare_lock(app: FastAPI) -> Lock:
 
 
 @asynccontextmanager
-async def _resolve_local_asgi_database(app: FastAPI) -> AsyncIterator[LocalDatabaseState]:
+async def _resolve_local_asgi_database(app: "FastAPI") -> AsyncIterator[LocalDatabaseState]:
     """Resolve database state for a local ASGI request."""
+    # Imported on first local-ASGI use so CLI startup never pays for FastAPI (#886).
+    from fastapi import Depends, Request
     from fastapi.dependencies.utils import get_dependant, solve_dependencies
 
     from basic_memory.deps import get_engine_factory
@@ -127,7 +131,7 @@ async def _resolve_local_asgi_database(app: FastAPI) -> AsyncIterator[LocalDatab
         yield await resolve_database_state(**solved.values)
 
 
-def _retain_prepared_local_asgi_database(app: FastAPI) -> bool:
+def _retain_prepared_local_asgi_database(app: "FastAPI") -> bool:
     """Retain an active local ASGI database preparation if one exists."""
     with _prepared_local_asgi_database_lock:
         active = _prepared_local_asgi_databases.get(app)
@@ -139,7 +143,7 @@ def _retain_prepared_local_asgi_database(app: FastAPI) -> bool:
 
 
 def _install_prepared_local_asgi_database(
-    app: FastAPI,
+    app: "FastAPI",
     database_state: LocalDatabaseState,
     dependency_context: AbstractAsyncContextManager[LocalDatabaseState],
 ) -> None:
@@ -163,7 +167,7 @@ def _install_prepared_local_asgi_database(
         )
 
 
-def _restore_local_asgi_state_attribute(app: FastAPI, name: str, previous_value: object) -> None:
+def _restore_local_asgi_state_attribute(app: "FastAPI", name: str, previous_value: object) -> None:
     """Restore a FastAPI app.state attribute captured before local ASGI preparation."""
     if previous_value is _MISSING_STATE_VALUE:
         if hasattr(app.state, name):
@@ -173,7 +177,7 @@ def _restore_local_asgi_state_attribute(app: FastAPI, name: str, previous_value:
 
 
 def _release_prepared_local_asgi_database(
-    app: FastAPI,
+    app: "FastAPI",
 ) -> AbstractAsyncContextManager[LocalDatabaseState] | None:
     """Release local ASGI database state after a client context exits."""
     with _prepared_local_asgi_database_lock:
@@ -196,7 +200,7 @@ def _release_prepared_local_asgi_database(
 
 
 @asynccontextmanager
-async def _prepared_local_asgi_database(app: FastAPI) -> AsyncIterator[None]:
+async def _prepared_local_asgi_database(app: "FastAPI") -> AsyncIterator[None]:
     """Initialize local ASGI database state before the first request."""
     prepare_lock = _get_prepared_local_asgi_database_prepare_lock(app)
     async with prepare_lock:
@@ -368,7 +372,8 @@ async def get_client(
     1. Factory injection.
     2. Explicit routing flags (--local/--cloud).
     3. Per-project mode routing when project_name is provided.
-    4. Local ASGI transport by default.
+    4. Cloud routing when a workspace selector is provided.
+    5. Local ASGI transport by default.
     """
     if _client_factory:
         async with _client_factory(workspace=workspace) as client:
@@ -428,6 +433,26 @@ async def get_client(
             yield client
         return
 
+    # --- Workspace-selector routing ---
+    # Trigger: caller passed a cloud workspace selector and nothing above routed.
+    # Why: a workspace names a cloud tenant — silently serving the request from
+    #   the local ASGI app sent writes to the wrong destination (#954: a cloud
+    #   project create either failed on the cloud-style path or landed locally).
+    # Outcome: route to the cloud proxy when credentials exist; without
+    #   credentials fail fast instead of pretending the operation succeeded.
+    if workspace is not None:
+        if not has_cloud_credentials(config):
+            raise RuntimeError(
+                f"A cloud workspace was requested ('{workspace}') but no cloud "
+                "credentials were found. Run 'bm cloud login' or "
+                "'bm cloud set-key <key>' first, or omit the workspace selector "
+                "for a local operation."
+            )
+        logger.debug(f"Workspace selector '{workspace}' provided - using cloud proxy client")
+        async with _cloud_client(config, timeout, workspace=workspace) as client:
+            yield client
+        return
+
     # --- Default fallback ---
     logger.debug("Default routing - using ASGI client for local Basic Memory API")
     async with _asgi_client(timeout) as client:

src/basic_memory/mcp/clients/directory.py

@@ -7,7 +7,9 @@ from typing import Optional, Any
 
 from httpx import AsyncClient
 
-from basic_memory.mcp.tools.utils import call_get
+# call_* helpers live in basic_memory.mcp.tools.utils; importing that at module
+# level executes the whole tools package (fastmcp + mcp SDK) during CLI startup,
+# so each method defers the import to call time instead (#886).
 
 
 class DirectoryClient:
@@ -55,6 +57,8 @@ class DirectoryClient:
         Raises:
             ToolError: If the request fails
         """
+        from basic_memory.mcp.tools.utils import call_get
+
         params: dict = {
             "dir_name": dir_name,
             "depth": depth,

src/basic_memory/mcp/clients/knowledge.py

@@ -8,7 +8,10 @@ from typing import Any
 from httpx import AsyncClient
 
 import logfire
-from basic_memory.mcp.tools.utils import call_get, call_post, call_put, call_patch, call_delete
+
+# call_* helpers live in basic_memory.mcp.tools.utils; importing that at module
+# level executes the whole tools package (fastmcp + mcp SDK) during CLI startup,
+# so each method defers the import to call time instead (#886).
 from basic_memory.schemas.response import (
     EntityResponse,
     DeleteEntitiesResponse,
@@ -57,6 +60,8 @@ class KnowledgeClient:
         Raises:
             ToolError: If the request fails
         """
+        from basic_memory.mcp.tools.utils import call_post
+
         with logfire.span(
             "mcp.client.knowledge.create_entity",
             client_name="knowledge",
@@ -89,6 +94,8 @@ class KnowledgeClient:
         Raises:
             ToolError: If the request fails
         """
+        from basic_memory.mcp.tools.utils import call_put
+
         with logfire.span(
             "mcp.client.knowledge.update_entity",
             client_name="knowledge",
@@ -116,6 +123,8 @@ class KnowledgeClient:
         Raises:
             ToolError: If the entity is not found or request fails
         """
+        from basic_memory.mcp.tools.utils import call_get
+
         with logfire.span(
             "mcp.client.knowledge.get_entity",
             client_name="knowledge",
@@ -147,6 +156,8 @@ class KnowledgeClient:
         Raises:
             ToolError: If the request fails
         """
+        from basic_memory.mcp.tools.utils import call_patch
+
         with logfire.span(
             "mcp.client.knowledge.patch_entity",
             client_name="knowledge",
@@ -174,6 +185,8 @@ class KnowledgeClient:
         Raises:
             ToolError: If the entity is not found or request fails
         """
+        from basic_memory.mcp.tools.utils import call_delete
+
         with logfire.span(
             "mcp.client.knowledge.delete_entity",
             client_name="knowledge",
@@ -201,6 +214,8 @@ class KnowledgeClient:
         Raises:
             ToolError: If the request fails
         """
+        from basic_memory.mcp.tools.utils import call_put
+
         with logfire.span(
             "mcp.client.knowledge.move_entity",
             client_name="knowledge",
@@ -231,6 +246,8 @@ class KnowledgeClient:
         Raises:
             ToolError: If the request fails
         """
+        from basic_memory.mcp.tools.utils import call_post
+
         with logfire.span(
             "mcp.client.knowledge.move_directory",
             client_name="knowledge",
@@ -261,6 +278,8 @@ class KnowledgeClient:
         Raises:
             ToolError: If the request fails
         """
+        from basic_memory.mcp.tools.utils import call_post
+
         with logfire.span(
             "mcp.client.knowledge.delete_directory",
             client_name="knowledge",
@@ -290,6 +309,8 @@ class KnowledgeClient:
         Raises:
             ToolError: If the file does not exist on disk or indexing fails
         """
+        from basic_memory.mcp.tools.utils import call_post
+
         with logfire.span(
             "mcp.client.knowledge.sync_file",
             client_name="knowledge",
@@ -309,6 +330,8 @@ class KnowledgeClient:
 
     async def get_orphans(self) -> list[GraphNode]:
         """Get entities that have no incoming or outgoing relations."""
+        from basic_memory.mcp.tools.utils import call_get
+
         with logfire.span(
             "mcp.client.knowledge.get_orphans",
             client_name="knowledge",
@@ -338,6 +361,8 @@ class KnowledgeClient:
         Raises:
             ToolError: If the identifier cannot be resolved
         """
+        from basic_memory.mcp.tools.utils import call_post
+
         with logfire.span(
             "mcp.client.knowledge.resolve_entity",
             client_name="knowledge",

src/basic_memory/mcp/clients/memory.py

@@ -8,7 +8,10 @@ from typing import Optional
 from httpx import AsyncClient
 
 import logfire
-from basic_memory.mcp.tools.utils import call_get
+
+# call_* helpers live in basic_memory.mcp.tools.utils; importing that at module
+# level executes the whole tools package (fastmcp + mcp SDK) during CLI startup,
+# so each method defers the import to call time instead (#886).
 from basic_memory.schemas.memory import GraphContext
 
 
@@ -63,6 +66,8 @@ class MemoryClient:
         Raises:
             ToolError: If the request fails
         """
+        from basic_memory.mcp.tools.utils import call_get
+
         params: dict = {
             "depth": depth,
             "page": page,
@@ -113,6 +118,8 @@ class MemoryClient:
         Raises:
             ToolError: If the request fails
         """
+        from basic_memory.mcp.tools.utils import call_get
+
         params: dict = {
             "timeframe": timeframe,
             "depth": depth,

src/basic_memory/mcp/clients/project.py

@@ -7,13 +7,9 @@ from typing import Any
 
 from httpx import AsyncClient
 
-from basic_memory.mcp.tools.utils import (
-    call_delete,
-    call_get,
-    call_patch,
-    call_post,
-    call_put,
-)
+# call_* helpers live in basic_memory.mcp.tools.utils; importing that at module
+# level executes the whole tools package (fastmcp + mcp SDK) during CLI startup,
+# so each method defers the import to call time instead (#886).
 from basic_memory.schemas import ProjectInfoResponse, SyncReportResponse
 from basic_memory.schemas.project_info import ProjectList, ProjectStatusResponse
 from basic_memory.schemas.v2 import ProjectResolveResponse
@@ -53,6 +49,8 @@ class ProjectClient:
         Raises:
             ToolError: If the request fails
         """
+        from basic_memory.mcp.tools.utils import call_get
+
         response = await call_get(
             self.http_client,
             "/v2/projects/",
@@ -71,6 +69,8 @@ class ProjectClient:
         Raises:
             ToolError: If the request fails
         """
+        from basic_memory.mcp.tools.utils import call_post
+
         response = await call_post(
             self.http_client,
             "/v2/projects/",
@@ -93,6 +93,8 @@ class ProjectClient:
         Raises:
             ToolError: If the request fails
         """
+        from basic_memory.mcp.tools.utils import call_delete
+
         url = f"/v2/projects/{project_external_id}"
         if delete_notes:
             url += "?delete_notes=true"
@@ -114,6 +116,8 @@ class ProjectClient:
         Raises:
             ToolError: If the request fails
         """
+        from basic_memory.mcp.tools.utils import call_post
+
         response = await call_post(
             self.http_client,
             "/v2/projects/resolve",
@@ -133,6 +137,8 @@ class ProjectClient:
         Raises:
             ToolError: If the request fails
         """
+        from basic_memory.mcp.tools.utils import call_put
+
         response = await call_put(
             self.http_client,
             f"/v2/projects/{project_external_id}/default",
@@ -154,6 +160,8 @@ class ProjectClient:
         Raises:
             ToolError: If the request fails
         """
+        from basic_memory.mcp.tools.utils import call_patch
+
         response = await call_patch(
             self.http_client,
             f"/v2/projects/{project_external_id}",
@@ -181,6 +189,8 @@ class ProjectClient:
         Raises:
             ToolError: If the request fails
         """
+        from basic_memory.mcp.tools.utils import call_post
+
         url = f"/v2/projects/{project_external_id}/sync"
         params = []
         if force_full:
@@ -204,6 +214,8 @@ class ProjectClient:
         Raises:
             ToolError: If the request fails
         """
+        from basic_memory.mcp.tools.utils import call_post
+
         response = await call_post(
             self.http_client,
             f"/v2/projects/{project_external_id}/status",
@@ -222,6 +234,8 @@ class ProjectClient:
         Raises:
             ToolError: If the request fails
         """
+        from basic_memory.mcp.tools.utils import call_get
+
         response = await call_get(
             self.http_client,
             f"/v2/projects/{project_external_id}/info",

src/basic_memory/mcp/clients/resource.py

@@ -6,7 +6,9 @@ Encapsulates all /v2/projects/{project_id}/resource/* endpoints.
 from httpx import AsyncClient, Response
 
 import logfire
-from basic_memory.mcp.tools.utils import call_get
+# call_* helpers live in basic_memory.mcp.tools.utils; importing that at module
+# level executes the whole tools package (fastmcp + mcp SDK) during CLI startup,
+# so each method defers the import to call time instead (#886).
 
 
 class ResourceClient:
@@ -49,6 +51,8 @@ class ResourceClient:
         Raises:
             ToolError: If the resource is not found or request fails
         """
+        from basic_memory.mcp.tools.utils import call_get
+
         with logfire.span(
             "mcp.client.resource.read",
             client_name="resource",

src/basic_memory/mcp/clients/schema.py

@@ -5,7 +5,9 @@ Encapsulates all /v2/projects/{project_id}/schema/* endpoints.
 
 from httpx import AsyncClient
 
-from basic_memory.mcp.tools.utils import call_post, call_get
+# call_* helpers live in basic_memory.mcp.tools.utils; importing that at module
+# level executes the whole tools package (fastmcp + mcp SDK) during CLI startup,
+# so each method defers the import to call time instead (#886).
 from basic_memory.schemas.schema import (
     ValidationReport,
     InferenceReport,
@@ -56,6 +58,8 @@ class SchemaClient:
         Raises:
             ToolError: If the request fails
         """
+        from basic_memory.mcp.tools.utils import call_post
+
         params: dict[str, str] = {}
         if note_type:
             params["note_type"] = note_type
@@ -87,6 +91,8 @@ class SchemaClient:
         Raises:
             ToolError: If the request fails
         """
+        from basic_memory.mcp.tools.utils import call_post
+
         response = await call_post(
             self.http_client,
             f"{self._base_path}/infer",
@@ -106,6 +112,8 @@ class SchemaClient:
         Raises:
             ToolError: If the request fails
         """
+        from basic_memory.mcp.tools.utils import call_get
+
         response = await call_get(
             self.http_client,
             f"{self._base_path}/diff/{note_type}",

src/basic_memory/mcp/clients/search.py

@@ -8,7 +8,10 @@ from typing import Any
 from httpx import AsyncClient
 
 import logfire
-from basic_memory.mcp.tools.utils import call_post
+
+# call_* helpers live in basic_memory.mcp.tools.utils; importing that at module
+# level executes the whole tools package (fastmcp + mcp SDK) during CLI startup,
+# so each method defers the import to call time instead (#886).
 from basic_memory.schemas.search import SearchResponse
 
 
@@ -57,6 +60,8 @@ class SearchClient:
         Raises:
             ToolError: If the request fails
         """
+        from basic_memory.mcp.tools.utils import call_post
+
         with logfire.span(
             "mcp.client.search.search",
             client_name="search",

src/basic_memory/mcp/project_context.py

@@ -8,10 +8,24 @@ The resolve_project_parameter function is a thin wrapper for backwards
 compatibility with existing MCP tools.
 """
 
+# PEP 563 lazy annotations keep `Context` usable in signatures without importing
+# fastmcp at module load — the fastmcp/mcp stack costs ~0.5s of CLI startup (#886).
+from __future__ import annotations
+
 import asyncio
 from contextlib import asynccontextmanager, nullcontext
+from typing import (
+    TYPE_CHECKING,
+    AsyncIterator,
+    Awaitable,
+    Callable,
+    List,
+    Optional,
+    Sequence,
+    Tuple,
+    cast,
+)
 from dataclasses import dataclass, field
-from typing import AsyncIterator, Awaitable, Callable, List, Optional, Sequence, Tuple, cast
 from uuid import UUID
 
 from httpx import AsyncClient
@@ -19,8 +33,6 @@ from httpx._types import (
     HeaderTypes,
 )
 from loguru import logger
-from fastmcp import Context
-from mcp.server.fastmcp.exceptions import ToolError
 
 import logfire
 from basic_memory.config import BasicMemoryConfig, ConfigManager, ProjectMode, has_cloud_credentials
@@ -46,6 +58,9 @@ from basic_memory.workspace_context import (
     workspace_permalink_context,
 )
 
+if TYPE_CHECKING:
+    from fastmcp import Context
+
 # --- Workspace provider injection ---
 # Mirrors the set_client_factory() pattern in async_client.py.
 # The cloud MCP server sets a provider that queries its own database directly,
@@ -54,6 +69,14 @@ _workspace_provider: Optional[Callable[[], Awaitable[list[WorkspaceInfo]]]] = No
 _WORKSPACE_PROJECT_INDEX_STATE_KEY = "workspace_project_index"
 
 
+class WorkspaceProjectLookupMiss(ValueError):
+    """A project was absent from the workspace index (as opposed to ambiguous).
+
+    Misses are retried once against a freshly rebuilt index, because the
+    session cache may simply predate an out-of-band project creation (#956).
+    """
+
+
 @dataclass(frozen=True)
 class WorkspaceProjectEntry:
     """A cloud project resolved together with the workspace that owns it."""
@@ -460,6 +483,17 @@ def _canonical_memory_path_for_workspace(
     # Outcome: lookups preserve the complete workspace/project canonical permalink.
     if not normalized_remainder:
         normalized_remainder = project_permalink
+
+    # Same index-form rule as _canonical_memory_path_for_active_route (#957):
+    # without an active workspace permalink context, stored permalinks are
+    # project-qualified and a workspace-prefixed pattern cannot match.
+    if "*" in normalized_remainder and current_workspace_permalink_context() is None:
+        return build_qualified_permalink_reference(
+            project_permalink,
+            normalized_remainder,
+            include_project=True,
+        )
+
     return build_qualified_permalink_reference(
         project_permalink,
         normalized_remainder,
@@ -477,6 +511,24 @@ def _canonical_memory_path_for_active_route(
 ) -> str:
     """Return the canonical permalink path for the currently routed project/workspace."""
     project_prefix = active_project.permalink
+
+    # Trigger: the path contains a glob wildcard (folder/*) and no server-side
+    #   workspace permalink context is active.
+    # Why: patterns match raw against the search index, so they must mirror the
+    #   stored permalink form. The contextvar is what qualified permalinks at
+    #   write time — when it is absent, stored rows are project-qualified and a
+    #   workspace prefix (from the client's cached_workspace display state)
+    #   guarantees zero matches (#957). Direct lookups keep full qualification
+    #   because the link resolver understands it; patterns have no fallback.
+    # Outcome: without the contextvar, qualify patterns with the project prefix
+    #   only; with it, fall through to normal workspace canonicalization.
+    if "*" in path and current_workspace_permalink_context() is None:
+        if not include_project:
+            return path
+        if path == project_prefix or path.startswith(f"{project_prefix}/"):
+            return path
+        return f"{project_prefix}/{path}"
+
     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
@@ -722,9 +774,15 @@ async def _fetch_workspace_project_entries(
 
 async def _ensure_workspace_project_index(
     context: Optional[Context] = None,
+    *,
+    force_refresh: bool = False,
 ) -> WorkspaceProjectIndex:
-    """Build or load the session-local workspace/project lookup index."""
-    if context:
+    """Build or load the session-local workspace/project lookup index.
+
+    force_refresh bypasses the cached index and rebuilds from discovery —
+    used by resolve_workspace_project_identifier when a lookup misses (#956).
+    """
+    if context and not force_refresh:
         cached_raw = await context.get_state(_WORKSPACE_PROJECT_INDEX_STATE_KEY)
         cached_index = _workspace_project_index_from_state(cached_raw)
         if cached_index is not None:
@@ -798,13 +856,99 @@ async def ensure_workspace_project_index(
     return await _ensure_workspace_project_index(context=context)
 
 
+def _match_workspace_identifier(
+    workspaces: tuple[WorkspaceInfo, ...],
+    workspace_identifier: str,
+) -> WorkspaceInfo:
+    """Resolve the first segment of a qualified route to a single workspace.
+
+    The edit_note/write_note contract advertises that the workspace segment may be a
+    slug, tenant_id, or display name. We honor those forms in a fixed priority order so
+    that adding tenant_id/name support never changes the meaning of an identifier that
+    already resolves today:
+
+    1. slug (casefold) — existing behavior, checked first so working routes are stable.
+    2. tenant_id — exact match against the opaque id (no casefolding, mirroring the
+       precedent in ``workspace_matches_exact_identifier``).
+    3. display name (casefold) — names are not guaranteed unique, so a name that matches
+       multiple workspaces is rejected rather than silently picking one.
+    """
+    # Trigger: identifier equals a workspace slug (casefold).
+    # Why: slug is the canonical routing key; resolving it first guarantees a workspace
+    # whose display name collides with another workspace's slug yields to the slug owner.
+    # Outcome: return the slug owner before tenant_id/name are considered.
+    slug_matches = [
+        workspace
+        for workspace in workspaces
+        if workspace.slug.casefold() == workspace_identifier.casefold()
+    ]
+    if slug_matches:
+        return slug_matches[0]
+
+    # Trigger: identifier exactly equals a workspace tenant_id (an opaque id).
+    # Why: tenant_ids are unique, so an exact hit is unambiguous and needs no tie-break.
+    tenant_matches = [
+        workspace for workspace in workspaces if workspace.tenant_id == workspace_identifier
+    ]
+    if tenant_matches:
+        return tenant_matches[0]
+
+    # Trigger: identifier matches one or more workspace display names (casefold).
+    # Why: names are not guaranteed unique; failing fast on collisions keeps routing
+    # deterministic and tells the caller exactly how to disambiguate.
+    name_matches = [
+        workspace
+        for workspace in workspaces
+        if workspace.name.casefold() == workspace_identifier.casefold()
+    ]
+    if len(name_matches) > 1:
+        candidates = ", ".join(workspace.slug for workspace in name_matches)
+        raise ValueError(
+            f"Workspace name '{workspace_identifier}' matched multiple workspaces "
+            f"(slugs: {candidates}). Use the workspace slug or tenant_id to disambiguate."
+        )
+    if name_matches:
+        return name_matches[0]
+
+    available = ", ".join(workspace.slug for workspace in workspaces)
+    raise ValueError(
+        f"Workspace '{workspace_identifier}' was not found by slug, tenant_id, or name. "
+        f"Available workspace slugs: {available}"
+    )
+
+
 async def resolve_workspace_project_identifier(
     project: str,
     context: Optional[Context] = None,
 ) -> WorkspaceProjectEntry:
     """Resolve a project by external_id (UUID), qualified name, or unqualified name."""
     index = await _ensure_workspace_project_index(context=context)
+    try:
+        return await _resolve_workspace_project_from_index(index, project, context)
+    except WorkspaceProjectLookupMiss:
+        # Trigger: the lookup missed the session-cached index.
+        # Why: a miss is exactly the signal the cache may be stale — projects
+        #   created out-of-band (CLI, a teammate in a shared workspace) post-date
+        #   the index built at session start (#956).
+        # Outcome: rebuild the index once and retry; a second miss is authoritative
+        #   and its error (with the refreshed project list) propagates.
+        logger.info(
+            f"Workspace project lookup missed for '{project}'; refreshing index and retrying"
+        )
+        refreshed = await _ensure_workspace_project_index(context=context, force_refresh=True)
+        return await _resolve_workspace_project_from_index(refreshed, project, context)
 
+
+async def _resolve_workspace_project_from_index(
+    index: WorkspaceProjectIndex,
+    project: str,
+    context: Optional[Context] = None,
+) -> WorkspaceProjectEntry:
+    """Resolve a project against one concrete index snapshot.
+
+    Raises WorkspaceProjectLookupMiss for absent projects (retryable via index
+    refresh) and plain ValueError for ambiguity, which a refresh cannot fix.
+    """
     # Fast path: direct lookup by external_id when the identifier is a UUID
     # Canonicalize via str(UUID(...)) so uppercase, brace-wrapped, or urn:uuid forms
     # all hash to the same lowercase-hyphenated key as the stored external_ids.
@@ -816,23 +960,14 @@ async def resolve_workspace_project_identifier(
     except ValueError:
         pass
 
-    workspace_slug, project_identifier = _split_qualified_project_identifier(project)
+    workspace_identifier, project_identifier = _split_qualified_project_identifier(project)
     project_permalink = generate_permalink(project_identifier)
 
-    if workspace_slug:
-        workspace_matches = [
-            workspace
-            for workspace in index.workspaces
-            if workspace.slug.casefold() == workspace_slug.casefold()
-        ]
-        if not workspace_matches:
-            available = ", ".join(workspace.slug for workspace in index.workspaces)
-            raise ValueError(
-                f"Workspace '{workspace_slug}' was not found. "
-                f"Available workspace slugs: {available}"
-            )
-
-        workspace = workspace_matches[0]
+    if workspace_identifier:
+        # Honor the documented "slug, name, or tenant_id" contract for the workspace
+        # segment; _match_workspace_identifier raises a clear error on ambiguous names
+        # and unknown identifiers, listing what forms were tried.
+        workspace = _match_workspace_identifier(index.workspaces, workspace_identifier)
         matches = [
             entry
             for entry in index.entries_by_permalink.get(project_permalink, ())
@@ -843,7 +978,7 @@ async def resolve_workspace_project_identifier(
                 failed_workspace.tenant_id == workspace.tenant_id
                 for failed_workspace in index.failed_workspaces
             ):
-                raise ValueError(
+                raise WorkspaceProjectLookupMiss(
                     f"Projects for workspace '{workspace.name}' ({workspace.slug}) "
                     "could not be loaded. Retry after workspace discovery recovers."
                 )
@@ -852,7 +987,7 @@ async def resolve_workspace_project_identifier(
                 for entry in index.entries
                 if entry.workspace.tenant_id == workspace.tenant_id
             )
-            raise ValueError(
+            raise WorkspaceProjectLookupMiss(
                 f"Project '{project_identifier}' was not found in workspace "
                 f"'{workspace.name}' ({workspace.slug}). Available projects: {available}"
             )
@@ -877,7 +1012,7 @@ async def resolve_workspace_project_identifier(
                 "retry or use a qualified project from an indexed workspace."
             )
         available = ", ".join(entry.qualified_name for entry in index.entries)
-        raise ValueError(
+        raise WorkspaceProjectLookupMiss(
             f"Project '{project}' was not found in indexed cloud workspaces. "
             f"Available projects: {available}.{failed_note}"
         )
@@ -1212,6 +1347,9 @@ async def resolve_project_and_path(
         # Why: allow project-scoped memory URLs without requiring a separate project parameter
         # Outcome: attempt to resolve the prefix as a project and route to it
         if project_prefix:
+            # Deferred: ToolError lives in the mcp SDK, which must not load at CLI startup (#886).
+            from mcp.server.fastmcp.exceptions import ToolError
+
             if cached_project and _project_matches_identifier(cached_project, project_prefix):
                 resolved_project = await resolve_project_parameter(project_prefix, context=context)
                 if resolved_project and generate_permalink(resolved_project) != generate_permalink(
@@ -1438,6 +1576,9 @@ async def get_project_client(
         is_factory_mode,
     )
 
+    # Deferred: ToolError lives in the mcp SDK, which must not load at CLI startup (#886).
+    from mcp.server.fastmcp.exceptions import ToolError
+
     # When project_id (UUID) is provided, prefer it as the resolution identifier.
     # external_id is unambiguous across workspaces; project name can collide.
     project_identifier = project_id if project_id else project

src/basic_memory/mcp/resources/discovery.py

@@ -0,0 +1,17 @@
+"""Shared loader for the bundled cloud-discovery markdown resources."""
+
+from pathlib import Path
+
+
+def load_discovery_resource(filename: str) -> str:
+    """Read a bundled discovery markdown file with promo placeholders rendered.
+
+    The markdown carries a {{OSS_DISCOUNT_CODE}} placeholder so the promo code
+    has one source of truth (cli.promo); substitute before it reaches users.
+    """
+    # Import here to avoid pulling CLI promo machinery (analytics, rich, config)
+    # into the MCP server import graph at module load.
+    from basic_memory.cli.promo import OSS_DISCOUNT_CODE
+
+    content = (Path(__file__).parent / filename).read_text(encoding="utf-8")
+    return content.replace("{{OSS_DISCOUNT_CODE}}", OSS_DISCOUNT_CODE)

src/basic_memory/mcp/tools/build_context.py

@@ -54,7 +54,10 @@ def _format_entity_block(result: ContextResult) -> str:
         lines.append("")
         lines.append("### Relations")
         for rel in relation_items:
-            lines.append(f"- {rel.relation_type} [[{rel.to_entity}]]")
+            # Unresolved forward references have no resolved entity yet; fall back
+            # to the literal target text instead of rendering [[None]] (#955)
+            target = rel.to_entity or rel.to_name
+            lines.append(f"- {rel.relation_type} [[{target}]]")
 
     # --- Related entities (non-relation related results) ---
     related_entities: list[EntitySummary | ObservationSummary] = [
@@ -112,6 +115,7 @@ def _format_context_markdown(graph: GraphContext, project: str) -> str:
 
 
 @mcp.tool(
+    title="Build Context",
     description="""Build context from a memory:// URI to continue conversations naturally.
 
     Use this to follow up on previous discussions or explore related topics.
@@ -131,6 +135,7 @@ def _format_context_markdown(graph: GraphContext, project: str) -> str:
     - "json" (default): Structured JSON with internal fields excluded
     - "text": Compact markdown text for LLM consumption
     """,
+    tags={"navigation", "notes"},
     annotations={"readOnlyHint": True, "openWorldHint": False},
 )
 async def build_context(

src/basic_memory/mcp/tools/canvas.py

@@ -17,7 +17,9 @@ from basic_memory.mcp.tools.utils import call_put, call_post, resolve_entity_id
 
 
 @mcp.tool(
+    title="Create Canvas",
     description="Create an Obsidian canvas file to visualize concepts and connections.",
+    tags={"canvas", "notes"},
     annotations={"destructiveHint": False, "idempotentHint": True, "openWorldHint": False},
 )
 async def canvas(

src/basic_memory/mcp/tools/chatgpt_tools.py

@@ -105,7 +105,9 @@ def _format_document_for_chatgpt(
 
 
 @mcp.tool(
+    title="Search Knowledge Base",
     description="Search for content across the knowledge base",
+    tags={"search"},
     annotations={"readOnlyHint": True, "openWorldHint": False},
 )
 async def search(
@@ -167,7 +169,9 @@ async def search(
 
 
 @mcp.tool(
+    title="Fetch Document",
     description="Fetch the full contents of a search result document",
+    tags={"search", "notes"},
     annotations={"readOnlyHint": True, "openWorldHint": False},
 )
 async def fetch(

src/basic_memory/mcp/tools/cloud_info.py

@@ -1,15 +1,15 @@
 """Cloud information MCP tool."""
 
-from pathlib import Path
-
+from basic_memory.mcp.resources.discovery import load_discovery_resource
 from basic_memory.mcp.server import mcp
 
 
 @mcp.tool(
     "cloud_info",
+    title="Cloud Info",
+    tags={"cloud"},
     annotations={"readOnlyHint": True, "openWorldHint": False},
 )
 def cloud_info() -> str:
     """Return optional Basic Memory Cloud information and setup guidance."""
-    content_path = Path(__file__).parent.parent / "resources" / "cloud_info.md"
-    return content_path.read_text(encoding="utf-8")
+    return load_discovery_resource("cloud_info.md")

src/basic_memory/mcp/tools/delete_note.py

@@ -182,7 +182,9 @@ def _directory_path_for_delete(
 
 
 @mcp.tool(
+    title="Delete Note",
     description="Delete a note or directory by title, permalink, or path",
+    tags={"notes"},
     annotations={"destructiveHint": True, "openWorldHint": False},
 )
 async def delete_note(

src/basic_memory/mcp/tools/edit_note.py

@@ -304,7 +304,9 @@ Error editing note '{identifier}': {error_message}
 
 
 @mcp.tool(
+    title="Edit Note",
     description="Edit an existing markdown note using various operations like append, prepend, find_replace, replace_section, insert_before_section, or insert_after_section.",
+    tags={"notes"},
     annotations={"destructiveHint": False, "openWorldHint": False},
 )
 async def edit_note(

src/basic_memory/mcp/tools/list_directory.py

@@ -11,7 +11,9 @@ from basic_memory.mcp.server import mcp
 
 
 @mcp.tool(
+    title="List Directory",
     description="List directory contents with filtering and depth control.",
+    tags={"navigation", "notes"},
     annotations={"readOnlyHint": True, "openWorldHint": False},
 )
 async def list_directory(

src/basic_memory/mcp/tools/move_note.py

@@ -357,7 +357,9 @@ delete_note("{identifier}")
 
 
 @mcp.tool(
+    title="Move Note",
     description="Move a note or directory to a new location, updating database and maintaining links.",
+    tags={"notes"},
     annotations={"destructiveHint": False, "openWorldHint": False},
 )
 async def move_note(

src/basic_memory/mcp/tools/project_management.py

@@ -357,6 +357,8 @@ def _format_project_list_json(
 
 @mcp.tool(
     "list_memory_projects",
+    title="List Memory Projects",
+    tags={"projects"},
     annotations={"readOnlyHint": True, "openWorldHint": False},
 )
 async def list_memory_projects(
@@ -475,10 +477,14 @@ async def _resolve_workspace_routing(
     if workspace is None:
         return None
 
-    explicit_cloud_routing = _explicit_routing() and not _force_local_mode()
+    forced_local = _explicit_routing() and _force_local_mode()
     config = ConfigManager().config
+    # Resolve whenever credentials make workspace discovery possible — not only
+    # under explicit --cloud. A workspace selector implies cloud routing
+    # (get_client routes it to the cloud proxy, #954), and the transport needs
+    # the tenant id in X-Workspace-ID, not a slug or display name.
     should_resolve_workspace = is_factory_mode() or (
-        explicit_cloud_routing and has_cloud_credentials(config)
+        has_cloud_credentials(config) and not forced_local
     )
     if not should_resolve_workspace:
         return workspace
@@ -495,6 +501,8 @@ async def _resolve_workspace_routing(
 
 @mcp.tool(
     "create_memory_project",
+    title="Create Memory Project",
+    tags={"projects"},
     annotations={"destructiveHint": False, "openWorldHint": False},
 )
 async def create_memory_project(
@@ -517,8 +525,9 @@ 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`. In local mode the selector is passed through
-            without slug resolution.
+            via `list_workspaces`. A workspace selector implies cloud routing:
+            without cloud credentials the call fails fast instead of silently
+            creating a local project (#954).
         output_format: "text" returns the existing human-readable result text.
             "json" returns structured project creation metadata.
         context: Optional FastMCP context for progress/status logging.
@@ -636,6 +645,8 @@ async def create_memory_project(
 
 
 @mcp.tool(
+    title="Delete Project",
+    tags={"projects"},
     annotations={"destructiveHint": True, "openWorldHint": False},
 )
 async def delete_project(
@@ -654,8 +665,9 @@ async def delete_project(
         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.
+            used. A workspace selector implies cloud routing: without cloud
+            credentials the call fails fast, matching create_memory_project
+            behavior (#954).
 
     Returns:
         Confirmation message about project deletion

src/basic_memory/mcp/tools/read_content.py

@@ -155,7 +155,9 @@ def optimize_image(img, content_length, max_output_bytes=350000):
 
 
 @mcp.tool(
+    title="Read Content",
     description="Read a file's raw content by path or permalink",
+    tags={"notes"},
     annotations={"readOnlyHint": True, "openWorldHint": False},
 )
 async def read_content(

src/basic_memory/mcp/tools/read_note.py

@@ -74,7 +74,9 @@ def _parse_opening_frontmatter(content: str) -> tuple[str, dict | None]:
 
 
 @mcp.tool(
+    title="Read Note",
     description="Read a markdown note by title or permalink.",
+    tags={"notes"},
     # TODO: re-enable once MCP client rendering is working
     # meta={"ui/resourceUri": "ui://basic-memory/note-preview"},
     annotations={"readOnlyHint": True, "openWorldHint": False},

src/basic_memory/mcp/tools/recent_activity.py

@@ -26,6 +26,7 @@ from basic_memory.schemas.search import SearchItemType
 
 
 @mcp.tool(
+    title="Recent Activity",
     description="""Get recent activity for a project or across all projects.
 
     Timeframe supports natural language formats like:
@@ -36,6 +37,7 @@ from basic_memory.schemas.search import SearchItemType
     - "3 weeks ago"
     Or standard formats like "7d"
     """,
+    tags={"navigation", "notes"},
     annotations={"readOnlyHint": True, "openWorldHint": False},
 )
 async def recent_activity(

src/basic_memory/mcp/tools/release_notes.py

@@ -1,15 +1,15 @@
 """Release notes MCP tool."""
 
-from pathlib import Path
-
+from basic_memory.mcp.resources.discovery import load_discovery_resource
 from basic_memory.mcp.server import mcp
 
 
 @mcp.tool(
     "release_notes",
+    title="Release Notes",
+    tags={"cloud"},
     annotations={"readOnlyHint": True, "openWorldHint": False},
 )
 def release_notes() -> str:
     """Return the latest product release notes for optional user review."""
-    content_path = Path(__file__).parent.parent / "resources" / "release_notes.md"
-    return content_path.read_text(encoding="utf-8")
+    return load_discovery_resource("release_notes.md")

src/basic_memory/mcp/tools/schema.py

@@ -204,7 +204,9 @@ def _no_schema_guidance(note_type: str, tool_name: str) -> str:
 
 
 @mcp.tool(
+    title="Validate Schema",
     description="Validate notes against their Picoschema definitions.",
+    tags={"schema"},
     annotations={"readOnlyHint": True, "openWorldHint": False},
 )
 async def schema_validate(
@@ -317,7 +319,9 @@ async def schema_validate(
 
 
 @mcp.tool(
+    title="Infer Schema",
     description="Analyze existing notes and suggest a Picoschema definition.",
+    tags={"schema"},
     annotations={"readOnlyHint": True, "openWorldHint": False},
 )
 async def schema_infer(
@@ -438,7 +442,9 @@ async def schema_infer(
 
 
 @mcp.tool(
+    title="Schema Diff",
     description="Detect drift between a schema definition and actual note usage.",
+    tags={"schema"},
     annotations={"readOnlyHint": True, "openWorldHint": False},
 )
 async def schema_diff(

src/basic_memory/mcp/tools/search.py

@@ -14,7 +14,7 @@ from basic_memory.config import ConfigManager, has_cloud_credentials
 from basic_memory.utils import (
     build_canonical_permalink,
     coerce_dict,
-    coerce_list,
+    parse_str_list,
     parse_tags,
     strict_search_tags,
 )
@@ -612,7 +612,9 @@ async def _search_all_projects(
 
 
 @mcp.tool(
+    title="Search Notes",
     description="Search across all content in the knowledge base with advanced syntax support.",
+    tags={"search"},
     # TODO: re-enable once MCP client rendering is working
     # meta={"ui/resourceUri": "ui://basic-memory/search-results"},
     annotations={"readOnlyHint": True, "openWorldHint": False},
@@ -649,24 +651,30 @@ async def search_notes(
     # Plural-vs-singular trips models constantly. Accept the singular too.
     note_types: Annotated[
         List[str] | None,
-        BeforeValidator(coerce_list),
+        # parse_str_list, not coerce_list: "note,task" must split into ["note", "task"]
+        # consistent with how tags are handled (#910/#930). coerce_list wraps the whole
+        # comma string as the single literal type ["note,task"], which matches nothing.
+        BeforeValidator(parse_str_list),
         Field(default=None, validation_alias=AliasChoices("note_types", "note_type", "types")),
         "Filter by the 'type' field in note frontmatter (e.g. 'note', 'chapter', 'person'). "
+        "Accepts a list, a comma-separated string (e.g. 'note,task'), or a JSON-array string. "
         "Case-insensitive.",
     ] = None,
     entity_types: Annotated[
         List[str] | None,
-        BeforeValidator(coerce_list),
+        BeforeValidator(parse_str_list),
         Field(default=None, validation_alias=AliasChoices("entity_types", "entity_type")),
         "Filter by knowledge graph item type: 'entity' (whole notes), 'observation', or "
         "'relation'. Defaults to 'entity'. Do NOT pass schema/frontmatter types like "
-        "'Chapter' here — use note_types instead.",
+        "'Chapter' here — use note_types instead. "
+        "Accepts a list, a comma-separated string (e.g. 'entity,observation'), or a JSON-array string.",
     ] = None,
     categories: Annotated[
         List[str] | None,
-        BeforeValidator(coerce_list),
+        BeforeValidator(parse_str_list),
         Field(default=None, validation_alias=AliasChoices("categories", "category")),
         "Filter observation results to these exact categories (e.g. ['requirement']). "
+        "Accepts a list, a comma-separated string (e.g. 'requirement,decision'), or a JSON-array string. "
         "Pair with entity_types=['observation'] to return only observations whose "
         "category matches exactly — not every row mentioning the word.",
     ] = None,
@@ -820,6 +828,11 @@ async def search_notes(
         Formatted markdown text (output_format="text"), dict (output_format="json"),
         or helpful error guidance string if search fails
 
+        Pagination note: `total` is exact only for text/title/permalink searches.
+        Vector and hybrid searches skip the count query (it would cost a second
+        semantic retrieval pass) and report `total: 0` even when results are
+        returned — use `has_more` for pagination in those modes.
+
     Examples:
         # Basic text search
         results = await search_notes("project planning")
@@ -893,6 +906,17 @@ async def search_notes(
     if page_size < 1:
         raise ValueError(f"page_size must be >= 1, got {page_size}")
 
+    # Trigger: list params arrived via a direct function call instead of the MCP layer.
+    # Why: the BeforeValidator annotations only run through MCP/Pydantic validation; direct
+    #      callers (e.g. `bm tool search-notes --type note,task` in cli/commands/tool.py,
+    #      which Typer collects as the one-element list ["note,task"]) would otherwise
+    #      forward the comma string as one literal type that matches nothing (#930).
+    # Outcome: comma-split/list normalization applies on every path; parse_str_list is
+    #          idempotent, so MCP-validated input passes through unchanged.
+    note_types = parse_str_list(note_types) if note_types is not None else []
+    entity_types = parse_str_list(entity_types) if entity_types is not None else []
+    categories = parse_str_list(categories) if categories is not None else []
+
     # Avoid mutable-default-argument footguns. Treat None as "no filter".
     # Lowercase note_types so "Chapter" matches the stored "chapter".
     note_types = [t.lower() for t in note_types] if note_types else []

src/basic_memory/mcp/tools/ui_sdk.py

@@ -18,7 +18,9 @@ def _text_block(message: str) -> List[ContentBlock]:
 
 
 @mcp.tool(
+    title="Search Notes (UI)",
     description="Search notes and return an embedded MCP-UI resource (raw HTML).",
+    tags={"search", "ui"},
     output_schema=None,
     annotations={"readOnlyHint": True, "openWorldHint": False},
 )
@@ -92,7 +94,9 @@ async def search_notes_ui(
 
 
 @mcp.tool(
+    title="Read Note (UI)",
     description="Read a note and return an embedded MCP-UI resource (raw HTML).",
+    tags={"notes", "ui"},
     output_schema=None,
     annotations={"readOnlyHint": True, "openWorldHint": False},
 )

src/basic_memory/mcp/tools/view_note.py

@@ -11,7 +11,9 @@ from basic_memory.mcp.tools.read_note import read_note
 
 
 @mcp.tool(
+    title="View Note",
     description="View a note as a formatted artifact for better readability.",
+    tags={"notes"},
     annotations={"readOnlyHint": True, "openWorldHint": False},
 )
 async def view_note(

src/basic_memory/mcp/tools/workspaces.py

@@ -45,7 +45,9 @@ def _workspace_list_response(workspaces: list[WorkspaceInfo]) -> WorkspaceListRe
 
 
 @mcp.tool(
+    title="List Workspaces",
     description="List available cloud workspaces (tenant_id, type, role, and name).",
+    tags={"cloud", "projects"},
     annotations={"readOnlyHint": True, "openWorldHint": False},
 )
 async def list_workspaces(

src/basic_memory/mcp/tools/write_note.py

@@ -25,8 +25,39 @@ from basic_memory.workspace_context import current_workspace_permalink_context
 TagType = Union[List[str], str, None]
 
 
+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}"
+
+
 @mcp.tool(
+    title="Write Note",
     description="Create a markdown note. If the note already exists, returns an error by default — pass overwrite=True to replace.",
+    tags={"notes"},
     annotations={"destructiveHint": True, "idempotentHint": False, "openWorldHint": False},
 )
 async def write_note(
@@ -38,6 +69,7 @@ async def write_note(
         Field(validation_alias=AliasChoices("directory", "folder", "dir", "path")),
     ],
     project: Optional[str] = None,
+    workspace: Optional[str] = None,
     project_id: Optional[str] = None,
     tags: list[str] | str | None = None,
     note_type: str = "note",
@@ -93,6 +125,8 @@ async def write_note(
                 form (or project_id) to disambiguate. If unknown, use
                 list_memory_projects() to discover available projects and their
                 qualified names.
+        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().
@@ -170,6 +204,11 @@ async def write_note(
     effective_overwrite = (
         overwrite if overwrite is not None else ConfigManager().config.write_note_overwrite_default
     )
+    project = _compose_workspace_project_route(
+        workspace=workspace,
+        project=project,
+        project_id=project_id,
+    )
 
     with logfire.span(
         "mcp.tool.write_note",

src/basic_memory/repository/entity_repository.py

@@ -7,12 +7,11 @@ from typing import List, Optional, Sequence, Union, Any
 from loguru import logger
 from sqlalchemy import exists, func, select
 from sqlalchemy.exc import IntegrityError
-from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker
+from sqlalchemy.ext.asyncio import AsyncSession
 from sqlalchemy.orm import load_only, selectinload
 from sqlalchemy.orm.interfaces import LoaderOption
 from sqlalchemy.engine import Row
 
-from basic_memory import db
 from basic_memory.models.knowledge import Entity, Observation, Relation
 from basic_memory.repository.repository import Repository
 
@@ -24,16 +23,17 @@ class EntityRepository(Repository[Entity]):
     to strings before passing to repository methods.
     """
 
-    def __init__(self, session_maker: async_sessionmaker[AsyncSession], project_id: int):
-        """Initialize with session maker and project_id filter.
+    def __init__(self, project_id: int):
+        """Initialize with project_id filter.
 
         Args:
-            session_maker: SQLAlchemy session maker
             project_id: Project ID to filter all operations by
         """
-        super().__init__(session_maker, Entity, project_id=project_id)
+        super().__init__(Entity, project_id=project_id)
 
-    async def get_by_id(self, entity_id: int, *, load_relations: bool = True) -> Optional[Entity]:
+    async def get_by_id(
+        self, session: AsyncSession, entity_id: int, *, load_relations: bool = True
+    ) -> Optional[Entity]:
         """Get entity by numeric ID.
 
         Args:
@@ -42,23 +42,24 @@ class EntityRepository(Repository[Entity]):
         Returns:
             Entity if found, None otherwise
         """
-        async with db.scoped_session(self.session_maker) as session:
-            if not load_relations:
-                result = await session.execute(self.select().where(Entity.id == entity_id))
-                return result.scalars().one_or_none()
+        if not load_relations:
+            result = await session.execute(self.select().where(Entity.id == entity_id))
+            return result.scalars().one_or_none()
 
-            return await self.select_by_id(session, entity_id)
+        return await self.select_by_id(session, entity_id)
 
-    async def _find_one_by_query(self, query, *, load_relations: bool) -> Optional[Entity]:
+    async def _find_one_by_query(
+        self, session: AsyncSession, query, *, load_relations: bool
+    ) -> Optional[Entity]:
         """Return one entity row with optional eager loading."""
         if load_relations:
-            return await self.find_one(query)
+            return await self.find_one(session, query)
 
-        result = await self.execute_query(query, use_query_options=False)
+        result = await self.execute_query(session, query, use_query_options=False)
         return result.scalars().one_or_none()
 
     async def get_by_external_id(
-        self, external_id: str, *, load_relations: bool = True
+        self, session: AsyncSession, external_id: str, *, load_relations: bool = True
     ) -> Optional[Entity]:
         """Get entity by external UUID.
 
@@ -69,10 +70,10 @@ class EntityRepository(Repository[Entity]):
             Entity if found, None otherwise
         """
         query = self.select().where(Entity.external_id == external_id)
-        return await self._find_one_by_query(query, load_relations=load_relations)
+        return await self._find_one_by_query(session, query, load_relations=load_relations)
 
     async def get_by_permalink(
-        self, permalink: str, *, load_relations: bool = True
+        self, session: AsyncSession, permalink: str, *, load_relations: bool = True
     ) -> Optional[Entity]:
         """Get entity by permalink.
 
@@ -80,9 +81,11 @@ class EntityRepository(Repository[Entity]):
             permalink: Unique identifier for the entity
         """
         query = self.select().where(Entity.permalink == permalink)
-        return await self._find_one_by_query(query, load_relations=load_relations)
+        return await self._find_one_by_query(session, query, load_relations=load_relations)
 
-    async def get_by_title(self, title: str, *, load_relations: bool = True) -> Sequence[Entity]:
+    async def get_by_title(
+        self, session: AsyncSession, title: str, *, load_relations: bool = True
+    ) -> Sequence[Entity]:
         """Get entities by title, ordered by shortest path first.
 
         When multiple entities share the same title (in different folders),
@@ -97,11 +100,11 @@ class EntityRepository(Repository[Entity]):
             .where(Entity.title == title)
             .order_by(func.length(Entity.file_path), Entity.file_path)
         )
-        result = await self.execute_query(query, use_query_options=load_relations)
+        result = await self.execute_query(session, query, use_query_options=load_relations)
         return list(result.scalars().all())
 
     async def get_by_file_path(
-        self, file_path: Union[Path, str], *, load_relations: bool = True
+        self, session: AsyncSession, file_path: Union[Path, str], *, load_relations: bool = True
     ) -> Optional[Entity]:
         """Get entity by file_path.
 
@@ -109,13 +112,13 @@ class EntityRepository(Repository[Entity]):
             file_path: Path to the entity file (will be converted to string internally)
         """
         query = self.select().where(Entity.file_path == Path(file_path).as_posix())
-        return await self._find_one_by_query(query, load_relations=load_relations)
+        return await self._find_one_by_query(session, query, load_relations=load_relations)
 
     # -------------------------------------------------------------------------
     # Lightweight methods for permalink resolution (no eager loading)
     # -------------------------------------------------------------------------
 
-    async def permalink_exists(self, permalink: str) -> bool:
+    async def permalink_exists(self, session: AsyncSession, permalink: str) -> bool:
         """Check if a permalink exists without loading the full entity.
 
         This is much faster than get_by_permalink() as it skips eager loading
@@ -129,10 +132,12 @@ class EntityRepository(Repository[Entity]):
         """
         query = select(Entity.id).where(Entity.permalink == permalink).limit(1)
         query = self._add_project_filter(query)
-        result = await self.execute_query(query, use_query_options=False)
+        result = await self.execute_query(session, query, use_query_options=False)
         return result.scalar_one_or_none() is not None
 
-    async def get_file_path_for_permalink(self, permalink: str) -> Optional[str]:
+    async def get_file_path_for_permalink(
+        self, session: AsyncSession, permalink: str
+    ) -> Optional[str]:
         """Get the file_path for a permalink without loading the full entity.
 
         Use when you only need the file_path, not the full entity with relations.
@@ -145,10 +150,12 @@ class EntityRepository(Repository[Entity]):
         """
         query = select(Entity.file_path).where(Entity.permalink == permalink)
         query = self._add_project_filter(query)
-        result = await self.execute_query(query, use_query_options=False)
+        result = await self.execute_query(session, query, use_query_options=False)
         return result.scalar_one_or_none()
 
-    async def get_permalink_for_file_path(self, file_path: Union[Path, str]) -> Optional[str]:
+    async def get_permalink_for_file_path(
+        self, session: AsyncSession, file_path: Union[Path, str]
+    ) -> Optional[str]:
         """Get the permalink for a file_path without loading the full entity.
 
         Use when you only need the permalink, not the full entity with relations.
@@ -161,10 +168,10 @@ class EntityRepository(Repository[Entity]):
         """
         query = select(Entity.permalink).where(Entity.file_path == Path(file_path).as_posix())
         query = self._add_project_filter(query)
-        result = await self.execute_query(query, use_query_options=False)
+        result = await self.execute_query(session, query, use_query_options=False)
         return result.scalar_one_or_none()
 
-    async def get_all_permalinks(self) -> List[str]:
+    async def get_all_permalinks(self, session: AsyncSession) -> List[str]:
         """Get all permalinks for this project.
 
         Optimized for bulk operations - returns only permalink strings
@@ -175,11 +182,11 @@ class EntityRepository(Repository[Entity]):
         """
         query = select(Entity.permalink)
         query = self._add_project_filter(query)
-        result = await self.execute_query(query, use_query_options=False)
+        result = await self.execute_query(session, query, use_query_options=False)
         return list(result.scalars().all())
 
     async def find_by_ids_for_hydration(
-        self, ids: List[int], *, include_cross_project: bool = False
+        self, session: AsyncSession, ids: List[int], *, include_cross_project: bool = False
     ) -> Sequence[Entity]:
         """Fetch minimal entity fields needed for context hydration.
 
@@ -203,10 +210,10 @@ class EntityRepository(Repository[Entity]):
         if not include_cross_project:
             query = self._add_project_filter(query)
 
-        result = await self.execute_query(query, use_query_options=False)
+        result = await self.execute_query(session, query, use_query_options=False)
         return list(result.scalars().all())
 
-    async def get_permalink_to_file_path_map(self) -> dict[str, str]:
+    async def get_permalink_to_file_path_map(self, session: AsyncSession) -> dict[str, str]:
         """Get a mapping of permalink -> file_path for all entities.
 
         Optimized for bulk permalink resolution - loads minimal data in one query.
@@ -216,10 +223,10 @@ class EntityRepository(Repository[Entity]):
         """
         query = select(Entity.permalink, Entity.file_path)
         query = self._add_project_filter(query)
-        result = await self.execute_query(query, use_query_options=False)
+        result = await self.execute_query(session, query, use_query_options=False)
         return {row.permalink: row.file_path for row in result.all()}
 
-    async def get_file_path_to_permalink_map(self) -> dict[str, str]:
+    async def get_file_path_to_permalink_map(self, session: AsyncSession) -> dict[str, str]:
         """Get a mapping of file_path -> permalink for all entities.
 
         Optimized for bulk permalink resolution - loads minimal data in one query.
@@ -229,7 +236,7 @@ class EntityRepository(Repository[Entity]):
         """
         query = select(Entity.file_path, Entity.permalink)
         query = self._add_project_filter(query)
-        result = await self.execute_query(query, use_query_options=False)
+        result = await self.execute_query(session, query, use_query_options=False)
         return {row.file_path: row.permalink for row in result.all()}
 
     async def get_by_file_paths(
@@ -262,7 +269,7 @@ class EntityRepository(Repository[Entity]):
         result = await session.execute(query)  # pragma: no cover
         return list(result.all())  # pragma: no cover
 
-    async def find_by_checksum(self, checksum: str) -> Sequence[Entity]:
+    async def find_by_checksum(self, session: AsyncSession, checksum: str) -> Sequence[Entity]:
         """Find entities with the given checksum.
 
         Used for move detection - finds entities that may have been moved to a new path.
@@ -276,10 +283,12 @@ class EntityRepository(Repository[Entity]):
         """
         query = self.select().where(Entity.checksum == checksum)
         # Don't load relationships for move detection - we only need file_path and checksum
-        result = await self.execute_query(query, use_query_options=False)
+        result = await self.execute_query(session, query, use_query_options=False)
         return list(result.scalars().all())
 
-    async def find_by_checksums(self, checksums: Sequence[str]) -> Sequence[Entity]:
+    async def find_by_checksums(
+        self, session: AsyncSession, checksums: Sequence[str]
+    ) -> Sequence[Entity]:
         """Find entities with any of the given checksums (batch query for move detection).
 
         This is a batch-optimized version of find_by_checksum() that queries multiple checksums
@@ -304,16 +313,18 @@ class EntityRepository(Repository[Entity]):
         # Query: SELECT * FROM entities WHERE checksum IN (checksum1, checksum2, ...)
         query = self.select().where(Entity.checksum.in_(checksums))  # pragma: no cover
         # Don't load relationships for move detection - we only need file_path and checksum
-        result = await self.execute_query(query, use_query_options=False)  # pragma: no cover
+        result = await self.execute_query(
+            session, query, use_query_options=False
+        )  # pragma: no cover
         return list(result.scalars().all())  # pragma: no cover
 
-    async def delete_by_file_path(self, file_path: Union[Path, str]) -> bool:
+    async def delete_by_file_path(self, session: AsyncSession, file_path: Union[Path, str]) -> bool:
         """Delete entity with the provided file_path.
 
         Args:
             file_path: Path to the entity file (will be converted to string internally)
         """
-        return await self.delete_by_fields(file_path=Path(file_path).as_posix())
+        return await self.delete_by_fields(session, file_path=Path(file_path).as_posix())
 
     def get_load_options(self) -> List[LoaderOption]:
         """Get SQLAlchemy loader options for eager loading relationships."""
@@ -327,7 +338,9 @@ class EntityRepository(Repository[Entity]):
             selectinload(Entity.incoming_relations).selectinload(Relation.to_entity),
         ]
 
-    async def find_by_permalinks(self, permalinks: List[str]) -> Sequence[Entity]:
+    async def find_by_permalinks(
+        self, session: AsyncSession, permalinks: List[str]
+    ) -> Sequence[Entity]:
         """Find multiple entities by their permalink.
 
         Args:
@@ -342,10 +355,10 @@ class EntityRepository(Repository[Entity]):
             self.select().options(*self.get_load_options()).where(Entity.permalink.in_(permalinks))
         )
 
-        result = await self.execute_query(query)
+        result = await self.execute_query(session, query)
         return list(result.scalars().all())
 
-    async def upsert_entity(self, entity: Entity) -> Entity:
+    async def upsert_entity(self, session: AsyncSession, entity: Entity) -> Entity:
         """Insert or update entity using simple try/catch with database-level conflict resolution.
 
         Handles file_path race conditions by checking for existing entity on IntegrityError.
@@ -357,99 +370,84 @@ class EntityRepository(Repository[Entity]):
         Returns:
             The inserted or updated entity
         """
-        async with db.scoped_session(self.session_maker) as session:
-            # Set project_id if applicable and not already set
-            self._set_project_id_if_needed(entity)
+        # Set project_id if applicable and not already set
+        self._set_project_id_if_needed(entity)
 
-            # Try simple insert first
-            try:
+        # Try simple insert first.
+        try:
+            async with session.begin_nested():
                 session.add(entity)
                 await session.flush()
+        except IntegrityError as e:
+            # Check if this is a FOREIGN KEY constraint failure
+            # SQLite: "FOREIGN KEY constraint failed"
+            # Postgres: "violates foreign key constraint"
+            error_str = str(e)
+            if (
+                "FOREIGN KEY constraint failed" in error_str
+                or "violates foreign key constraint" in error_str
+            ):
+                # Import locally to avoid circular dependency (repository -> services -> repository)
+                from basic_memory.services.exceptions import SyncFatalError
 
-                # Return with relationships loaded
-                query = (
-                    self.select()
-                    .where(Entity.file_path == entity.file_path)
-                    .options(*self.get_load_options())
+                # Project doesn't exist in database - this is a fatal sync error
+                raise SyncFatalError(
+                    f"Cannot sync file '{entity.file_path}': "
+                    f"project_id={entity.project_id} does not exist in database. "
+                    f"The project may have been deleted. This sync will be terminated."
+                ) from e
+
+            # Re-query after the nested rollback to get a fresh, attached entity.
+            existing_result = await session.execute(
+                select(Entity)
+                .where(Entity.file_path == entity.file_path, Entity.project_id == entity.project_id)
+                .options(*self.get_load_options())
+            )
+            existing_entity = existing_result.scalar_one_or_none()
+
+            if existing_entity:
+                # File path conflict - update the existing entity
+                logger.debug(
+                    f"Resolving file_path conflict for {entity.file_path}, "
+                    f"entity_id={existing_entity.id}, observations={len(entity.observations)}"
                 )
-                result = await session.execute(query)
-                found = result.scalar_one_or_none()
-                if not found:  # pragma: no cover
-                    raise RuntimeError(
-                        f"Failed to retrieve entity after insert: {entity.file_path}"
-                    )
-                return found
+                # Use merge to avoid session state conflicts. Preserve stable
+                # external_id so external references survive re-indexing.
+                entity.id = existing_entity.id
+                entity.external_id = existing_entity.external_id
 
-            except IntegrityError as e:
-                # Check if this is a FOREIGN KEY constraint failure
-                # SQLite: "FOREIGN KEY constraint failed"
-                # Postgres: "violates foreign key constraint"
-                error_str = str(e)
-                if (
-                    "FOREIGN KEY constraint failed" in error_str
-                    or "violates foreign key constraint" in error_str
-                ):
-                    # Import locally to avoid circular dependency (repository -> services -> repository)
-                    from basic_memory.services.exceptions import SyncFatalError
+                # Ensure observations reference the correct entity_id.
+                for obs in entity.observations:
+                    obs.entity_id = existing_entity.id
+                    obs.id = None
 
-                    # Project doesn't exist in database - this is a fatal sync error
-                    raise SyncFatalError(
-                        f"Cannot sync file '{entity.file_path}': "
-                        f"project_id={entity.project_id} does not exist in database. "
-                        f"The project may have been deleted. This sync will be terminated."
-                    ) from e
+                merged_entity = await session.merge(entity)
+                await session.flush()
 
-                await session.rollback()
-
-                # Re-query after rollback to get a fresh, attached entity
-                existing_result = await session.execute(
+                # Re-query to get proper relationships loaded.
+                final_result = await session.execute(
                     select(Entity)
-                    .where(
-                        Entity.file_path == entity.file_path, Entity.project_id == entity.project_id
-                    )
+                    .where(Entity.id == merged_entity.id)
                     .options(*self.get_load_options())
                 )
-                existing_entity = existing_result.scalar_one_or_none()
+                return final_result.scalar_one()
 
-                if existing_entity:
-                    # File path conflict - update the existing entity
-                    logger.debug(
-                        f"Resolving file_path conflict for {entity.file_path}, "
-                        f"entity_id={existing_entity.id}, observations={len(entity.observations)}"
-                    )
-                    # Use merge to avoid session state conflicts
-                    # Set the ID to update existing entity
-                    entity.id = existing_entity.id
-                    # Preserve the stable external_id so that external references
-                    # (e.g. public share links) survive re-indexing
-                    entity.external_id = existing_entity.external_id
+            # No file_path conflict - must be permalink conflict.
+            return await self._handle_permalink_conflict(entity, session)
 
-                    # Ensure observations reference the correct entity_id
-                    for obs in entity.observations:
-                        obs.entity_id = existing_entity.id
-                        # Clear any existing ID to force INSERT as new observation
-                        obs.id = None
+        # Return with relationships loaded.
+        query = (
+            self.select()
+            .where(Entity.file_path == entity.file_path)
+            .options(*self.get_load_options())
+        )
+        result = await session.execute(query)
+        found = result.scalar_one_or_none()
+        if not found:  # pragma: no cover
+            raise RuntimeError(f"Failed to retrieve entity after insert: {entity.file_path}")
+        return found
 
-                    # Merge the entity which will update the existing one
-                    merged_entity = await session.merge(entity)
-
-                    await session.commit()
-
-                    # Re-query to get proper relationships loaded
-                    final_result = await session.execute(
-                        select(Entity)
-                        .where(Entity.id == merged_entity.id)
-                        .options(*self.get_load_options())
-                    )
-                    return final_result.scalar_one()
-
-                else:
-                    # No file_path conflict - must be permalink conflict
-                    # Generate unique permalink and retry
-                    entity = await self._handle_permalink_conflict(entity, session)
-                    return entity
-
-    async def get_all_file_paths(self) -> List[str]:
+    async def get_all_file_paths(self, session: AsyncSession) -> List[str]:
         """Get all file paths for this project - optimized for deletion detection.
 
         Returns only file_path strings without loading entities or relationships.
@@ -461,10 +459,10 @@ class EntityRepository(Repository[Entity]):
         query = select(Entity.file_path)
         query = self._add_project_filter(query)
 
-        result = await self.execute_query(query, use_query_options=False)
+        result = await self.execute_query(session, query, use_query_options=False)
         return list(result.scalars().all())
 
-    async def find_without_relations(self) -> Sequence[Entity]:
+    async def find_without_relations(self, session: AsyncSession) -> 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.
@@ -477,10 +475,10 @@ class EntityRepository(Repository[Entity]):
         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)
+        result = await self.execute_query(session, query, use_query_options=False)
         return list(result.scalars().all())
 
-    async def get_distinct_directories(self) -> List[str]:
+    async def get_distinct_directories(self, session: AsyncSession) -> List[str]:
         """Extract unique directory paths from file_path column.
 
         Optimized method for getting directory structure without loading full entities
@@ -494,7 +492,7 @@ class EntityRepository(Repository[Entity]):
         query = self._add_project_filter(query)
 
         # Execute with use_query_options=False to skip eager loading
-        result = await self.execute_query(query, use_query_options=False)
+        result = await self.execute_query(session, query, use_query_options=False)
         file_paths = [row for row in result.scalars().all()]
 
         # Parse file paths to extract unique directories
@@ -508,7 +506,9 @@ class EntityRepository(Repository[Entity]):
 
         return sorted(directories)
 
-    async def find_by_directory_prefix(self, directory_prefix: str) -> Sequence[Entity]:
+    async def find_by_directory_prefix(
+        self, session: AsyncSession, directory_prefix: str
+    ) -> Sequence[Entity]:
         """Find entities whose file_path starts with the given directory prefix.
 
         Optimized method for listing directory contents without loading all entities.
@@ -524,7 +524,7 @@ class EntityRepository(Repository[Entity]):
         # Build SQL LIKE pattern
         if directory_prefix == "" or directory_prefix == "/":
             # Root directory - return all entities
-            return await self.find_all()
+            return await self.find_all(session)
 
         # Remove leading/trailing slashes for consistency
         directory_prefix = directory_prefix.strip("/")
@@ -537,7 +537,7 @@ class EntityRepository(Repository[Entity]):
         query = self.select().where(Entity.file_path.like(pattern))
 
         # Skip eager loading - we only need basic entity fields for directory trees
-        result = await self.execute_query(query, use_query_options=False)
+        result = await self.execute_query(session, query, use_query_options=False)
         return list(result.scalars().all())
 
     async def _handle_permalink_conflict(self, entity: Entity, session: AsyncSession) -> Entity:

src/basic_memory/repository/note_content_repository.py

@@ -4,9 +4,8 @@ from pathlib import Path
 from typing import Any, Mapping, Optional
 
 from sqlalchemy import select
-from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker
+from sqlalchemy.ext.asyncio import AsyncSession
 
-from basic_memory import db
 from basic_memory.models import Entity, NoteContent
 from basic_memory.repository.repository import Repository
 
@@ -30,9 +29,9 @@ NOTE_CONTENT_MUTABLE_FIELDS = frozenset(
 class NoteContentRepository(Repository[NoteContent]):
     """Repository for project-scoped note materialization state."""
 
-    def __init__(self, session_maker: async_sessionmaker[AsyncSession], project_id: int):
-        """Initialize with session maker and project-scoped filtering."""
-        super().__init__(session_maker, NoteContent, project_id=project_id)
+    def __init__(self, project_id: int):
+        """Initialize with project-scoped filtering."""
+        super().__init__(NoteContent, project_id=project_id)
 
     def _coerce_note_content(
         self, data: Mapping[str, Any] | NoteContent
@@ -75,16 +74,22 @@ class NoteContentRepository(Repository[NoteContent]):
         note_content.external_id = entity.external_id
         note_content.file_path = Path(entity.file_path).as_posix()
 
-    async def get_by_entity_id(self, entity_id: int) -> Optional[NoteContent]:
+    async def get_by_entity_id(
+        self, session: AsyncSession, entity_id: int
+    ) -> Optional[NoteContent]:
         """Get note content by the owning entity identifier."""
-        return await self.find_by_id(entity_id)
+        return await self.find_by_id(session, entity_id)
 
-    async def get_by_external_id(self, external_id: str) -> Optional[NoteContent]:
+    async def get_by_external_id(
+        self, session: AsyncSession, external_id: str
+    ) -> Optional[NoteContent]:
         """Get note content by the mirrored entity external identifier."""
         query = self.select().where(NoteContent.external_id == external_id)
-        return await self.find_one(query)
+        return await self.find_one(session, query)
 
-    async def get_by_file_path(self, file_path: Path | str) -> Optional[NoteContent]:
+    async def get_by_file_path(
+        self, session: AsyncSession, file_path: Path | str
+    ) -> Optional[NoteContent]:
         """Get note content by file path, preferring rows whose entity still owns that path."""
         normalized_path = Path(file_path).as_posix()
 
@@ -104,88 +109,88 @@ class NoteContentRepository(Repository[NoteContent]):
             .options(*self.get_load_options())
         )
 
-        async with db.scoped_session(self.session_maker) as session:
-            result = await session.execute(query)
-            return result.scalars().first()
+        result = await session.execute(query)
+        return result.scalars().first()
 
-    async def create(self, data: Mapping[str, Any] | NoteContent) -> NoteContent:
+    async def create(
+        self, session: AsyncSession, data: Mapping[str, Any] | NoteContent
+    ) -> NoteContent:
         """Create a note_content row aligned to its owning entity."""
         note_content, _ = self._coerce_note_content(data)
 
-        async with db.scoped_session(self.session_maker) as session:
-            await self._align_identity_fields(session, note_content)
-            session.add(note_content)
-            await session.flush()
+        await self._align_identity_fields(session, note_content)
+        session.add(note_content)
+        await session.flush()
 
-            created = await self.select_by_id(session, note_content.entity_id)
-            if created is None:  # pragma: no cover
-                raise ValueError(
-                    f"Can't find NoteContent for entity {note_content.entity_id} after add"
-                )
-            return created
+        created = await self.select_by_id(session, note_content.entity_id)
+        if created is None:  # pragma: no cover
+            raise ValueError(
+                f"Can't find NoteContent for entity {note_content.entity_id} after add"
+            )
+        return created
 
-    async def upsert(self, data: Mapping[str, Any] | NoteContent) -> NoteContent:
+    async def upsert(
+        self, session: AsyncSession, data: Mapping[str, Any] | NoteContent
+    ) -> NoteContent:
         """Insert or update note_content while keeping mirrored identity fields in sync."""
         note_content, provided_fields = self._coerce_note_content(data)
 
-        async with db.scoped_session(self.session_maker) as session:
-            await self._align_identity_fields(session, note_content)
-            existing = await self.select_by_id(session, note_content.entity_id)
-
-            if existing is None:
-                session.add(note_content)
-                await session.flush()
-                created = await self.select_by_id(session, note_content.entity_id)
-                if created is None:  # pragma: no cover
-                    raise ValueError(
-                        f"Can't find NoteContent for entity {note_content.entity_id} after upsert"
-                    )
-                return created
-
-            fields_to_update = (provided_fields - {"entity_id"}) | {
-                "project_id",
-                "external_id",
-                "file_path",
-            }
-            for column_name in fields_to_update:
-                setattr(existing, column_name, getattr(note_content, column_name))
+        await self._align_identity_fields(session, note_content)
+        existing = await self.select_by_id(session, note_content.entity_id)
 
+        if existing is None:
+            session.add(note_content)
             await session.flush()
-            updated = await self.select_by_id(session, existing.entity_id)
-            if updated is None:  # pragma: no cover
+            created = await self.select_by_id(session, note_content.entity_id)
+            if created is None:  # pragma: no cover
                 raise ValueError(
-                    f"Can't find NoteContent for entity {existing.entity_id} after upsert"
+                    f"Can't find NoteContent for entity {note_content.entity_id} after upsert"
                 )
-            return updated
+            return created
 
-    async def update_state_fields(self, entity_id: int, **updates: Any) -> Optional[NoteContent]:
+        fields_to_update = (provided_fields - {"entity_id"}) | {
+            "project_id",
+            "external_id",
+            "file_path",
+        }
+        for column_name in fields_to_update:
+            setattr(existing, column_name, getattr(note_content, column_name))
+
+        await session.flush()
+        updated = await self.select_by_id(session, existing.entity_id)
+        if updated is None:  # pragma: no cover
+            raise ValueError(f"Can't find NoteContent for entity {existing.entity_id} after upsert")
+        return updated
+
+    async def update_state_fields(
+        self, session: AsyncSession, entity_id: int, **updates: Any
+    ) -> Optional[NoteContent]:
         """Update sync fields and re-align project_id, external_id, and file_path from entity."""
         invalid_fields = set(updates) - NOTE_CONTENT_MUTABLE_FIELDS
         if invalid_fields:
             invalid_list = ", ".join(sorted(invalid_fields))
             raise ValueError(f"Unsupported note_content update fields: {invalid_list}")
 
-        async with db.scoped_session(self.session_maker) as session:
-            note_content = await self.select_by_id(session, entity_id)
-            if note_content is None:
-                return None
+        note_content = await self.select_by_id(session, entity_id)
+        if note_content is None:
+            return None
 
-            await self._align_identity_fields(session, note_content)
-            for field_name, value in updates.items():
-                setattr(note_content, field_name, value)
+        await self._align_identity_fields(session, note_content)
+        for field_name, value in updates.items():
+            setattr(note_content, field_name, value)
 
-            await session.flush()
-            updated = await self.select_by_id(session, entity_id)
-            if updated is None:  # pragma: no cover
-                raise ValueError(f"Can't find NoteContent for entity {entity_id} after update")
-            return updated
+        await session.flush()
+        updated = await self.select_by_id(session, entity_id)
+        if updated is None:  # pragma: no cover
+            raise ValueError(f"Can't find NoteContent for entity {entity_id} after update")
+        return updated
 
-    async def delete_by_entity_id(self, entity_id: int) -> bool:
+    async def delete_by_entity_id(self, session: AsyncSession, entity_id: int) -> bool:
         """Delete note_content by entity identifier."""
-        async with db.scoped_session(self.session_maker) as session:
-            note_content = await self.select_by_id(session, entity_id)
-            if note_content is None:
-                return False
+        note_content = await self.select_by_id(session, entity_id)
+        if note_content is None:
+            return False
 
-            await session.delete(note_content)
-            return True
+        await session.delete(note_content)
+        await session.flush()
+        return True

src/basic_memory/repository/observation_repository.py

@@ -3,7 +3,7 @@
 from typing import Dict, List, Sequence
 
 from sqlalchemy import select
-from sqlalchemy.ext.asyncio import async_sessionmaker
+from sqlalchemy.ext.asyncio import AsyncSession
 from sqlalchemy.orm import selectinload
 from sqlalchemy.orm.interfaces import LoaderOption
 
@@ -14,44 +14,46 @@ from basic_memory.repository.repository import Repository
 class ObservationRepository(Repository[Observation]):
     """Repository for Observation model with memory-specific operations."""
 
-    def __init__(self, session_maker: async_sessionmaker, project_id: int):
-        """Initialize with session maker and project_id filter.
+    def __init__(self, project_id: int):
+        """Initialize with project_id filter.
 
         Args:
-            session_maker: SQLAlchemy session maker
             project_id: Project ID to filter all operations by
         """
-        super().__init__(session_maker, Observation, project_id=project_id)
+        super().__init__(Observation, project_id=project_id)
 
     def get_load_options(self) -> List[LoaderOption]:
         """Eager-load parent entity to prevent N+1 if obs.entity is accessed."""
         return [selectinload(Observation.entity)]
 
-    async def find_by_entity(self, entity_id: int) -> Sequence[Observation]:
+    async def find_by_entity(self, session: AsyncSession, entity_id: int) -> Sequence[Observation]:
         """Find all observations for a specific entity."""
-        query = select(Observation).filter(Observation.entity_id == entity_id)
-        result = await self.execute_query(query)
+        query = self.select().filter(Observation.entity_id == entity_id)
+        result = await self.execute_query(session, query)
         return result.scalars().all()
 
-    async def find_by_context(self, context: str) -> Sequence[Observation]:
+    async def find_by_context(self, session: AsyncSession, context: str) -> Sequence[Observation]:
         """Find observations with a specific context."""
-        query = select(Observation).filter(Observation.context == context)
-        result = await self.execute_query(query)
+        query = self.select().filter(Observation.context == context)
+        result = await self.execute_query(session, query)
         return result.scalars().all()
 
-    async def find_by_category(self, category: str) -> Sequence[Observation]:
+    async def find_by_category(self, session: AsyncSession, category: str) -> Sequence[Observation]:
         """Find observations with a specific context."""
-        query = select(Observation).filter(Observation.category == category)
-        result = await self.execute_query(query)
+        query = self.select().filter(Observation.category == category)
+        result = await self.execute_query(session, query)
         return result.scalars().all()
 
-    async def observation_categories(self) -> Sequence[str]:
+    async def observation_categories(self, session: AsyncSession) -> Sequence[str]:
         """Return a list of all observation categories."""
         query = select(Observation.category).distinct()
-        result = await self.execute_query(query, use_query_options=False)
+        query = self._add_project_filter(query)
+        result = await self.execute_query(session, query, use_query_options=False)
         return result.scalars().all()
 
-    async def find_by_entities(self, entity_ids: List[int]) -> Dict[int, List[Observation]]:
+    async def find_by_entities(
+        self, session: AsyncSession, entity_ids: List[int]
+    ) -> Dict[int, List[Observation]]:
         """Find all observations for multiple entities in a single query.
 
         Args:
@@ -64,8 +66,8 @@ class ObservationRepository(Repository[Observation]):
             return {}
 
         # Query observations for all entities in the list
-        query = select(Observation).filter(Observation.entity_id.in_(entity_ids))
-        result = await self.execute_query(query)
+        query = self.select().filter(Observation.entity_id.in_(entity_ids))
+        result = await self.execute_query(session, query)
         observations = result.scalars().all()
 
         # Group observations by entity_id

src/basic_memory/repository/postgres_search_repository.py

@@ -18,6 +18,7 @@ from basic_memory.repository.search_index_row import SearchIndexRow
 from basic_memory.repository.search_repository_base import (
     SearchRepositoryBase,
     VectorChunkState,
+    relaxed_query_words,
 )
 from basic_memory.repository.metadata_filters import parse_metadata_filters
 from basic_memory.repository.semantic_errors import SemanticDependenciesMissingError
@@ -176,6 +177,14 @@ class PostgresSearchRepository(SearchRepositoryBase):
         # For non-Boolean queries, prepare single term
         return self._prepare_single_term(term, is_prefix)
 
+    @staticmethod
+    def _relaxed_tsquery_text(search_text: Optional[str]) -> Optional[str]:
+        """OR-relaxed tsquery expression for a failed strict query, or None."""
+        words = relaxed_query_words(search_text)
+        if not words:
+            return None
+        return " | ".join(f"{word}:*" for word in words)
+
     def _prepare_boolean_query(self, query: str) -> str:
         """Convert Boolean query to tsquery format.
 
@@ -236,7 +245,12 @@ class PostgresSearchRepository(SearchRepositoryBase):
 
         # Handle multi-word queries
         if " " in cleaned_term:
-            words = [w for w in cleaned_term.split() if w.strip()]
+            # Strip sentence punctuation from word edges so question-form
+            # queries produce clean lexemes (parity with SQLite FTS5 prep).
+            # The tsquery tokenizer ignores this punctuation anyway; leaving it
+            # in only risks tsquery syntax errors. Interior characters are kept.
+            words = [w.strip("?!.,;") for w in cleaned_term.split()]
+            words = [w for w in words if w]
             if not words:
                 # All characters were special chars, search won't match anything
                 # Return a safe search term that won't cause syntax errors
@@ -249,8 +263,11 @@ class PostgresSearchRepository(SearchRepositoryBase):
             # Join with AND operator
             return " & ".join(prepared_words)
 
-        # Single word
-        cleaned_term = cleaned_term.strip()
+        # Single word: strip edge punctuation; guard the now-empty case so a
+        # bare ":*"/"" never reaches tsquery.
+        cleaned_term = cleaned_term.strip().strip("?!.,;")
+        if not cleaned_term:
+            return "NOSPECIALCHARS:*"
         if is_prefix:
             return f"{cleaned_term}:*"
         else:
@@ -908,6 +925,8 @@ class PostgresSearchRepository(SearchRepositoryBase):
         min_similarity: Optional[float] = None,
         limit: int = 10,
         offset: int = 0,
+        allow_relaxed: bool = False,
+        session: AsyncSession | None = None,
     ) -> List[SearchIndexRow]:
         """Search across all indexed content using PostgreSQL tsvector."""
         # --- Dispatch vector / hybrid modes (shared logic) ---
@@ -978,10 +997,32 @@ class PostgresSearchRepository(SearchRepositoryBase):
         """
 
         logger.trace(f"Search {sql} params: {params}")
-        try:
-            async with db.scoped_session(self.session_maker) as session:
-                result = await session.execute(text(sql), params)
+
+        async def run_search(active_session: AsyncSession):
+            result = await active_session.execute(text(sql), params)
+            rows = result.fetchall()
+            # Trigger: multi-word natural-language query matched nothing
+            # under the default all-terms-AND tsquery semantics.
+            # Why: questions rarely have every word in one document;
+            # without relaxation the FTS half of hybrid search contributes
+            # zero candidates (parity with the SQLite path).
+            # Outcome: one retry with OR-joined prefix lexemes; ts_rank
+            # still ranks multi-term matches first.
+            relaxed = (
+                self._relaxed_tsquery_text(search_text) if allow_relaxed and not rows else None
+            )
+            if relaxed and params.get("text"):
+                params["text"] = relaxed
+                result = await active_session.execute(text(sql), params)
                 rows = result.fetchall()
+            return rows
+
+        try:
+            if session is not None:
+                rows = await run_search(session)
+            else:
+                async with db.scoped_session(self.session_maker) as owned_session:
+                    rows = await run_search(owned_session)
         except Exception as e:
             if self._is_tsquery_syntax_error(e):
                 logger.warning(f"tsquery syntax error for search term: {search_text}, error: {e}")

src/basic_memory/repository/project_info_repository.py

@@ -5,6 +5,6 @@ from basic_memory.models.project import Project
 class ProjectInfoRepository(Repository):
     """Repository for statistics queries."""
 
-    def __init__(self, session_maker):
+    def __init__(self):
         # Initialize with Project model as a reference
-        super().__init__(session_maker, Project)
+        super().__init__(Project)

src/basic_memory/repository/project_repository.py

@@ -7,9 +7,8 @@ from typing import Optional, Sequence, Union
 from loguru import logger
 from sqlalchemy import Executable, inspect as sa_inspect, select, text
 from sqlalchemy.exc import NoResultFound, OperationalError
-from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker
+from sqlalchemy.ext.asyncio import AsyncSession
 
-from basic_memory import db
 from basic_memory.models.project import Project
 from basic_memory.repository.repository import Repository
 
@@ -79,20 +78,22 @@ class ProjectRepository(Repository[Project]):
     Each entity, observation, and relation belongs to a specific project.
     """
 
-    def __init__(self, session_maker: async_sessionmaker[AsyncSession]):
-        """Initialize with session maker."""
-        super().__init__(session_maker, Project)
+    def __init__(self):
+        """Initialize the repository."""
+        super().__init__(Project)
 
-    async def get_by_name(self, name: str) -> Optional[Project]:
+    async def get_by_name(self, session: AsyncSession, name: str) -> Optional[Project]:
         """Get project by name (exact match).
 
         Args:
             name: Unique name of the project
         """
         query = self.select().where(Project.name == name)
-        return await self.find_one(query)
+        return await self.find_one(session, query)
 
-    async def get_by_name_case_insensitive(self, name: str) -> Optional[Project]:
+    async def get_by_name_case_insensitive(
+        self, session: AsyncSession, name: str
+    ) -> Optional[Project]:
         """Get project by name (case-insensitive match).
 
         Args:
@@ -102,27 +103,27 @@ class ProjectRepository(Repository[Project]):
             Project if found, None otherwise
         """
         query = self.select().where(Project.name.ilike(name))
-        return await self.find_one(query)
+        return await self.find_one(session, query)
 
-    async def get_by_permalink(self, permalink: str) -> Optional[Project]:
+    async def get_by_permalink(self, session: AsyncSession, permalink: str) -> Optional[Project]:
         """Get project by permalink.
 
         Args:
             permalink: URL-friendly identifier for the project
         """
         query = self.select().where(Project.permalink == permalink)
-        return await self.find_one(query)
+        return await self.find_one(session, query)
 
-    async def get_by_path(self, path: Union[Path, str]) -> Optional[Project]:
+    async def get_by_path(self, session: AsyncSession, path: Union[Path, str]) -> Optional[Project]:
         """Get project by filesystem path.
 
         Args:
             path: Path to the project directory (will be converted to string internally)
         """
         query = self.select().where(Project.path == Path(path).as_posix())
-        return await self.find_one(query)
+        return await self.find_one(session, query)
 
-    async def get_by_id(self, project_id: int) -> Optional[Project]:
+    async def get_by_id(self, session: AsyncSession, project_id: int) -> Optional[Project]:
         """Get project by numeric ID.
 
         Args:
@@ -131,10 +132,11 @@ class ProjectRepository(Repository[Project]):
         Returns:
             Project if found, None otherwise
         """
-        async with db.scoped_session(self.session_maker) as session:
-            return await self.select_by_id(session, project_id)
+        return await self.select_by_id(session, project_id)
 
-    async def get_by_external_id(self, external_id: str) -> Optional[Project]:
+    async def get_by_external_id(
+        self, session: AsyncSession, external_id: str
+    ) -> Optional[Project]:
         """Get project by external UUID.
 
         Args:
@@ -144,20 +146,20 @@ class ProjectRepository(Repository[Project]):
             Project if found, None otherwise
         """
         query = self.select().where(Project.external_id == external_id)
-        return await self.find_one(query)
+        return await self.find_one(session, query)
 
-    async def get_default_project(self) -> Optional[Project]:
+    async def get_default_project(self, session: AsyncSession) -> Optional[Project]:
         """Get the default project (the one marked as is_default=True)."""
         query = self.select().where(Project.is_default.is_(True))
-        return await self.find_one(query)
+        return await self.find_one(session, query)
 
-    async def get_active_projects(self) -> Sequence[Project]:
+    async def get_active_projects(self, session: AsyncSession) -> Sequence[Project]:
         """Get all active projects."""
         query = self.select().where(Project.is_active == True)  # noqa: E712
-        result = await self.execute_query(query)
+        result = await self.execute_query(session, query)
         return list(result.scalars().all())
 
-    async def set_as_default(self, project_id: int) -> Optional[Project]:
+    async def set_as_default(self, session: AsyncSession, project_id: int) -> Optional[Project]:
         """Set a project as the default and unset previous default.
 
         Args:
@@ -166,22 +168,21 @@ class ProjectRepository(Repository[Project]):
         Returns:
             The updated project if found, None otherwise
         """
-        async with db.scoped_session(self.session_maker) as session:
-            # First, clear the default flag for all projects using direct SQL
-            await session.execute(
-                text("UPDATE project SET is_default = NULL WHERE is_default IS NOT NULL")
-            )
+        # First, clear the default flag for all projects using direct SQL
+        await session.execute(
+            text("UPDATE project SET is_default = NULL WHERE is_default IS NOT NULL")
+        )
+        await session.flush()
+
+        # Set the new default project
+        target_project = await self.select_by_id(session, project_id)
+        if target_project:
+            target_project.is_default = True
             await session.flush()
+            return target_project
+        return None  # pragma: no cover
 
-            # Set the new default project
-            target_project = await self.select_by_id(session, project_id)
-            if target_project:
-                target_project.is_default = True
-                await session.flush()
-                return target_project
-            return None  # pragma: no cover
-
-    async def delete(self, entity_id: int) -> bool:
+    async def delete(self, session: AsyncSession, entity_id: int) -> bool:
         """Delete a project and its derived search rows in one transaction.
 
         The cascade picture differs by backend:
@@ -204,62 +205,60 @@ class ProjectRepository(Repository[Project]):
         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
+        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"
+        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())
+        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_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},
+            )
 
-            # 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
+        await session.delete(project)
+        await session.flush()
+        logger.debug(f"Deleted Project and search rows for project_id: {entity_id}")
+        return True
 
     async def scalar_vec_query(
-        self, query: Executable, params: Optional[dict] = None
+        self, session: AsyncSession, query: Executable, params: Optional[dict] = None
     ) -> Optional[int]:
         """Run a scalar COUNT query that reads the sqlite-vec vec0 table.
 
@@ -271,16 +270,17 @@ class ProjectRepository(Repository[Project]):
         Returns None when sqlite-vec cannot be loaded on this Python build, so
         callers can fall back to the genuinely-missing-dependency path.
         """
-        async with db.scoped_session(self.session_maker) as session:
-            # Trigger: query reads the vec0-backed search_vector_embeddings table.
-            # Why: vec0 modules are only visible on a connection that loaded sqlite-vec.
-            # Outcome: load the extension here, or signal absence so the caller degrades.
-            if not await _load_sqlite_vec_on_session(session):
-                return None
-            result = await session.execute(query, params)
-            return result.scalar()
+        # Trigger: query reads the vec0-backed search_vector_embeddings table.
+        # Why: vec0 modules are only visible on a connection that loaded sqlite-vec.
+        # Outcome: load the extension here, or signal absence so the caller degrades.
+        if not await _load_sqlite_vec_on_session(session):
+            return None
+        result = await session.execute(query, params)
+        return result.scalar()
 
-    async def update_path(self, project_id: int, new_path: str) -> Optional[Project]:
+    async def update_path(
+        self, session: AsyncSession, project_id: int, new_path: str
+    ) -> Optional[Project]:
         """Update project path.
 
         Args:
@@ -290,10 +290,9 @@ class ProjectRepository(Repository[Project]):
         Returns:
             The updated project if found, None otherwise
         """
-        async with db.scoped_session(self.session_maker) as session:
-            project = await self.select_by_id(session, project_id)
-            if project:
-                project.path = new_path
-                await session.flush()
-                return project
-            return None
+        project = await self.select_by_id(session, project_id)
+        if project:
+            project.path = new_path
+            await session.flush()
+            return project
+        return None

src/basic_memory/repository/relation_repository.py

@@ -6,11 +6,10 @@ from sqlalchemy import and_, delete, select
 from sqlalchemy.engine import CursorResult
 from sqlalchemy.dialects.postgresql import insert as pg_insert
 from sqlalchemy.dialects.sqlite import insert as sqlite_insert
-from sqlalchemy.ext.asyncio import async_sessionmaker
+from sqlalchemy.ext.asyncio import AsyncSession
 from sqlalchemy.orm import selectinload, aliased
 from sqlalchemy.orm.interfaces import LoaderOption
 
-from basic_memory import db
 from basic_memory.models import Relation, Entity
 from basic_memory.repository.repository import Repository
 
@@ -18,17 +17,20 @@ from basic_memory.repository.repository import Repository
 class RelationRepository(Repository[Relation]):
     """Repository for Relation model with memory-specific operations."""
 
-    def __init__(self, session_maker: async_sessionmaker, project_id: int):
-        """Initialize with session maker and project_id filter.
+    def __init__(self, project_id: int):
+        """Initialize with project_id filter.
 
         Args:
-            session_maker: SQLAlchemy session maker
             project_id: Project ID to filter all operations by
         """
-        super().__init__(session_maker, Relation, project_id=project_id)
+        super().__init__(Relation, project_id=project_id)
 
     async def find_relation(
-        self, from_permalink: str, to_permalink: str, relation_type: str
+        self,
+        session: AsyncSession,
+        from_permalink: str,
+        to_permalink: str,
+        relation_type: str,
     ) -> Optional[Relation]:
         """Find a relation by its from and to path IDs."""
         from_entity = aliased(Entity)
@@ -46,36 +48,44 @@ class RelationRepository(Repository[Relation]):
                 )
             )
         )
-        return await self.find_one(query)
+        query = self._add_project_filter(query)
+        return await self.find_one(session, query)
 
-    async def find_by_entities(self, from_id: int, to_id: int) -> Sequence[Relation]:
+    async def find_by_entities(
+        self, session: AsyncSession, from_id: int, to_id: int
+    ) -> Sequence[Relation]:
         """Find all relations between two entities."""
-        query = select(Relation).where((Relation.from_id == from_id) & (Relation.to_id == to_id))
-        result = await self.execute_query(query)
+        query = self.select().where((Relation.from_id == from_id) & (Relation.to_id == to_id))
+        result = await self.execute_query(session, query)
         return result.scalars().all()
 
-    async def find_by_type(self, relation_type: str) -> Sequence[Relation]:
+    async def find_by_type(self, session: AsyncSession, relation_type: str) -> Sequence[Relation]:
         """Find all relations of a specific type."""
-        query = select(Relation).filter(Relation.relation_type == relation_type)
-        result = await self.execute_query(query)
+        query = self.select().filter(Relation.relation_type == relation_type)
+        result = await self.execute_query(session, query)
         return result.scalars().all()
 
-    async def delete_outgoing_relations_from_entity(self, entity_id: int) -> None:
+    async def delete_outgoing_relations_from_entity(
+        self, session: AsyncSession, entity_id: int
+    ) -> None:
         """Delete outgoing relations for an entity.
 
         Only deletes relations where this entity is the source (from_id),
         as these are the ones owned by this entity's markdown file.
         """
-        async with db.scoped_session(self.session_maker) as session:
-            await session.execute(delete(Relation).where(Relation.from_id == entity_id))
+        query = delete(Relation).where(Relation.from_id == entity_id)
+        query = query.where(Relation.project_id == self.project_id)
+        await session.execute(query)
 
-    async def find_unresolved_relations(self) -> Sequence[Relation]:
+    async def find_unresolved_relations(self, session: AsyncSession) -> Sequence[Relation]:
         """Find all unresolved relations, where to_id is null."""
-        query = select(Relation).filter(Relation.to_id.is_(None))
-        result = await self.execute_query(query)
+        query = self.select().filter(Relation.to_id.is_(None))
+        result = await self.execute_query(session, query)
         return result.scalars().all()
 
-    async def find_unresolved_relations_for_entity(self, entity_id: int) -> Sequence[Relation]:
+    async def find_unresolved_relations_for_entity(
+        self, session: AsyncSession, entity_id: int
+    ) -> Sequence[Relation]:
         """Find unresolved relations for a specific entity.
 
         Args:
@@ -84,11 +94,13 @@ class RelationRepository(Repository[Relation]):
         Returns:
             List of unresolved relations where this entity is the source.
         """
-        query = select(Relation).filter(Relation.from_id == entity_id, Relation.to_id.is_(None))
-        result = await self.execute_query(query)
+        query = self.select().filter(Relation.from_id == entity_id, Relation.to_id.is_(None))
+        result = await self.execute_query(session, query)
         return result.scalars().all()
 
-    async def add_all_ignore_duplicates(self, relations: List[Relation]) -> int:
+    async def add_all_ignore_duplicates(
+        self, session: AsyncSession, relations: List[Relation]
+    ) -> int:
         """Bulk insert relations, ignoring duplicates.
 
         Uses ON CONFLICT DO NOTHING to skip relations that would violate the
@@ -120,27 +132,23 @@ class RelationRepository(Repository[Relation]):
             for r in relations
         ]
 
-        async with db.scoped_session(self.session_maker) as session:
-            # Check dialect to use appropriate insert
-            dialect_name = session.bind.dialect.name if session.bind else "sqlite"
+        # Check dialect to use appropriate insert
+        dialect_name = session.bind.dialect.name if session.bind else "sqlite"
 
-            if dialect_name == "postgresql":  # pragma: no cover
-                # PostgreSQL: use RETURNING to count inserted rows
-                # (rowcount is 0 for ON CONFLICT DO NOTHING)
-                stmt = (  # pragma: no cover
-                    pg_insert(Relation)
-                    .values(values)
-                    .on_conflict_do_nothing()
-                    .returning(Relation.id)
-                )
-                result = await session.execute(stmt)  # pragma: no cover
-                return len(result.fetchall())  # pragma: no cover
-            else:
-                # SQLite: rowcount works correctly
-                stmt = sqlite_insert(Relation).values(values)
-                stmt = stmt.on_conflict_do_nothing()
-                result = cast(CursorResult[Any], await session.execute(stmt))
-                return result.rowcount if result.rowcount > 0 else 0
+        if dialect_name == "postgresql":  # pragma: no cover
+            # PostgreSQL: use RETURNING to count inserted rows
+            # (rowcount is 0 for ON CONFLICT DO NOTHING)
+            stmt = (  # pragma: no cover
+                pg_insert(Relation).values(values).on_conflict_do_nothing().returning(Relation.id)
+            )
+            result = await session.execute(stmt)  # pragma: no cover
+            return len(result.fetchall())  # pragma: no cover
+        else:
+            # SQLite: rowcount works correctly
+            stmt = sqlite_insert(Relation).values(values)
+            stmt = stmt.on_conflict_do_nothing()
+            result = cast(CursorResult[Any], await session.execute(stmt))
+            return result.rowcount if result.rowcount > 0 else 0
 
     def get_load_options(self) -> List[LoaderOption]:
         return [selectinload(Relation.from_entity), selectinload(Relation.to_entity)]

src/basic_memory/repository/repository.py

@@ -1,7 +1,6 @@
 """Base repository implementation."""
 
-from typing import Type, Optional, Any, Sequence, TypeVar, List, Dict, cast
-
+from typing import Optional, Any, Sequence, TypeVar, List, Dict, cast
 
 from loguru import logger
 from sqlalchemy import (
@@ -16,27 +15,23 @@ from sqlalchemy import (
     update as sqlalchemy_update,
 )
 from sqlalchemy.engine import CursorResult
-from sqlalchemy.exc import NoResultFound
-from sqlalchemy.ext.asyncio import async_sessionmaker, AsyncSession
+from sqlalchemy.ext.asyncio import AsyncSession
 from sqlalchemy.orm.interfaces import LoaderOption
 from sqlalchemy.sql.elements import ColumnElement
 
-from basic_memory import db
 from basic_memory.models import Base
 
 T = TypeVar("T", bound=Base)
 
 
 class Repository[T: Base]:
-    """Base repository implementation with generic CRUD operations."""
+    """Base repository implementation with explicit caller-owned sessions."""
 
     def __init__(
         self,
-        session_maker: async_sessionmaker[AsyncSession],
-        Model: Type[T],
+        Model: type[T],
         project_id: Optional[int] = None,
     ):
-        self.session_maker = session_maker
         self.project_id = project_id
         if Model:
             self.Model = Model
@@ -98,62 +93,61 @@ class Repository[T: Base]:
         result = await session.execute(query)
         return result.scalars().all()
 
-    async def add(self, model: T) -> T:
+    async def add(self, session: AsyncSession, model: T) -> T:
         """
         Add a model to the repository. This will also add related objects
+        :param session: the caller-owned session to use
         :param model: the model to add
         :return: the added model instance
         """
-        async with db.scoped_session(self.session_maker) as session:
-            # Set project_id if applicable and not already set
-            self._set_project_id_if_needed(model)
+        # Set project_id if applicable and not already set
+        self._set_project_id_if_needed(model)
 
-            session.add(model)
-            await session.flush()
+        session.add(model)
+        await session.flush()
 
-            # Query within same session
-            found = await self.select_by_id(session, model.id)  # pyright: ignore [reportAttributeAccessIssue]
-            if found is None:  # pragma: no cover
-                logger.error(
-                    "Failed to retrieve model after add",
-                    model_type=self.Model.__name__,
-                    model_id=model.id,  # pyright: ignore
-                )
-                raise ValueError(
-                    f"Can't find {self.Model.__name__} with ID {model.id} after session.add"  # pyright: ignore
-                )
-            return found
+        # Query within same session
+        found = await self.select_by_id(session, model.id)  # pyright: ignore [reportAttributeAccessIssue]
+        if found is None:  # pragma: no cover
+            logger.error(
+                "Failed to retrieve model after add",
+                model_type=self.Model.__name__,
+                model_id=model.id,  # pyright: ignore
+            )
+            raise ValueError(
+                f"Can't find {self.Model.__name__} with ID {model.id} after session.add"  # pyright: ignore
+            )
+        return found
 
-    async def add_all(self, models: List[T]) -> Sequence[T]:
+    async def add_all(self, session: AsyncSession, models: List[T]) -> Sequence[T]:
         """
         Add a list of models to the repository. This will also add related objects
+        :param session: the caller-owned session to use
         :param models: the models to add
         :return: the added models instances
         """
-        async with db.scoped_session(self.session_maker) as session:
-            # set the project id if not present in models
-            for model in models:
-                self._set_project_id_if_needed(model)
+        # set the project id if not present in models
+        for model in models:
+            self._set_project_id_if_needed(model)
 
-            session.add_all(models)
-            await session.flush()
+        session.add_all(models)
+        await session.flush()
 
-            # Query within same session
-            return await self.select_by_ids(session, [m.id for m in models])  # pyright: ignore [reportAttributeAccessIssue]
+        # Query within same session
+        return await self.select_by_ids(session, [m.id for m in models])  # pyright: ignore [reportAttributeAccessIssue]
 
-    async def add_all_no_return(self, models: List[T]) -> int:
+    async def add_all_no_return(self, session: AsyncSession, models: List[T]) -> int:
         """Insert models without reloading them afterward."""
         if not models:
             return 0
 
-        async with db.scoped_session(self.session_maker) as session:
-            for model in models:
-                self._set_project_id_if_needed(model)
+        for model in models:
+            self._set_project_id_if_needed(model)
 
-            session.add_all(models)
-            await session.flush()
-            logger.debug(f"Added {len(models)} {self.Model.__name__} records")
-            return len(models)
+        session.add_all(models)
+        await session.flush()
+        logger.debug(f"Added {len(models)} {self.Model.__name__} records")
+        return len(models)
 
     def select(self, *entities: Any) -> Select:
         """Create a new SELECT statement.
@@ -170,55 +164,55 @@ class Repository[T: Base]:
         return self._add_project_filter(query)
 
     async def find_all(
-        self, skip: int = 0, limit: Optional[int] = None, use_load_options: bool = True
+        self,
+        session: AsyncSession,
+        skip: int = 0,
+        limit: Optional[int] = None,
+        use_load_options: bool = True,
     ) -> Sequence[T]:
         """Fetch records from the database with pagination.
 
         Args:
+            session: The caller-owned session to use
             skip: Number of records to skip
             limit: Maximum number of records to return
             use_load_options: Whether to apply eager loading options (default: True)
         """
         logger.debug(f"Finding all {self.Model.__name__} (skip={skip}, limit={limit})")
 
-        async with db.scoped_session(self.session_maker) as session:
-            query = select(self.Model).offset(skip)
+        query = select(self.Model).offset(skip)
 
-            # Only apply load options if requested
-            if use_load_options:
-                query = query.options(*self.get_load_options())
+        # Only apply load options if requested
+        if use_load_options:
+            query = query.options(*self.get_load_options())
 
-            # Add project filter if applicable
-            query = self._add_project_filter(query)
+        # Add project filter if applicable
+        query = self._add_project_filter(query)
 
-            if limit:
-                query = query.limit(limit)
+        if limit:
+            query = query.limit(limit)
 
-            result = await session.execute(query)
+        result = await session.execute(query)
 
-            items = result.scalars().all()
-            logger.debug(f"Found {len(items)} {self.Model.__name__} records")
-            return items
+        items = result.scalars().all()
+        logger.debug(f"Found {len(items)} {self.Model.__name__} records")
+        return items
 
-    async def find_by_id(self, entity_id: int) -> Optional[T]:
+    async def find_by_id(self, session: AsyncSession, entity_id: Any) -> Optional[T]:
         """Fetch an entity by its unique identifier."""
         logger.debug(f"Finding {self.Model.__name__} by ID: {entity_id}")
+        return await self.select_by_id(session, entity_id)
 
-        async with db.scoped_session(self.session_maker) as session:
-            return await self.select_by_id(session, entity_id)
-
-    async def find_by_ids(self, ids: List[int]) -> Sequence[T]:
+    async def find_by_ids(self, session: AsyncSession, ids: List[Any]) -> Sequence[T]:
         """Fetch multiple entities by their identifiers in a single query."""
         logger.debug(f"Finding {self.Model.__name__} by IDs: {ids}")
+        return await self.select_by_ids(session, ids)
 
-        async with db.scoped_session(self.session_maker) as session:
-            return await self.select_by_ids(session, ids)
-
-    async def find_one(self, query: Select[tuple[T]]) -> Optional[T]:
+    async def find_one(self, session: AsyncSession, query: Select[tuple[T]]) -> Optional[T]:
         """Execute a query and retrieve a single record."""
         # add in load options
         query = query.options(*self.get_load_options())
-        result = await self.execute_query(query)
+        result = await self.execute_query(session, query)
         entity = result.scalars().one_or_none()
 
         if entity:
@@ -227,12 +221,42 @@ class Repository[T: Base]:
             logger.trace(f"No {self.Model.__name__} found")
         return entity
 
-    async def create(self, data: dict) -> T:
+    async def create(self, session: AsyncSession, data: dict[str, Any]) -> T:
         """Create a new record from a model instance."""
         logger.debug(f"Creating {self.Model.__name__} from entity_data: {data}")
-        async with db.scoped_session(self.session_maker) as session:
-            # Only include valid columns that are provided in entity_data
-            model_data = self.get_model_data(data)
+        # Only include valid columns that are provided in entity_data
+        model_data = self.get_model_data(data)
+
+        # Add project_id if applicable and not already provided
+        if self.has_project_id and self.project_id is not None and "project_id" not in model_data:
+            model_data["project_id"] = self.project_id
+
+        model = self.Model(**model_data)
+        session.add(model)
+        await session.flush()
+
+        return_instance = await self.select_by_id(session, model.id)  # pyright: ignore [reportAttributeAccessIssue]
+        if return_instance is None:  # pragma: no cover
+            logger.error(
+                "Failed to retrieve model after create",
+                model_type=self.Model.__name__,
+                model_id=model.id,  # pyright: ignore
+            )
+            raise ValueError(
+                f"Can't find {self.Model.__name__} with ID {model.id} after session.add"  # pyright: ignore
+            )
+        return return_instance
+
+    async def create_all(
+        self, session: AsyncSession, data_list: List[dict[str, Any]]
+    ) -> Sequence[T]:
+        """Create multiple records in a single transaction."""
+        logger.debug(f"Bulk creating {len(data_list)} {self.Model.__name__} instances")
+
+        # Only include valid columns that are provided in entity_data
+        model_list = []
+        for d in data_list:
+            model_data = self.get_model_data(d)
 
             # Add project_id if applicable and not already provided
             if (
@@ -240,169 +264,126 @@ class Repository[T: Base]:
                 and self.project_id is not None
                 and "project_id" not in model_data
             ):
-                model_data["project_id"] = self.project_id
+                model_data["project_id"] = self.project_id  # pragma: no cover
 
-            model = self.Model(**model_data)
-            session.add(model)
-            await session.flush()
+            model_list.append(self.Model(**model_data))
 
-            return_instance = await self.select_by_id(session, model.id)  # pyright: ignore [reportAttributeAccessIssue]
-            if return_instance is None:  # pragma: no cover
-                logger.error(
-                    "Failed to retrieve model after create",
-                    model_type=self.Model.__name__,
-                    model_id=model.id,  # pyright: ignore
-                )
-                raise ValueError(
-                    f"Can't find {self.Model.__name__} with ID {model.id} after session.add"  # pyright: ignore
-                )
-            return return_instance
+        session.add_all(model_list)
+        await session.flush()
 
-    async def create_all(self, data_list: List[dict]) -> Sequence[T]:
-        """Create multiple records in a single transaction."""
-        logger.debug(f"Bulk creating {len(data_list)} {self.Model.__name__} instances")
+        return await self.select_by_ids(session, [model.id for model in model_list])  # pyright: ignore [reportAttributeAccessIssue]
 
-        async with db.scoped_session(self.session_maker) as session:
-            # Only include valid columns that are provided in entity_data
-            model_list = []
-            for d in data_list:
-                model_data = self.get_model_data(d)
-
-                # Add project_id if applicable and not already provided
-                if (
-                    self.has_project_id
-                    and self.project_id is not None
-                    and "project_id" not in model_data
-                ):
-                    model_data["project_id"] = self.project_id  # pragma: no cover
-
-                model_list.append(self.Model(**model_data))
-
-            session.add_all(model_list)
-            await session.flush()
-
-            return await self.select_by_ids(session, [model.id for model in model_list])  # pyright: ignore [reportAttributeAccessIssue]
-
-    async def update(self, entity_id: int, entity_data: dict[str, Any] | T) -> Optional[T]:
+    async def update(
+        self,
+        session: AsyncSession,
+        entity_id: Any,
+        entity_data: dict[str, Any] | T,
+    ) -> Optional[T]:
         """Update an entity with the given data."""
         logger.debug(f"Updating {self.Model.__name__} {entity_id} with data: {entity_data}")
-        async with db.scoped_session(self.session_maker) as session:
-            try:
-                result = await session.execute(
-                    select(self.Model).filter(self.primary_key == entity_id)
-                )
-                entity = result.scalars().one()
+        entity = await self.select_by_id(session, entity_id)
+        if entity is None:
+            logger.debug(f"No {self.Model.__name__} found to update: {entity_id}")
+            return None
 
-                if isinstance(entity_data, dict):
-                    update_data = cast(dict[str, Any], entity_data)
-                    for key in self.valid_columns:
-                        if key in update_data:
-                            setattr(entity, key, update_data[key])
+        if isinstance(entity_data, dict):
+            update_data = cast(dict[str, Any], entity_data)
+            for key in self.valid_columns:
+                if key in update_data:
+                    setattr(entity, key, update_data[key])
 
-                elif isinstance(entity_data, self.Model):
-                    for column in self.valid_columns:
-                        setattr(entity, column, getattr(entity_data, column))
+        elif isinstance(entity_data, self.Model):
+            for column in self.valid_columns:
+                setattr(entity, column, getattr(entity_data, column))
 
-                await session.flush()  # Make sure changes are flushed
-                await session.refresh(entity)  # Refresh
+        await session.flush()
+        await session.refresh(entity)
 
-                logger.debug(f"Updated {self.Model.__name__}: {entity_id}")
-                return await self.select_by_id(session, entity.id)  # pyright: ignore [reportAttributeAccessIssue]
+        logger.debug(f"Updated {self.Model.__name__}: {entity_id}")
+        return await self.select_by_id(session, entity.id)  # pyright: ignore [reportAttributeAccessIssue]
 
-            except NoResultFound:
-                logger.debug(f"No {self.Model.__name__} found to update: {entity_id}")
-                return None
-
-    async def update_fields(self, entity_id: Any, entity_data: dict[str, Any]) -> bool:
+    async def update_fields(
+        self, session: AsyncSession, entity_id: Any, entity_data: dict[str, Any]
+    ) -> bool:
         """Update columns without reloading the model graph afterward."""
         update_data = {k: v for k, v in entity_data.items() if k in self.valid_columns}
         if not update_data:
             return True
 
-        async with db.scoped_session(self.session_maker) as session:
-            conditions = [self.primary_key == entity_id]
-            if self.has_project_id and self.project_id is not None:
-                conditions.append(getattr(self.Model, "project_id") == self.project_id)
+        conditions = [self.primary_key == entity_id]
+        if self.has_project_id and self.project_id is not None:
+            conditions.append(getattr(self.Model, "project_id") == self.project_id)
 
-            result = cast(
-                CursorResult[Any],
-                await session.execute(
-                    sqlalchemy_update(self.Model).where(and_(*conditions)).values(**update_data)
-                ),
-            )
-            return result.rowcount > 0
+        result = cast(
+            CursorResult[Any],
+            await session.execute(
+                sqlalchemy_update(self.Model).where(and_(*conditions)).values(**update_data)
+            ),
+        )
+        return result.rowcount > 0
 
-    async def delete(self, entity_id: int) -> bool:
+    async def delete(self, session: AsyncSession, entity_id: int) -> bool:
         """Delete an entity from the database."""
         logger.debug(f"Deleting {self.Model.__name__}: {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)
-                )
-                entity = result.scalars().one()
-                await session.delete(entity)
+        entity = await self.select_by_id(session, entity_id)
+        if entity is None:
+            logger.debug(f"No {self.Model.__name__} found to delete: {entity_id}")
+            return False
 
-                logger.debug(f"Deleted {self.Model.__name__}: {entity_id}")
-                return True
-            except NoResultFound:
-                logger.debug(f"No {self.Model.__name__} found to delete: {entity_id}")
-                return False
+        await session.delete(entity)
+        await session.flush()
 
-    async def delete_by_ids(self, ids: List[int]) -> int:
+        logger.debug(f"Deleted {self.Model.__name__}: {entity_id}")
+        return True
+
+    async def delete_by_ids(self, session: AsyncSession, ids: List[int]) -> int:
         """Delete records matching given IDs."""
         logger.debug(f"Deleting {self.Model.__name__} by ids: {ids}")
-        async with db.scoped_session(self.session_maker) as session:
-            conditions = [self.primary_key.in_(ids)]
+        conditions = [self.primary_key.in_(ids)]
 
-            # Add project_id filter if applicable
-            if self.has_project_id and self.project_id is not None:  # pragma: no cover
-                conditions.append(getattr(self.Model, "project_id") == self.project_id)
+        # Add project_id filter if applicable
+        if self.has_project_id and self.project_id is not None:  # pragma: no cover
+            conditions.append(getattr(self.Model, "project_id") == self.project_id)
 
-            query = delete(self.Model).where(and_(*conditions))
-            result = cast(CursorResult[Any], await session.execute(query))
-            logger.debug(f"Deleted {result.rowcount} records")
-            return result.rowcount
+        query = delete(self.Model).where(and_(*conditions))
+        result = cast(CursorResult[Any], await session.execute(query))
+        logger.debug(f"Deleted {result.rowcount} records")
+        return result.rowcount
 
-    async def delete_by_fields(self, **filters: Any) -> bool:
+    async def delete_by_fields(self, session: AsyncSession, **filters: Any) -> bool:
         """Delete records matching given field values."""
         logger.debug(f"Deleting {self.Model.__name__} by fields: {filters}")
-        async with db.scoped_session(self.session_maker) as session:
-            conditions = [getattr(self.Model, field) == value for field, value in filters.items()]
+        conditions = [getattr(self.Model, field) == value for field, value in filters.items()]
 
-            # Add project_id filter if applicable
-            if self.has_project_id and self.project_id is not None:
-                conditions.append(getattr(self.Model, "project_id") == self.project_id)
+        # Add project_id filter if applicable
+        if self.has_project_id and self.project_id is not None:
+            conditions.append(getattr(self.Model, "project_id") == self.project_id)
 
-            query = delete(self.Model).where(and_(*conditions))
-            result = cast(CursorResult[Any], await session.execute(query))
-            deleted = result.rowcount > 0
-            logger.debug(f"Deleted {result.rowcount} records")
-            return deleted
+        query = delete(self.Model).where(and_(*conditions))
+        result = cast(CursorResult[Any], await session.execute(query))
+        deleted = result.rowcount > 0
+        logger.debug(f"Deleted {result.rowcount} records")
+        return deleted
 
-    async def count(self, query: Executable | None = None) -> int:
+    async def count(self, session: AsyncSession, query: Executable | None = None) -> int:
         """Count entities in the database table."""
-        async with db.scoped_session(self.session_maker) as session:
-            if query is None:
-                query = select(func.count()).select_from(self.Model)
-                # Add project filter if applicable
-                if (
-                    isinstance(query, Select)
-                    and self.has_project_id
-                    and self.project_id is not None
-                ):
-                    query = query.where(
-                        getattr(self.Model, "project_id") == self.project_id
-                    )  # pragma: no cover
+        if query is None:
+            query = select(func.count()).select_from(self.Model)
+            # Add project filter if applicable
+            if isinstance(query, Select) and self.has_project_id and self.project_id is not None:
+                query = query.where(
+                    getattr(self.Model, "project_id") == self.project_id
+                )  # pragma: no cover
 
-            result = await session.execute(query)
-            scalar = result.scalar()
-            count = scalar if scalar is not None else 0
-            logger.debug(f"Counted {count} {self.Model.__name__} records")
-            return count
+        result = await session.execute(query)
+        scalar = result.scalar()
+        count = scalar if scalar is not None else 0
+        logger.debug(f"Counted {count} {self.Model.__name__} records")
+        return count
 
     async def execute_query(
         self,
+        session: AsyncSession,
         query: Executable,
         params: Optional[Dict[str, Any]] = None,
         use_query_options: bool = True,
@@ -411,9 +392,8 @@ class Repository[T: Base]:
 
         query = query.options(*self.get_load_options()) if use_query_options else query
         logger.trace(f"Executing query: {query}, params: {params}")
-        async with db.scoped_session(self.session_maker) as session:
-            result = await session.execute(query, params)
-            return result
+        result = await session.execute(query, params)
+        return result
 
     def get_load_options(self) -> List[LoaderOption]:
         """Get list of loader options for eager loading relationships.

src/basic_memory/repository/search_index_row.py

@@ -36,6 +36,7 @@ class SearchIndexRow:
     category: Optional[str] = None  # observations
     from_id: Optional[int] = None  # relations
     to_id: Optional[int] = None  # relations
+    to_name: Optional[str] = None  # relations: literal target text, set even when unresolved
     relation_type: Optional[str] = None  # relations
 
     # Matched chunk text from vector search (the actual content that matched the query)
@@ -94,6 +95,7 @@ class SearchIndexRow:
             else self.metadata,
             "from_id": self.from_id,
             "to_id": self.to_id,
+            "to_name": self.to_name,
             "relation_type": self.relation_type,
             "entity_id": self.entity_id,
             "category": self.category,

src/basic_memory/repository/search_repository.py

@@ -48,6 +48,8 @@ class SearchRepository(Protocol):
         min_similarity: Optional[float] = None,
         limit: int = 10,
         offset: int = 0,
+        allow_relaxed: bool = False,
+        session: AsyncSession | None = None,
     ) -> List[SearchIndexRow]:
         """Search across indexed content."""
         ...

src/basic_memory/repository/search_repository_base.py

@@ -40,6 +40,55 @@ BULLET_PATTERN = re.compile(r"^[\-\*]\s+")
 OVERSIZED_ENTITY_VECTOR_SHARD_SIZE = 256
 _SQLITE_MAX_PREPARE_WINDOW = 8
 
+# Interrogative/function words contribute lexical noise when a strict
+# full-text query is relaxed: "when OR did OR a" matches loud wrong documents
+# that displace genuine results from the ranking window.
+RELAXATION_STOPWORDS = frozenset(
+    "a an and are as at be but by did do does for from had has have how i in is it of on "
+    "or that the their they this to was we were what when where which who whom whose why "
+    "will with you your".split()
+)
+
+
+def relaxed_query_words(search_text: Optional[str]) -> Optional[list[str]]:
+    """Content-bearing words for OR-relaxing a strict full-text query.
+
+    Returns None when relaxation must not apply. These eligibility rules match
+    SearchService._is_relaxed_fts_fallback_eligible so the hybrid FTS branch
+    relaxes exactly the same query shapes as the service-level FTS path:
+
+    - empty / quoted / explicit-boolean queries (user intent is not
+      second-guessed);
+    - fewer than three alphanumeric tokens (short queries like "New Feature"
+      over-broaden under OR — and in hybrid the relaxed FTS-only rows normalize
+      to 1.0 and can outrank the vector result the user wanted);
+    - any pure-digit token ("root note 1", "SPEC 16") — identifier-like queries
+      over-broaden and create false positives under OR.
+    """
+    if not search_text:
+        return None
+    stripped = search_text.strip()
+    if '"' in stripped or any(op in f" {stripped} " for op in (" AND ", " OR ", " NOT ")):
+        return None
+    # Eligibility checks run on raw alphanumeric tokens (parity with the
+    # service), before stopword filtering.
+    tokens = re.findall(r"[A-Za-z0-9]+", stripped.lower())
+    if len(tokens) < 3 or any(token.isdigit() for token in tokens):
+        return None
+    words = [word.strip("?!.,;:") for word in stripped.split()]
+    words = [
+        word
+        for word in words
+        if word and word.isalnum() and word.lower() not in RELAXATION_STOPWORDS
+    ]
+    return words or None
+
+
+# Entity, observation, and relation rows in search_index carry ids from independent
+# auto-increment sequences, so a bare id is ambiguous across row types. Every map in
+# the vector/hybrid retrieval path must key rows by (type, id) to avoid collisions.
+type SearchIndexKey = tuple[str, int]
+
 
 @dataclass
 class VectorSyncBatchResult:
@@ -224,6 +273,7 @@ class SearchRepositoryBase(ABC):
         min_similarity: Optional[float] = None,
         limit: int = 10,
         offset: int = 0,
+        allow_relaxed: bool = False,
     ) -> List[SearchIndexRow]:
         """Search across all indexed content.
 
@@ -1857,7 +1907,7 @@ class SearchRepositoryBase(ABC):
     # ------------------------------------------------------------------
 
     @staticmethod
-    def _parse_chunk_key(chunk_key: str) -> tuple[str, int]:
+    def _parse_chunk_key(chunk_key: str) -> SearchIndexKey:
         """Parse a chunk_key like 'observation:5:0' into (type, search_index_id)."""
         parts = chunk_key.split(":")
         return parts[0], int(parts[1])
@@ -1932,26 +1982,27 @@ class SearchRepositoryBase(ABC):
 
         hydrate_start = time.perf_counter()
         # Build per-search_index_row similarity scores from chunk-level results.
-        # Each chunk_key encodes the search_index row type and id.
+        # Each chunk_key encodes the search_index row type and id; keep both as the
+        # key because different row types can share the same numeric id (#982).
         # Track the best similarity per row (for ranking) and all chunks (for context).
-        similarity_by_si_id: dict[int, float] = {}
-        chunks_by_si_id: dict[int, list[tuple[float, str]]] = {}
+        similarity_by_si_key: dict[SearchIndexKey, float] = {}
+        chunks_by_si_key: dict[SearchIndexKey, list[tuple[float, str]]] = {}
         for row in vector_rows:
             chunk_key = row.get("chunk_key", "")
             distance = float(row["best_distance"])
             similarity = self._distance_to_similarity(distance)
             chunk_text = row.get("chunk_text", "")
             try:
-                _, si_id = self._parse_chunk_key(chunk_key)
+                si_key = self._parse_chunk_key(chunk_key)
             except (ValueError, IndexError):
                 # Fallback: group by entity_id for chunks without parseable keys
                 continue
-            current = similarity_by_si_id.get(si_id)
+            current = similarity_by_si_key.get(si_key)
             if current is None or similarity > current:
-                similarity_by_si_id[si_id] = similarity
-            chunks_by_si_id.setdefault(si_id, []).append((similarity, chunk_text))
+                similarity_by_si_key[si_key] = similarity
+            chunks_by_si_key.setdefault(si_key, []).append((similarity, chunk_text))
 
-        if not similarity_by_si_id:
+        if not similarity_by_si_key:
             hydrate_ms = (time.perf_counter() - hydrate_start) * 1000
             _log_vector_summary()
             return []
@@ -1962,16 +2013,17 @@ class SearchRepositoryBase(ABC):
             min_similarity if min_similarity is not None else self._semantic_min_similarity
         )
         if effective_min_similarity > 0.0:
-            similarity_by_si_id = {
-                k: v for k, v in similarity_by_si_id.items() if v >= effective_min_similarity
+            similarity_by_si_key = {
+                k: v for k, v in similarity_by_si_key.items() if v >= effective_min_similarity
             }
-            if not similarity_by_si_id:
+            if not similarity_by_si_key:
                 hydrate_ms = (time.perf_counter() - hydrate_start) * 1000
                 _log_vector_summary()
                 return []
 
-        # Fetch the actual search_index rows
-        si_ids = list(similarity_by_si_id.keys())
+        # Fetch the actual search_index rows. Colliding (type, id) keys share one
+        # bare id, so deduplicate while preserving first-seen order.
+        si_ids = list(dict.fromkeys(si_id for _, si_id in similarity_by_si_key))
         search_index_rows = await self._fetch_search_index_rows_by_ids(si_ids)
 
         # Apply optional filters if requested
@@ -2003,16 +2055,14 @@ class SearchRepositoryBase(ABC):
                 limit=VECTOR_FILTER_SCAN_LIMIT,
                 offset=0,
             )
-            # Use (id, type) tuples to avoid collisions between different
+            # Use (type, id) tuples to avoid collisions between different
             # search_index row types that share the same auto-increment id.
-            allowed_keys = {(row.id, row.type) for row in filtered_rows if row.id is not None}
-            search_index_rows = {
-                k: v for k, v in search_index_rows.items() if (v.id, v.type) in allowed_keys
-            }
+            allowed_keys = {(row.type, row.id) for row in filtered_rows if row.id is not None}
+            search_index_rows = {k: v for k, v in search_index_rows.items() if k in allowed_keys}
 
         ranked_rows: list[SearchIndexRow] = []
-        for si_id, similarity in similarity_by_si_id.items():
-            row = search_index_rows.get(si_id)
+        for si_key, similarity in similarity_by_si_key.items():
+            row = search_index_rows.get(si_key)
             if row is None:
                 continue
 
@@ -2022,7 +2072,7 @@ class SearchRepositoryBase(ABC):
             if content_snippet and len(content_snippet) <= SMALL_NOTE_CONTENT_LIMIT:
                 matched_chunk_text = content_snippet
             else:
-                si_chunks = chunks_by_si_id.get(si_id, [])
+                si_chunks = chunks_by_si_key.get(si_key, [])
                 si_chunks.sort(key=lambda c: c[0], reverse=True)
                 top_texts = [text for _, text in si_chunks[:TOP_CHUNKS_PER_RESULT]]
                 matched_chunk_text = "\n---\n".join(top_texts) if top_texts else None
@@ -2088,8 +2138,12 @@ class SearchRepositoryBase(ABC):
 
     async def _fetch_search_index_rows_by_ids(
         self, row_ids: list[int]
-    ) -> dict[int, SearchIndexRow]:
-        """Fetch search_index rows by their primary key (id), any type."""
+    ) -> dict[SearchIndexKey, SearchIndexRow]:
+        """Fetch search_index rows by id, keyed by (type, id) to disambiguate types.
+
+        A bare id can match one row per type (independent id sequences), so the
+        result must carry every matching row rather than letting one clobber another.
+        """
         if not row_ids:
             return {}
         placeholders = ",".join(f":id_{idx}" for idx in range(len(row_ids)))
@@ -2106,11 +2160,11 @@ class SearchRepositoryBase(ABC):
             WHERE project_id = :project_id
               AND id IN ({placeholders})
         """
-        result: dict[int, SearchIndexRow] = {}
+        result: dict[SearchIndexKey, SearchIndexRow] = {}
         async with db.scoped_session(self.session_maker) as session:
             row_result = await session.execute(text(sql), params)
             for row in row_result.fetchall():
-                result[row.id] = SearchIndexRow(
+                result[(row.type, row.id)] = SearchIndexRow(
                     project_id=self.project_id,
                     id=row.id,
                     title=row.title,
@@ -2156,7 +2210,7 @@ class SearchRepositoryBase(ABC):
     ) -> List[SearchIndexRow]:
         """Fuse FTS and vector results using score-based fusion.
 
-        Uses search_index row id as the fusion key. The formula
+        Uses the search_index (type, id) pair as the fusion key. The formula
         ``max(vec, fts) + FUSION_BONUS * min(vec, fts)`` preserves
         the dominant signal and rewards dual-source agreement.
         """
@@ -2165,6 +2219,9 @@ class SearchRepositoryBase(ABC):
         query_start = time.perf_counter()
         candidate_limit = max(self._semantic_vector_k, (limit + offset) * 10)
         fts_start = time.perf_counter()
+        # allow_relaxed: question-form queries rarely AND-match, and a dead FTS
+        # branch silently degrades hybrid to vector-only ranking. Fusion plus
+        # bm25 keep relaxed lexical candidates from dominating precision.
         fts_results = await self.search(
             search_text=search_text,
             permalink=permalink,
@@ -2178,6 +2235,7 @@ class SearchRepositoryBase(ABC):
             retrieval_mode=SearchRetrievalMode.FTS,
             limit=candidate_limit,
             offset=0,
+            allow_relaxed=True,
         )
         fts_ms = (time.perf_counter() - fts_start) * 1000
         vector_start = time.perf_counter()
@@ -2199,17 +2257,19 @@ class SearchRepositoryBase(ABC):
         vector_ms = (time.perf_counter() - vector_start) * 1000
         fusion_start = time.perf_counter()
 
-        # --- Score-based fusion keyed on search_index row id ---
+        # --- Score-based fusion keyed on (type, id) ---
+        # A bare row id collides across row types (independent id sequences), so
+        # fusion must key on (type, id) or distinct rows would merge (#982).
         # FTS scores are normalized to [0, 1] (BM25 is unbounded).
         # Vector scores are used raw — already calibrated [0, 1] by _distance_to_similarity().
-        rows_by_id: dict[int, SearchIndexRow] = {}
+        rows_by_key: dict[SearchIndexKey, SearchIndexRow] = {}
 
         # Normalize FTS scores to [0, 1] — handles both SQLite (negative bm25)
         # and Postgres (positive ts_rank) by using absolute values
         fts_abs = [abs(row.score or 0.0) for row in fts_results]
         fts_max = max(fts_abs) if fts_abs else 1.0
 
-        fts_scores: dict[int, float] = {}
+        fts_scores: dict[SearchIndexKey, float] = {}
         for row in fts_results:
             if row.id is None:
                 continue
@@ -2217,32 +2277,32 @@ class SearchRepositoryBase(ABC):
             # Gate: FTS scores below threshold contribute zero
             if norm < FTS_GATE_THRESHOLD:
                 norm = 0.0
-            fts_scores[row.id] = norm
-            rows_by_id[row.id] = row
+            fts_scores[(row.type, row.id)] = norm
+            rows_by_key[(row.type, row.id)] = row
 
-        vec_scores: dict[int, float] = {}
+        vec_scores: dict[SearchIndexKey, float] = {}
         for row in vector_results:
             if row.id is None:
                 continue
             # Trigger: no re-normalization by vec_max
             # Why: vector similarity is already calibrated [0, 1]; re-normalizing
             # inflates weak matches when the entire result set is mediocre
-            vec_scores[row.id] = row.score or 0.0
-            rows_by_id[row.id] = row
+            vec_scores[(row.type, row.id)] = row.score or 0.0
+            rows_by_key[(row.type, row.id)] = row
 
         # Fuse: max(v, f) + FUSION_BONUS * min(v, f)
         # Preserves the dominant signal; bonus rewards dual-source agreement.
         # Output range: [0, 1.3] for dual-source, [0, 1.0] for single-source.
-        fused_scores: dict[int, float] = {}
-        for row_id in fts_scores.keys() | vec_scores.keys():
-            v = vec_scores.get(row_id, 0.0)
-            f = fts_scores.get(row_id, 0.0)
-            fused_scores[row_id] = max(v, f) + FUSION_BONUS * min(v, f)
+        fused_scores: dict[SearchIndexKey, float] = {}
+        for row_key in fts_scores.keys() | vec_scores.keys():
+            v = vec_scores.get(row_key, 0.0)
+            f = fts_scores.get(row_key, 0.0)
+            fused_scores[row_key] = max(v, f) + FUSION_BONUS * min(v, f)
 
         ranked = sorted(fused_scores.items(), key=lambda item: item[1], reverse=True)
         output: list[SearchIndexRow] = []
-        for row_id, fused_score in ranked[offset : offset + limit]:
-            row = rows_by_id[row_id]
+        for row_key, fused_score in ranked[offset : offset + limit]:
+            row = rows_by_key[row_key]
             # Trigger: FTS-only results have no matched_chunk_text from vector search.
             # Why: without chunk text, API falls back to truncated content, losing answer text.
             # Outcome: FTS-only results get full content_snippet as matched_chunk.

src/basic_memory/repository/sqlite_search_repository.py

@@ -23,7 +23,10 @@ from basic_memory.models.search import (
 from basic_memory.repository.embedding_provider import EmbeddingProvider
 from basic_memory.repository.embedding_provider_factory import create_embedding_provider
 from basic_memory.repository.search_index_row import SearchIndexRow
-from basic_memory.repository.search_repository_base import SearchRepositoryBase
+from basic_memory.repository.search_repository_base import (
+    SearchRepositoryBase,
+    relaxed_query_words,
+)
 from basic_memory.repository.metadata_filters import parse_metadata_filters, build_sqlite_json_path
 from basic_memory.repository.semantic_errors import SemanticDependenciesMissingError
 from basic_memory.schemas.search import SearchItemType, SearchRetrievalMode
@@ -255,6 +258,19 @@ class SQLiteSearchRepository(SearchRepositoryBase):
         if "*" in term and all(c.isalnum() or c in "*_-" for c in term):
             return term
 
+        # Natural-language queries arrive with sentence punctuation that FTS5
+        # treats as syntax ("When did Melanie paint a sunrise?"). The tokenizer
+        # ignores this punctuation in the INDEX, so stripping it from word
+        # edges loses nothing — but leaving it forces the whole question into
+        # an exact-phrase match that returns zero rows, silently disabling the
+        # FTS half of hybrid search. Interior characters (hyphens, slashes —
+        # permalinks and paths) are untouched.
+        if " " in term:
+            words = [word.strip("?!.,;:") for word in term.split()]
+            term = " ".join(word for word in words if word)
+            if not term:
+                return ""
+
         # Characters that can cause FTS5 syntax errors when used as operators
         # We're more conservative here - only quote when we detect problematic patterns
         problematic_chars = [
@@ -351,6 +367,14 @@ class SQLiteSearchRepository(SearchRepositoryBase):
         # For non-Boolean queries, use the single term preparation logic
         return self._prepare_single_term(term, is_prefix)
 
+    @staticmethod
+    def _relaxed_fts_text(search_text: Optional[str]) -> Optional[str]:
+        """OR-relaxed FTS5 expression for a failed strict query, or None."""
+        words = relaxed_query_words(search_text)
+        if not words:
+            return None
+        return " OR ".join(f"{word}*" for word in words)
+
     # ------------------------------------------------------------------
     # sqlite-vec extension loading (SQLite-specific)
     # ------------------------------------------------------------------
@@ -953,8 +977,16 @@ class SQLiteSearchRepository(SearchRepositoryBase):
         min_similarity: Optional[float] = None,
         limit: int = 10,
         offset: int = 0,
+        allow_relaxed: bool = False,
+        session: AsyncSession | None = None,
     ) -> List[SearchIndexRow]:
-        """Search across all indexed content using SQLite FTS5."""
+        """Search across all indexed content using SQLite FTS5.
+
+        ``allow_relaxed=True`` retries a zero-result strict multi-word query
+        with OR-joined content terms. Only the hybrid path opts in: its FTS
+        branch otherwise contributes nothing for question-form queries.
+        Service-level FTS searches keep their own conservative fallback.
+        """
         # --- Dispatch vector / hybrid modes (shared logic) ---
         dispatched = await self._dispatch_retrieval_mode(
             search_text=search_text,
@@ -1017,10 +1049,31 @@ class SQLiteSearchRepository(SearchRepositoryBase):
         """
 
         logger.trace(f"Search {sql} params: {params}")
-        try:
-            async with db.scoped_session(self.session_maker) as session:
-                result = await session.execute(text(sql), params)
+
+        async def run_search(active_session: AsyncSession):
+            result = await active_session.execute(text(sql), params)
+            rows = result.fetchall()
+            # Trigger: multi-word natural-language query matched nothing
+            # under the default all-terms-AND semantics.
+            # Why: questions ("when did X do Y") rarely have every word in
+            # one document; without relaxation the FTS half of hybrid
+            # search contributes zero candidates and ranking degrades to
+            # vector-only.
+            # Outcome: one retry with OR-joined prefix terms; bm25 still
+            # ranks multi-term matches first.
+            relaxed = self._relaxed_fts_text(search_text) if allow_relaxed and not rows else None
+            if relaxed and params.get("text"):
+                params["text"] = relaxed
+                result = await active_session.execute(text(sql), params)
                 rows = result.fetchall()
+            return rows
+
+        try:
+            if session is not None:
+                rows = await run_search(session)
+            else:
+                async with db.scoped_session(self.session_maker) as owned_session:
+                    rows = await run_search(owned_session)
         except Exception as e:
             # Handle FTS5 syntax errors and provide user-friendly feedback
             if self._is_fts5_syntax_error(e):  # pragma: no cover

src/basic_memory/schemas/base.py

@@ -19,7 +19,6 @@ from pathlib import Path
 from typing import List, Optional, Annotated, Dict
 
 from annotated_types import MinLen, MaxLen
-from dateparser import parse
 
 from pydantic import BaseModel, BeforeValidator, Field, model_validator, computed_field
 
@@ -92,6 +91,10 @@ def parse_timeframe(timeframe: str) -> datetime:
         parse_timeframe('1d') -> 2025-06-04 14:50:00-07:00 (24 hours ago with local timezone)
         parse_timeframe('1 week ago') -> 2025-05-29 14:50:00-07:00 (1 week ago with local timezone)
     """
+    # Deferred: dateparser costs ~0.13s to import; schemas load on every CLI
+    # start, but timeframe parsing only happens per request (#886).
+    from dateparser import parse
+
     if timeframe.lower() == "today":
         # For "today", return 1 day ago to ensure we capture recent activity across timezones
         # This handles the case where client and server are in different timezones

src/basic_memory/schemas/memory.py

@@ -155,6 +155,9 @@ class RelationSummary(BaseModel):
     from_entity_id: Optional[int] = None
     from_entity_external_id: Optional[str] = None
     to_entity: Optional[str] = None
+    # Literal target text from the markdown; present even when the relation is
+    # an unresolved forward reference (to_entity is None until the target exists)
+    to_name: Optional[str] = None
     to_entity_id: Optional[int] = None
     to_entity_external_id: Optional[str] = None
     created_at: Annotated[

src/basic_memory/services/context_service.py

@@ -2,15 +2,18 @@
 
 from __future__ import annotations
 
+from contextlib import asynccontextmanager
 from dataclasses import dataclass, field
 from datetime import datetime, timezone
-from typing import Any, List, Optional, Tuple, TYPE_CHECKING
+from typing import Any, AsyncIterator, List, Optional, Tuple, TYPE_CHECKING
 
 
 from loguru import logger
 from sqlalchemy import text
+from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker
 
 import logfire
+from basic_memory import db
 from basic_memory.repository.entity_repository import EntityRepository
 from basic_memory.repository.observation_repository import ObservationRepository
 from basic_memory.repository.postgres_search_repository import PostgresSearchRepository
@@ -18,6 +21,7 @@ from basic_memory.repository.search_repository import SearchRepository, SearchIn
 from basic_memory.schemas.memory import MemoryUrl, memory_url_path
 from basic_memory.schemas.search import SearchItemType
 from basic_memory.utils import generate_permalink
+from basic_memory.workspace_context import workspace_slug_for_canonical_permalinks
 
 if TYPE_CHECKING:
     from basic_memory.services.link_resolver import LinkResolver
@@ -36,6 +40,7 @@ class ContextResultRow:
     from_id: Optional[int] = None
     to_id: Optional[int] = None
     relation_type: Optional[str] = None
+    to_name: Optional[str] = None
     content: Optional[str] = None
     category: Optional[str] = None
     entity_id: Optional[int] = None
@@ -89,11 +94,21 @@ class ContextService:
         entity_repository: EntityRepository,
         observation_repository: ObservationRepository,
         link_resolver: Optional[LinkResolver] = None,
+        session_maker: async_sessionmaker[AsyncSession] | None = None,
     ):
         self.search_repository = search_repository
         self.entity_repository = entity_repository
         self.observation_repository = observation_repository
         self.link_resolver = link_resolver
+        self.session_maker = session_maker
+
+    @asynccontextmanager
+    async def _session_scope(self) -> AsyncIterator[AsyncSession]:
+        """Open a service-owned transaction for core repository reads."""
+        if self.session_maker is None:  # pragma: no cover
+            raise ValueError("session_maker is required for ContextService")
+        async with db.scoped_session(self.session_maker) as session:
+            yield session
 
     async def build_context(
         self,
@@ -143,6 +158,29 @@ class ContextService:
                         primary = await self.search_repository.search(
                             permalink_match=normalized_path, limit=fetch_limit, offset=offset
                         )
+
+                        # Trigger: a workspace-qualified pattern matched nothing while a
+                        #   workspace permalink context is active.
+                        # Why: rows written before workspace canonicalization (or via
+                        #   clients that didn't forward workspace headers) store
+                        #   project-qualified permalinks; a workspace-prefixed pattern
+                        #   can never match those legacy rows (#957).
+                        # Outcome: retry once with the workspace prefix stripped so the
+                        #   pattern matches the index form the rows actually carry.
+                        if not primary:
+                            workspace_slug = workspace_slug_for_canonical_permalinks()
+                            ws_prefix = f"{workspace_slug}/" if workspace_slug else None
+                            if ws_prefix and normalized_path.startswith(ws_prefix):
+                                fallback_path = normalized_path.removeprefix(ws_prefix)
+                                logger.debug(
+                                    f"Pattern search fallback without workspace prefix: "
+                                    f"'{fallback_path}'"
+                                )
+                                primary = await self.search_repository.search(
+                                    permalink_match=fallback_path,
+                                    limit=fetch_limit,
+                                    offset=offset,
+                                )
                     else:
                         normalized_path = generate_permalink(path, split_extension=False)
                         logger.debug(f"Direct lookup for '{normalized_path}'")
@@ -151,9 +189,13 @@ class ContextService:
                         )
 
                         if not primary and self.link_resolver:
-                            entity = await self.link_resolver.resolve_link(
-                                path, use_search=True, strict=False
-                            )
+                            async with self._session_scope() as session:
+                                entity = await self.link_resolver.resolve_link(
+                                    path,
+                                    use_search=True,
+                                    strict=False,
+                                    session=session,
+                                )
                             if entity:
                                 logger.debug(
                                     f"LinkResolver resolved '{path}' to permalink '{entity.permalink}'"
@@ -209,9 +251,10 @@ class ContextService:
                     phase="load_observations",
                     result_count=len(entity_ids),
                 ):
-                    observations_by_entity = await self.observation_repository.find_by_entities(
-                        entity_ids
-                    )
+                    async with self._session_scope() as session:
+                        observations_by_entity = await self.observation_repository.find_by_entities(
+                            session, entity_ids
+                        )
                 logger.debug(f"Found observations for {len(observations_by_entity)} entities")
 
             metadata = ContextMetadata(
@@ -392,6 +435,7 @@ class ContextService:
                 from_id=row.from_id,
                 to_id=row.to_id,
                 relation_type=row.relation_type,
+                to_name=row.to_name,
                 content=row.content,
                 category=row.category,
                 entity_id=row.entity_id,
@@ -426,6 +470,7 @@ class ContextService:
                 CAST(NULL AS INTEGER) as from_id,
                 CAST(NULL AS INTEGER) as to_id,
                 CAST(NULL AS TEXT) as relation_type,
+                CAST(NULL AS TEXT) as to_name,
                 CAST(NULL AS TEXT) as content,
                 CAST(NULL AS TEXT) as category,
                 CAST(NULL AS INTEGER) as entity_id,
@@ -478,6 +523,10 @@ class ContextService:
                     WHEN step_type = 1 THEN r.relation_type
                     ELSE NULL
                 END as relation_type,
+                CASE
+                    WHEN step_type = 1 THEN r.to_name
+                    ELSE NULL
+                END as to_name,
                 CAST(NULL AS TEXT) as content,
                 CAST(NULL AS TEXT) as category,
                 CAST(NULL AS INTEGER) as entity_id,
@@ -541,6 +590,7 @@ class ContextService:
             from_id,
             to_id,
             relation_type,
+            to_name,
             content,
             category,
             entity_id,
@@ -550,7 +600,7 @@ class ContextService:
         FROM entity_graph
         WHERE depth > 0
         GROUP BY type, id, title, permalink, file_path, from_id, to_id,
-                 relation_type, content, category, entity_id, root_id, created_at
+                 relation_type, to_name, content, category, entity_id, root_id, created_at
         ORDER BY depth, type, id
         LIMIT :max_results
        """)
@@ -579,6 +629,7 @@ class ContextService:
                 NULL as from_id,
                 NULL as to_id,
                 NULL as relation_type,
+                NULL as to_name,
                 NULL as content,
                 NULL as category,
                 NULL as entity_id,
@@ -606,6 +657,7 @@ class ContextService:
                 r.from_id,
                 r.to_id,
                 r.relation_type,
+                r.to_name,
                 NULL as content,
                 NULL as category,
                 NULL as entity_id,
@@ -644,6 +696,7 @@ class ContextService:
                 NULL as from_id,
                 NULL as to_id,
                 NULL as relation_type,
+                NULL as to_name,
                 NULL as content,
                 NULL as category,
                 NULL as entity_id,
@@ -677,6 +730,7 @@ class ContextService:
             from_id,
             to_id,
             relation_type,
+            to_name,
             content,
             category,
             entity_id,
@@ -686,7 +740,7 @@ class ContextService:
         FROM entity_graph
         WHERE depth > 0
         GROUP BY type, id, title, permalink, file_path, from_id, to_id,
-                 relation_type, content, category, entity_id, root_id, created_at
+                 relation_type, to_name, content, category, entity_id, root_id, created_at
         ORDER BY depth, type, id
         LIMIT :max_results
        """)

src/basic_memory/services/directory_service.py

@@ -3,10 +3,14 @@
 import fnmatch
 import logging
 import os
+from contextlib import asynccontextmanager
 from datetime import datetime
-from typing import Dict, List, Optional, Sequence
+from typing import AsyncIterator, Dict, List, Optional, Sequence
 
 
+from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker
+
+from basic_memory import db
 from basic_memory.models import Entity
 from basic_memory.repository import EntityRepository
 from basic_memory.schemas.directory import DirectoryNode
@@ -28,19 +32,31 @@ def _mtime_to_datetime(entity: Entity) -> datetime:
 class DirectoryService:
     """Service for working with directory trees."""
 
-    def __init__(self, entity_repository: EntityRepository):
+    def __init__(
+        self,
+        entity_repository: EntityRepository,
+        session_maker: async_sessionmaker[AsyncSession],
+    ):
         """Initialize the directory service.
 
         Args:
             entity_repository: Directory repository for data access.
         """
         self.entity_repository = entity_repository
+        self.session_maker = session_maker
+
+    @asynccontextmanager
+    async def _session_scope(self) -> AsyncIterator[AsyncSession]:
+        """Open a service-owned transaction."""
+        async with db.scoped_session(self.session_maker) as session:
+            yield session
 
     async def get_directory_tree(self) -> DirectoryNode:
         """Build a hierarchical directory tree from indexed files."""
 
         # Get all files from DB (flat list)
-        entity_rows = await self.entity_repository.find_all()
+        async with self._session_scope() as session:
+            entity_rows = await self.entity_repository.find_all(session)
 
         # Create a root directory node
         root_node = DirectoryNode(name="Root", directory_path="/", type="directory")
@@ -114,7 +130,8 @@ class DirectoryService:
             DirectoryNode tree containing only folders (type="directory")
         """
         # Get unique directories without loading entities
-        directories = await self.entity_repository.get_distinct_directories()
+        async with self._session_scope() as session:
+            directories = await self.entity_repository.get_distinct_directories(session)
 
         # Create a root directory node
         root_node = DirectoryNode(name="Root", directory_path="/", type="directory")
@@ -179,7 +196,8 @@ class DirectoryService:
         # Optimize: Query only entities in the target directory
         # instead of loading the entire tree
         dir_prefix = dir_name.lstrip("/")
-        entity_rows = await self.entity_repository.find_by_directory_prefix(dir_prefix)
+        async with self._session_scope() as session:
+            entity_rows = await self.entity_repository.find_by_directory_prefix(session, dir_prefix)
 
         # Build a partial tree from only the relevant entities
         root_tree = self._build_directory_tree_from_entities(entity_rows, dir_name)

src/basic_memory/services/entity_service.py

@@ -1,16 +1,18 @@
 """Service for managing entities in the database."""
 
-import asyncio
 from collections.abc import Callable
+from contextlib import asynccontextmanager
 from copy import deepcopy
 from dataclasses import dataclass
 from pathlib import Path
-from typing import Any, List, Optional, Sequence, Tuple, Union
+from typing import Any, AsyncIterator, List, Optional, Sequence, Tuple, Union
 
 import frontmatter
 import yaml
 from loguru import logger
+from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker
 
+from basic_memory import db
 from basic_memory.config import ProjectConfig, BasicMemoryConfig
 from basic_memory.file_utils import (
     has_frontmatter,
@@ -101,6 +103,7 @@ class EntityService(BaseService[EntityModel]):
         relation_repository: RelationRepository,
         file_service: FileService,
         link_resolver: LinkResolver,
+        session_maker: async_sessionmaker[AsyncSession],
         search_service: Optional[SearchService] = None,
         app_config: Optional[BasicMemoryConfig] = None,
     ):
@@ -110,6 +113,7 @@ class EntityService(BaseService[EntityModel]):
         self.entity_parser = entity_parser
         self.file_service = file_service
         self.link_resolver = link_resolver
+        self.session_maker = session_maker
         self.search_service = search_service
         self.app_config = app_config
         self._project_permalink: Optional[str] = None
@@ -117,8 +121,23 @@ class EntityService(BaseService[EntityModel]):
         # Default returns None for local/CLI usage. Cloud overrides this to read from UserContext.
         self.get_user_id: Callable[[], Optional[str]] = lambda: None
 
+    @asynccontextmanager
+    async def _session_scope(
+        self, session: AsyncSession | None = None
+    ) -> AsyncIterator[AsyncSession]:
+        """Use the caller's session or open a service-owned transaction."""
+        if session is not None:
+            yield session
+            return
+
+        async with db.scoped_session(self.session_maker) as owned_session:
+            yield owned_session
+
     async def detect_file_path_conflicts(
-        self, file_path: str, skip_check: bool = False
+        self,
+        file_path: str,
+        skip_check: bool = False,
+        session: AsyncSession | None = None,
     ) -> List[str]:
         """Detect potential file path conflicts for a given file path.
 
@@ -142,7 +161,8 @@ class EntityService(BaseService[EntityModel]):
 
         # Load only file paths. Conflict detection is on the hot write path and
         # does not need observations or relations.
-        existing_paths = await self.repository.get_all_file_paths()
+        async with self._session_scope(session) as active_session:
+            existing_paths = await self.repository.get_all_file_paths(active_session)
 
         # Use the enhanced conflict detection utility
         return detect_potential_file_conflicts(file_path, existing_paths)
@@ -152,6 +172,7 @@ class EntityService(BaseService[EntityModel]):
         file_path: Permalink | Path,
         markdown: Optional[EntityMarkdown] = None,
         skip_conflict_check: bool = False,
+        session: AsyncSession | None = None,
     ) -> str:
         """Get or generate unique permalink for an entity.
 
@@ -169,71 +190,74 @@ class EntityService(BaseService[EntityModel]):
         file_path_str = Path(file_path).as_posix()
 
         # Check for potential file path conflicts before resolving permalink
-        conflicts = await self.detect_file_path_conflicts(
-            file_path_str, skip_check=skip_conflict_check
-        )
-        if conflicts:
-            logger.warning(
-                f"Detected potential file path conflicts for '{file_path_str}': {conflicts}"
+        async with self._session_scope(session) as active_session:
+            conflicts = await self.detect_file_path_conflicts(
+                file_path_str, skip_check=skip_conflict_check, session=active_session
             )
+            if conflicts:
+                logger.warning(
+                    f"Detected potential file path conflicts for '{file_path_str}': {conflicts}"
+                )
 
-        # If markdown has explicit permalink, try to validate it
-        if markdown and markdown.frontmatter.permalink:
-            desired_permalink = markdown.frontmatter.permalink
-            # Use lightweight method - we only need to check file_path
-            existing_file_path = await self.repository.get_file_path_for_permalink(
-                desired_permalink
+            # If markdown has explicit permalink, try to validate it
+            if markdown and markdown.frontmatter.permalink:
+                desired_permalink = markdown.frontmatter.permalink
+                # Use lightweight method - we only need to check file_path
+                existing_file_path = await self.repository.get_file_path_for_permalink(
+                    active_session, desired_permalink
+                )
+
+                # If no conflict or it's our own file, use as is
+                if not existing_file_path or existing_file_path == file_path_str:
+                    return desired_permalink
+
+            # For existing files, try to find current permalink
+            # Use lightweight method - we only need the permalink
+            existing_permalink = await self.repository.get_permalink_for_file_path(
+                active_session, file_path_str
             )
+            if existing_permalink:
+                return existing_permalink
 
-            # If no conflict or it's our own file, use as is
-            if not existing_file_path or existing_file_path == file_path_str:
-                return desired_permalink
+            # New file - generate permalink
+            if markdown and markdown.frontmatter.permalink:
+                desired_permalink = markdown.frontmatter.permalink
+            else:
+                # Trigger: generating a permalink for a new file
+                # Why: canonical permalinks may require project prefix for global addressing
+                # Outcome: include project slug when enabled in config
+                include_project = True
+                if self.app_config:
+                    include_project = self.app_config.permalinks_include_project
 
-        # For existing files, try to find current permalink
-        # Use lightweight method - we only need the permalink
-        existing_permalink = await self.repository.get_permalink_for_file_path(file_path_str)
-        if existing_permalink:
-            return existing_permalink
+                workspace_permalink = workspace_slug_for_canonical_permalinks()
+                project_permalink = None
+                # Trigger: project-prefixed permalinks are enabled, or organization workspace
+                #   context requires a complete workspace/project canonical permalink.
+                # Why: project slug is the stable middle segment for globally addressable links.
+                # Outcome: fetch and cache the project's permalink before building the canonical URL.
+                if include_project or workspace_permalink:
+                    project_permalink = await self._get_project_permalink(active_session)
 
-        # New file - generate permalink
-        if markdown and markdown.frontmatter.permalink:
-            desired_permalink = markdown.frontmatter.permalink
-        else:
-            # Trigger: generating a permalink for a new file
-            # Why: canonical permalinks may require project prefix for global addressing
-            # Outcome: include project slug when enabled in config
-            include_project = True
-            if self.app_config:
-                include_project = self.app_config.permalinks_include_project
+                desired_permalink = build_canonical_permalink(
+                    project_permalink,
+                    file_path_str,
+                    include_project=include_project,
+                    workspace_permalink=workspace_permalink,
+                )
 
-            workspace_permalink = workspace_slug_for_canonical_permalinks()
-            project_permalink = None
-            # Trigger: project-prefixed permalinks are enabled, or organization workspace
-            #   context requires a complete workspace/project canonical permalink.
-            # Why: project slug is the stable middle segment for globally addressable links.
-            # Outcome: fetch and cache the project's permalink before building the canonical URL.
-            if include_project or workspace_permalink:
-                project_permalink = await self._get_project_permalink()
-
-            desired_permalink = build_canonical_permalink(
-                project_permalink,
-                file_path_str,
-                include_project=include_project,
-                workspace_permalink=workspace_permalink,
-            )
-
-        # Make unique if needed - enhanced to handle character conflicts
-        # Use lightweight existence check instead of loading full entity
-        permalink = desired_permalink
-        suffix = 1
-        while await self.repository.permalink_exists(permalink):
-            permalink = f"{desired_permalink}-{suffix}"
-            suffix += 1
-            logger.debug(f"creating unique permalink: {permalink}")
+            # Make unique if needed - enhanced to handle character conflicts
+            # Use lightweight existence check instead of loading full entity
+            permalink = desired_permalink
+            suffix = 1
+            while await self.repository.permalink_exists(active_session, permalink):
+                permalink = f"{desired_permalink}-{suffix}"
+                suffix += 1
+                logger.debug(f"creating unique permalink: {permalink}")
 
         return permalink
 
-    async def _get_project_permalink(self) -> Optional[str]:
+    async def _get_project_permalink(self, session: AsyncSession) -> Optional[str]:
         """Get and cache the current project's permalink."""
         if self._project_permalink is not None:
             return self._project_permalink
@@ -242,8 +266,8 @@ class EntityService(BaseService[EntityModel]):
         if project_id is None:  # pragma: no cover
             return None  # pragma: no cover
 
-        project_repository = ProjectRepository(self.repository.session_maker)
-        project = await project_repository.get_by_id(project_id)
+        project_repository = ProjectRepository()
+        project = await project_repository.get_by_id(session, project_id)
         if project:
             self._project_permalink = project.permalink
         return self._project_permalink
@@ -343,6 +367,7 @@ class EntityService(BaseService[EntityModel]):
         current_permalink: str | None = None,
         content_markdown: EntityMarkdown | None = None,
         skip_conflict_check: bool = False,
+        session: AsyncSession | None = None,
     ) -> str | None:
         """Resolve the canonical permalink for a create/update write."""
         if self.app_config and self.app_config.disable_permalinks:
@@ -360,6 +385,7 @@ class EntityService(BaseService[EntityModel]):
             file_path,
             content_markdown,
             skip_conflict_check=skip_conflict_check,
+            session=session,
         )
         schema._permalink = resolved_permalink
         return resolved_permalink
@@ -437,6 +463,7 @@ class EntityService(BaseService[EntityModel]):
         *,
         check_storage_exists: bool = True,
         skip_conflict_check: bool = False,
+        session: AsyncSession | None = None,
     ) -> PreparedEntityWrite:
         """Derive accepted markdown and entity fields for a new note.
 
@@ -469,6 +496,7 @@ class EntityService(BaseService[EntityModel]):
             file_path=file_path,
             content_markdown=content_markdown,
             skip_conflict_check=skip_conflict_check,
+            session=session,
         )
 
         # Build the final markdown once here. Local mode will write it immediately; cloud mode can
@@ -496,6 +524,7 @@ class EntityService(BaseService[EntityModel]):
         existing_content: str,
         *,
         skip_conflict_check: bool = False,
+        session: AsyncSession | None = None,
     ) -> PreparedEntityWrite:
         """Derive accepted markdown and entity fields for a full note replacement.
 
@@ -533,6 +562,7 @@ class EntityService(BaseService[EntityModel]):
             current_permalink=current_permalink,
             content_markdown=content_markdown,
             skip_conflict_check=skip_conflict_check,
+            session=session,
         )
 
         post = await schema_to_markdown(schema)
@@ -573,6 +603,7 @@ class EntityService(BaseService[EntityModel]):
         find_text: Optional[str] = None,
         expected_replacements: int = 1,
         skip_conflict_check: bool = False,
+        session: AsyncSession | None = None,
     ) -> PreparedEntityWrite:
         """Derive accepted markdown and entity fields for an edit request.
 
@@ -621,6 +652,7 @@ class EntityService(BaseService[EntityModel]):
                         file_path,
                         content_markdown,
                         skip_conflict_check=skip_conflict_check,
+                        session=session,
                     )
 
             normalized_metadata = normalize_frontmatter_metadata(content_frontmatter or {})
@@ -676,30 +708,34 @@ class EntityService(BaseService[EntityModel]):
     async def create_entity_with_content(self, schema: EntitySchema) -> EntityWriteResult:
         """Create a new entity and return both the entity row and written markdown."""
         logger.debug(f"Creating entity: {schema.title}")
-        # --- Prepare Accepted State ---
-        # Derive the canonical markdown/entity fields before touching the filesystem.
-        prepared = await self.prepare_create_entity_content(schema)
-        self._sync_prepared_schema_state(schema, prepared)
-        # --- Persist File, Then Indexable DB State ---
-        # Local mode still writes the file immediately; the prepare object keeps semantics separate
-        # from that persistence step.
-        checksum = await self.file_service.write_file(prepared.file_path, prepared.markdown_content)
-        entity = await self.upsert_entity_from_markdown(
-            prepared.file_path,
-            prepared.entity_markdown,
-            is_new=True,
-        )
-        updated = await self.repository.update(entity.id, {"checksum": checksum})
-        if not updated:  # pragma: no cover
-            raise ValueError(f"Failed to update entity checksum after create: {entity.id}")
-        persisted_content, search_content = await self._read_persisted_write_content(
-            prepared.file_path
-        )
-        return EntityWriteResult(
-            entity=updated,
-            content=persisted_content,
-            search_content=search_content,
-        )
+        async with self._session_scope() as session:
+            # --- Prepare Accepted State ---
+            # Derive the canonical markdown/entity fields before touching the filesystem.
+            prepared = await self.prepare_create_entity_content(schema, session=session)
+            self._sync_prepared_schema_state(schema, prepared)
+            # --- Persist File, Then Indexable DB State ---
+            # Local mode still writes the file immediately; the prepare object keeps semantics separate
+            # from that persistence step.
+            checksum = await self.file_service.write_file(
+                prepared.file_path, prepared.markdown_content
+            )
+            entity = await self.upsert_entity_from_markdown(
+                prepared.file_path,
+                prepared.entity_markdown,
+                is_new=True,
+                session=session,
+            )
+            updated = await self.repository.update(session, entity.id, {"checksum": checksum})
+            if not updated:  # pragma: no cover
+                raise ValueError(f"Failed to update entity checksum after create: {entity.id}")
+            persisted_content, search_content = await self._read_persisted_write_content(
+                prepared.file_path
+            )
+            return EntityWriteResult(
+                entity=updated,
+                content=persisted_content,
+                search_content=search_content,
+            )
 
     async def update_entity(self, entity: EntityModel, schema: EntitySchema) -> EntityModel:
         """Update an entity's content and metadata."""
@@ -716,58 +752,63 @@ class EntityService(BaseService[EntityModel]):
             f"Updating entity with permalink: {entity.permalink} content-type: {schema.content_type}"
         )
 
-        # --- Read Current File State ---
-        # Full replacements merge with existing frontmatter, so local mode still needs the current
-        # file contents as input to the prepare step.
-        existing_content = await self.file_service.read_file_content(entity.file_path)
-        prepared = await self.prepare_update_entity_content(
-            entity,
-            schema,
-            existing_content,
-        )
-        self._sync_prepared_schema_state(schema, prepared)
-        previous_file_path = Path(entity.file_path)
-        # Trigger: a full replacement also renames the note to a different canonical path.
-        # Why: Path.replace() overwrites existing files, so the destination must be conflict-free
-        #      before we write or we can clobber another note and only fail later at the DB layer.
-        # Outcome: conflicting rename attempts fail before touching either file on disk.
-        if (
-            prepared.file_path.as_posix() != previous_file_path.as_posix()
-            and await self.file_service.exists(prepared.file_path)
-            and not self._paths_share_storage_target(previous_file_path, prepared.file_path)
-        ):
-            raise EntityAlreadyExistsError(
-                f"file already exists at destination path: {prepared.file_path.as_posix()}"
+        async with self._session_scope() as session:
+            # --- Read Current File State ---
+            # Full replacements merge with existing frontmatter, so local mode still needs the current
+            # file contents as input to the prepare step.
+            existing_content = await self.file_service.read_file_content(entity.file_path)
+            prepared = await self.prepare_update_entity_content(
+                entity,
+                schema,
+                existing_content,
+                session=session,
+            )
+            self._sync_prepared_schema_state(schema, prepared)
+            previous_file_path = Path(entity.file_path)
+            # Trigger: a full replacement also renames the note to a different canonical path.
+            # Why: Path.replace() overwrites existing files, so the destination must be conflict-free
+            #      before we write or we can clobber another note and only fail later at the DB layer.
+            # Outcome: conflicting rename attempts fail before touching either file on disk.
+            if (
+                prepared.file_path.as_posix() != previous_file_path.as_posix()
+                and await self.file_service.exists(prepared.file_path)
+                and not self._paths_share_storage_target(previous_file_path, prepared.file_path)
+            ):
+                raise EntityAlreadyExistsError(
+                    f"file already exists at destination path: {prepared.file_path.as_posix()}"
+                )
+            # --- Persist Prepared State ---
+            checksum = await self.file_service.write_file(
+                prepared.file_path,
+                prepared.markdown_content,
+            )
+            entity = await self.upsert_entity_from_markdown(
+                prepared.file_path,
+                prepared.entity_markdown,
+                is_new=False,
+                existing_entity=entity,
+                session=session,
+            )
+            if prepared.file_path.as_posix() != previous_file_path.as_posix():
+                # Trigger: a full replacement changed the canonical note path.
+                # Why: the new file has already been written and the entity now points at it.
+                # Outcome: remove the stale old file so local Basic Memory mirrors cloud's PGQ cleanup.
+                if not self._paths_share_storage_target(previous_file_path, prepared.file_path):
+                    await self.file_service.delete_file(previous_file_path)
+            entity = await self.repository.update(session, entity.id, {"checksum": checksum})
+            if not entity:  # pragma: no cover
+                raise ValueError(
+                    f"Failed to update entity checksum after update: {prepared.file_path}"
+                )
+            persisted_content, search_content = await self._read_persisted_write_content(
+                prepared.file_path
             )
-        # --- Persist Prepared State ---
-        checksum = await self.file_service.write_file(
-            prepared.file_path,
-            prepared.markdown_content,
-        )
-        entity = await self.upsert_entity_from_markdown(
-            prepared.file_path,
-            prepared.entity_markdown,
-            is_new=False,
-            existing_entity=entity,
-        )
-        if prepared.file_path.as_posix() != previous_file_path.as_posix():
-            # Trigger: a full replacement changed the canonical note path.
-            # Why: the new file has already been written and the entity now points at it.
-            # Outcome: remove the stale old file so local Basic Memory mirrors cloud's PGQ cleanup.
-            if not self._paths_share_storage_target(previous_file_path, prepared.file_path):
-                await self.file_service.delete_file(previous_file_path)
-        entity = await self.repository.update(entity.id, {"checksum": checksum})
-        if not entity:  # pragma: no cover
-            raise ValueError(f"Failed to update entity checksum after update: {prepared.file_path}")
-        persisted_content, search_content = await self._read_persisted_write_content(
-            prepared.file_path
-        )
 
-        return EntityWriteResult(
-            entity=entity,
-            content=persisted_content,
-            search_content=search_content,
-        )
+            return EntityWriteResult(
+                entity=entity,
+                content=persisted_content,
+                search_content=search_content,
+            )
 
     async def delete_entity(self, permalink_or_id: str | int) -> bool:
         """Delete entity and its file."""
@@ -812,7 +853,8 @@ class EntityService(BaseService[EntityModel]):
             # Trigger: repository.delete returns False when entity is already gone (NoResultFound)
             # Why: concurrent delete_directory requests can race to delete the same entity
             # Outcome: treat as success since the entity is deleted either way
-            deleted = await self.repository.delete(entity.id)
+            async with self._session_scope() as session:
+                deleted = await self.repository.delete(session, entity.id)
             if not deleted:
                 logger.info("Entity already removed from DB", entity_id=permalink_or_id)
             return True
@@ -824,7 +866,8 @@ class EntityService(BaseService[EntityModel]):
     async def get_by_permalink(self, permalink: str) -> EntityModel:
         """Get entity by type and name combination."""
         logger.debug(f"Getting entity by permalink: {permalink}")
-        db_entity = await self.repository.get_by_permalink(permalink)
+        async with self._session_scope() as session:
+            db_entity = await self.repository.get_by_permalink(session, permalink)
         if not db_entity:
             raise EntityNotFoundError(f"Entity not found: {permalink}")
         return db_entity
@@ -832,19 +875,25 @@ class EntityService(BaseService[EntityModel]):
     async def get_entities_by_id(self, ids: List[int]) -> Sequence[EntityModel]:
         """Get specific entities and their relationships."""
         logger.debug(f"Getting entities: {ids}")
-        return await self.repository.find_by_ids(ids)
+        async with self._session_scope() as session:
+            return await self.repository.find_by_ids(session, ids)
 
     async def get_entities_by_permalinks(self, permalinks: List[str]) -> Sequence[EntityModel]:
         """Get specific nodes and their relationships."""
         logger.debug(f"Getting entities permalinks: {permalinks}")
-        return await self.repository.find_by_permalinks(permalinks)
+        async with self._session_scope() as session:
+            return await self.repository.find_by_permalinks(session, permalinks)
 
     async def delete_entity_by_file_path(self, file_path: Union[str, Path]) -> None:
         """Delete entity by file path."""
-        await self.repository.delete_by_file_path(str(file_path))
+        async with self._session_scope() as session:
+            await self.repository.delete_by_file_path(session, str(file_path))
 
     async def create_entity_from_markdown(
-        self, file_path: Path, markdown: EntityMarkdown
+        self,
+        file_path: Path,
+        markdown: EntityMarkdown,
+        session: AsyncSession | None = None,
     ) -> EntityModel:
         """Create entity and observations only.
 
@@ -867,12 +916,13 @@ class EntityService(BaseService[EntityModel]):
             model.created_by = user_id
             model.last_updated_by = user_id
 
-        # Use UPSERT to handle conflicts cleanly
-        try:
-            return await self.repository.upsert_entity(model)
-        except Exception as e:
-            logger.error(f"Failed to upsert entity for {file_path}: {e}")
-            raise EntityCreationError(f"Failed to create entity: {str(e)}") from e
+        async with self._session_scope(session) as active_session:
+            # Use UPSERT to handle conflicts cleanly
+            try:
+                return await self.repository.upsert_entity(active_session, model)
+            except Exception as e:
+                logger.error(f"Failed to upsert entity for {file_path}: {e}")
+                raise EntityCreationError(f"Failed to create entity: {str(e)}") from e
 
     async def update_entity_and_observations(
         self,
@@ -880,6 +930,7 @@ class EntityService(BaseService[EntityModel]):
         markdown: EntityMarkdown,
         *,
         existing_entity: EntityModel | None = None,
+        session: AsyncSession | None = None,
     ) -> EntityModel:
         """Update entity fields and observations.
 
@@ -888,65 +939,53 @@ class EntityService(BaseService[EntityModel]):
         """
         logger.debug(f"Updating entity and observations: {file_path}")
 
-        if existing_entity is not None:
-            db_entity = await self.repository.get_by_id(
-                existing_entity.id,
-                load_relations=False,
+        async with self._session_scope(session) as active_session:
+            if existing_entity is not None:
+                db_entity = await self.repository.get_by_id(
+                    active_session,
+                    existing_entity.id,
+                    load_relations=False,
+                )
+            else:
+                db_entity = await self.repository.get_by_file_path(
+                    active_session,
+                    file_path.as_posix(),
+                    load_relations=False,
+                )
+            if db_entity is None:  # pragma: no cover
+                raise EntityNotFoundError(f"Entity not found for file path: {file_path}")
+
+            # Observations are owned by the markdown file, so re-indexing replaces the old set.
+            # We only need the entity id here; loading the old relationship collection is wasted work.
+            await self.observation_repository.delete_by_fields(
+                active_session, entity_id=db_entity.id
             )
-        else:
-            db_entity = await self.repository.get_by_file_path(
-                file_path.as_posix(),
-                load_relations=False,
-            )
-        if db_entity is None:  # pragma: no cover
-            raise EntityNotFoundError(f"Entity not found for file path: {file_path}")
 
-        # Observations are owned by the markdown file, so re-indexing replaces the old set.
-        # We only need the entity id here; loading the old relationship collection is wasted work.
-        await self.observation_repository.delete_by_fields(entity_id=db_entity.id)
+            observations = [
+                Observation(
+                    project_id=self.observation_repository.project_id,
+                    entity_id=db_entity.id,
+                    content=obs.content,
+                    category=obs.category,
+                    context=obs.context,
+                    tags=obs.tags,
+                )
+                for obs in markdown.observations
+            ]
+            await self.observation_repository.add_all_no_return(active_session, observations)
 
-        observations = [
-            Observation(
-                project_id=self.observation_repository.project_id,
-                entity_id=db_entity.id,
-                content=obs.content,
-                category=obs.category,
-                context=obs.context,
-                tags=obs.tags,
-            )
-            for obs in markdown.observations
-        ]
-        await self.observation_repository.add_all_no_return(observations)
+            self._apply_markdown_entity_fields(db_entity, file_path, markdown)
 
-        self._apply_markdown_entity_fields(db_entity, file_path, markdown)
+            # checksum value is None == not finished with sync
+            db_entity.checksum = None
 
-        # checksum value is None == not finished with sync
-        db_entity.checksum = None
+            # Set last_updated_by for cloud usage (preserve existing created_by)
+            user_id = self.get_user_id()
+            if user_id is not None:
+                db_entity.last_updated_by = user_id
 
-        # Set last_updated_by for cloud usage (preserve existing created_by)
-        user_id = self.get_user_id()
-        if user_id is not None:
-            db_entity.last_updated_by = user_id
-
-        entity_updates = {
-            "title": db_entity.title,
-            "note_type": db_entity.note_type,
-            "permalink": db_entity.permalink,
-            "file_path": db_entity.file_path,
-            "content_type": db_entity.content_type,
-            "created_at": db_entity.created_at,
-            "updated_at": db_entity.updated_at,
-            "entity_metadata": db_entity.entity_metadata,
-            "checksum": db_entity.checksum,
-            "last_updated_by": db_entity.last_updated_by,
-        }
-        updated = await self.repository.update_fields(
-            db_entity.id,
-            entity_updates,
-        )
-        if not updated:  # pragma: no cover
-            raise EntityNotFoundError(f"Entity not found for file path: {file_path}")
-        return db_entity
+            await active_session.flush()
+            return db_entity
 
     def _apply_markdown_entity_fields(
         self,
@@ -981,23 +1020,29 @@ class EntityService(BaseService[EntityModel]):
         existing_entity: EntityModel | None = None,
         resolve_relations: bool = True,
         reload_entity: bool = True,
+        session: AsyncSession | None = None,
     ) -> EntityModel:
         """Create/update entity and relations from parsed markdown."""
-        if is_new:
-            created = await self.create_entity_from_markdown(file_path, markdown)
-        else:
-            created = await self.update_entity_and_observations(
-                file_path,
+        async with self._session_scope(session) as active_session:
+            if is_new:
+                created = await self.create_entity_from_markdown(
+                    file_path, markdown, session=active_session
+                )
+            else:
+                created = await self.update_entity_and_observations(
+                    file_path,
+                    markdown,
+                    existing_entity=existing_entity,
+                    session=active_session,
+                )
+            # Pass the entity through so relation work does not have to rediscover the source row.
+            return await self.update_entity_relations(
+                created,
                 markdown,
-                existing_entity=existing_entity,
+                resolve_targets=resolve_relations,
+                reload_entity=reload_entity,
+                session=active_session,
             )
-        # Pass the entity through so relation work does not have to rediscover the source row.
-        return await self.update_entity_relations(
-            created,
-            markdown,
-            resolve_targets=resolve_relations,
-            reload_entity=reload_entity,
-        )
 
     async def update_entity_relations(
         self,
@@ -1006,6 +1051,7 @@ class EntityService(BaseService[EntityModel]):
         *,
         resolve_targets: bool = True,
         reload_entity: bool = True,
+        session: AsyncSession | None = None,
     ) -> EntityModel:
         """Update relations for entity.
 
@@ -1015,69 +1061,79 @@ class EntityService(BaseService[EntityModel]):
         entity_id = entity.id
         logger.debug(f"Updating relations for entity: {entity.file_path}")
 
-        # Clear existing relations first
-        await self.relation_repository.delete_outgoing_relations_from_entity(entity_id)
+        async with self._session_scope(session) as active_session:
+            # Clear existing relations first
+            await self.relation_repository.delete_outgoing_relations_from_entity(
+                active_session, entity_id
+            )
 
-        if markdown.relations:
-            if resolve_targets:
-                # Exact target resolution is useful for local sync, but expensive for cloud
-                # one-file jobs. Cloud can write unresolved rows and let a relation repair pass
-                # fill in to_id later.
-                resolved_entities = await asyncio.gather(
-                    *(
-                        self.link_resolver.resolve_link(
-                            rel.target,
-                            strict=True,
-                            load_relations=False,
+            if markdown.relations:
+                if resolve_targets:
+                    # Exact target resolution is useful for local sync, but expensive for cloud
+                    # one-file jobs. Cloud can write unresolved rows and let a relation repair pass
+                    # fill in to_id later.
+                    resolved_entities = []
+                    for rel in markdown.relations:
+                        try:
+                            resolved_entities.append(
+                                await self.link_resolver.resolve_link(
+                                    rel.target,
+                                    strict=True,
+                                    load_relations=False,
+                                    session=active_session,
+                                )
+                            )
+                        except Exception as exc:
+                            resolved_entities.append(exc)
+                else:
+                    resolved_entities = [None] * len(markdown.relations)
+
+                # Process results and create relation records
+                relations_to_add = []
+                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):
+                        # Relation target resolution keeps exceptions as values so a failed lookup
+                        # becomes an unresolved forward reference instead of aborting the write.
+                        target_entity = resolved
+
+                    if target_entity is None and not resolve_targets:
+                        target_entity = await self._resolve_deferred_self_relation(
+                            rel.target, entity, session=active_session
                         )
-                        for rel in markdown.relations
-                    ),
-                    return_exceptions=True,
-                )
-            else:
-                resolved_entities = [None] * len(markdown.relations)
 
-            # Process results and create relation records
-            relations_to_add = []
-            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, BaseException):
-                    # asyncio.gather(..., return_exceptions=True) can return any BaseException.
-                    target_entity = resolved
+                    # if the target is found, store the id
+                    target_id = target_entity.id if target_entity else None
+                    # if the target is found, store the title, otherwise add the target for a "forward link"
+                    target_name = target_entity.title if target_entity else rel.target
 
-                if target_entity is None and not resolve_targets:
-                    target_entity = await self._resolve_deferred_self_relation(rel.target, entity)
+                    # Create the relation
+                    relation = Relation(
+                        project_id=self.relation_repository.project_id,
+                        from_id=entity_id,
+                        to_id=target_id,
+                        to_name=target_name,
+                        relation_type=rel.type,
+                        context=rel.context,
+                    )
+                    relations_to_add.append(relation)
 
-                # if the target is found, store the id
-                target_id = target_entity.id if target_entity else None
-                # if the target is found, store the title, otherwise add the target for a "forward link"
-                target_name = target_entity.title if target_entity else rel.target
+                # Batch insert all relations
+                if relations_to_add:
+                    await self.relation_repository.add_all_ignore_duplicates(
+                        active_session, relations_to_add
+                    )
 
-                # Create the relation
-                relation = Relation(
-                    project_id=self.relation_repository.project_id,
-                    from_id=entity_id,
-                    to_id=target_id,
-                    to_name=target_name,
-                    relation_type=rel.type,
-                    context=rel.context,
-                )
-                relations_to_add.append(relation)
+            if not reload_entity:
+                return entity
 
-            # Batch insert all relations
-            if relations_to_add:
-                await self.relation_repository.add_all_ignore_duplicates(relations_to_add)
-
-        if not reload_entity:
-            return entity
-
-        # Reload entity with relations via PK lookup (faster than get_by_file_path string match).
-        reloaded = await self.repository.find_by_ids([entity_id])
-        return reloaded[0]
+            # Reload entity with relations via PK lookup (faster than get_by_file_path string match).
+            reloaded = await self.repository.find_by_ids(active_session, [entity_id])
+            return reloaded[0]
 
     async def _resolve_deferred_self_relation(
-        self, target: str, entity: EntityModel
+        self, target: str, entity: EntityModel, session: AsyncSession | None = None
     ) -> EntityModel | None:
         """Resolve only self-relations that are safe to identify in deferred mode."""
         clean_target = target.strip()
@@ -1101,9 +1157,12 @@ class EntityService(BaseService[EntityModel]):
         # Title-only links are ambiguous because Basic Memory allows duplicate titles.
         # Collapse them to self only when the title lookup proves this source is the sole candidate;
         # otherwise leave the relation unresolved so we do not create a wrong permanent edge.
-        title_matches = await self.repository.get_by_title(clean_target, load_relations=False)
-        if len(title_matches) == 1 and title_matches[0].id == entity.id:
-            return entity
+        async with self._session_scope(session) as active_session:
+            title_matches = await self.repository.get_by_title(
+                active_session, clean_target, load_relations=False
+            )
+            if len(title_matches) == 1 and title_matches[0].id == entity.id:
+                return entity
 
         return None
 
@@ -1166,43 +1225,46 @@ class EntityService(BaseService[EntityModel]):
 
         file_path = Path(entity.file_path)
         current_content, _ = await self.file_service.read_file(file_path)
-        # --- Prepare Against Explicit Base Content ---
-        # The edit operation is the semantic step; file/DB writes below are just persistence of that
-        # accepted result.
-        prepared = await self.prepare_edit_entity_content(
-            entity,
-            current_content,
-            operation=operation,
-            content=content,
-            section=section,
-            find_text=find_text,
-            expected_replacements=expected_replacements,
-        )
+        async with self._session_scope() as session:
+            # --- Prepare Against Explicit Base Content ---
+            # The edit operation is the semantic step; file/DB writes below are just persistence of that
+            # accepted result.
+            prepared = await self.prepare_edit_entity_content(
+                entity,
+                current_content,
+                operation=operation,
+                content=content,
+                section=section,
+                find_text=find_text,
+                expected_replacements=expected_replacements,
+                session=session,
+            )
 
-        checksum = await self.file_service.write_file(
-            file_path,
-            prepared.markdown_content,
-        )
+            checksum = await self.file_service.write_file(
+                file_path,
+                prepared.markdown_content,
+            )
 
-        # --- Rebuild Structured Knowledge State ---
-        # Non-fast edits remain fully synchronous locally: once the file write succeeds, we refresh
-        # observations, relations, and checksum in the same request.
-        entity = await self.upsert_entity_from_markdown(
-            file_path,
-            prepared.entity_markdown,
-            is_new=False,
-        )
+            # --- Rebuild Structured Knowledge State ---
+            # Non-fast edits remain fully synchronous locally: once the file write succeeds, we refresh
+            # observations, relations, and checksum in the same request.
+            entity = await self.upsert_entity_from_markdown(
+                file_path,
+                prepared.entity_markdown,
+                is_new=False,
+                session=session,
+            )
 
-        entity = await self.repository.update(entity.id, {"checksum": checksum})
-        if not entity:  # pragma: no cover
-            raise ValueError(f"Failed to update entity checksum after edit: {file_path}")
-        persisted_content, search_content = await self._read_persisted_write_content(file_path)
+            entity = await self.repository.update(session, entity.id, {"checksum": checksum})
+            if not entity:  # pragma: no cover
+                raise ValueError(f"Failed to update entity checksum after edit: {file_path}")
+            persisted_content, search_content = await self._read_persisted_write_content(file_path)
 
-        return EntityWriteResult(
-            entity=entity,
-            content=persisted_content,
-            search_content=search_content,
-        )
+            return EntityWriteResult(
+                entity=entity,
+                content=persisted_content,
+                search_content=search_content,
+            )
 
     def apply_edit_operation(
         self,
@@ -1528,11 +1590,12 @@ class EntityService(BaseService[EntityModel]):
             updates["checksum"] = new_checksum
 
             # 9. Update database
-            updated_entity = await self.repository.update(entity.id, updates)
-            if not updated_entity:
-                raise ValueError(f"Failed to update entity in database: {entity.id}")
+            async with self._session_scope() as session:
+                updated_entity = await self.repository.update(session, entity.id, updates)
+                if not updated_entity:
+                    raise ValueError(f"Failed to update entity in database: {entity.id}")
 
-            return updated_entity
+                return updated_entity
 
         except Exception as e:
             # Rollback: try to restore original file location if move succeeded
@@ -1581,7 +1644,8 @@ class EntityService(BaseService[EntityModel]):
         destination_directory = destination_directory.strip("/")
 
         # Find all entities in the source directory
-        entities = await self.repository.find_by_directory_prefix(source_directory)
+        async with self._session_scope() as session:
+            entities = await self.repository.find_by_directory_prefix(session, source_directory)
 
         if not entities:
             logger.warning(f"No entities found in directory: {source_directory}")
@@ -1665,7 +1729,8 @@ class EntityService(BaseService[EntityModel]):
         directory = directory.strip("/")
 
         # Find all entities in the directory
-        entities = await self.repository.find_by_directory_prefix(directory)
+        async with self._session_scope() as session:
+            entities = await self.repository.find_by_directory_prefix(session, directory)
 
         if not entities:
             logger.warning(f"No entities found in directory: {directory}")