fix(mcp): fix tool-docs generator and regenerate artifact

Fixes all reviewer-blocking and minor issues from the initial review of
the feat/404-tool-docs-artifact implementation.

BLOCKING fixes:
- Replace the naïve Annotated[...] regex with a bracket-aware character
  scan (_unwrap_annotated) so types like Dict[str, Any] | None and
  List[str] | None are extracted correctly instead of being truncated or
  emitting internal validator details (BeforeValidator, AliasChoices, etc.)
- Escape unescaped | characters in table cells (_escape_table_cell) so
  union types like list[str] | str | None render correctly in GitHub
  Flavoured Markdown tables instead of creating spurious extra columns

Minor fixes:
- Fix _extract_examples_section to detect the next top-level section
  (Raises:, Returns:, etc.) and stop there; previously the Raises: block
  was fenced inside the Python code example
- Add Description column data: _format_args_section now returns a parsed
  dict of arg descriptions (_parse_args_block) which populates the table
  Description column; fix indent-detection so the first arg line is not
  stripped of its leading spaces by .strip()
- Add deduplication: drop the docstring first line when normalised it is
  identical to the decorator description
- Demote ### sub-headers in docstring bodies to #### so they don't
  pollute GitHub's outline sidebar at the same level as tool headings
- Fix TOC anchor collision: the `search` tool anchor would resolve to the
  same #search as the ## Search group header; _tool_anchor detects
  collisions and appends -tool; an HTML <a id> anchor is injected in
  render_tool_section so the link resolves correctly
- Add comment explaining why ui_sdk.py is excluded from TOOL_FILES
- Format script with ruff (was failing CI ruff format --check gate)

Co-Authored-By: Claude <noreply@anthropic.com>
Signed-off-by: Drew Cain <groksrc@gmail.com>

.claude-plugin/marketplace.json

@@ -6,14 +6,14 @@
   },
   "metadata": {
     "description": "Official Basic Memory plugins from the canonical basic-memory repository",
-    "version": "0.22.1"
+    "version": "0.22.0"
   },
   "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": "0.22.1",
+      "version": "0.22.0",
       "author": {
         "name": "Basic Machines"
       },

.claude/commands/release/release.md

@@ -28,10 +28,7 @@ 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 **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)
+   - CHANGELOG.md contains entry for target version
    - Entry includes all major features and fixes
    - Breaking changes are documented
 
@@ -44,15 +41,11 @@ just release <version>
 The justfile target handles:
 - ✅ Version format validation
 - ✅ Git status and branch checks
-- ✅ Changelog entry check (must already be on `main`)
-- ✅ Quality checks (`just lint` + `just typecheck`)
+- ✅ Quality checks (`just check` - lint, format, type-check, tests)
 - ✅ Version update across all consolidated manifests via `just set-version` (Python
   package + Claude Code plugin/marketplaces + Codex plugin + Hermes + OpenClaw)
-- ✅ 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
+- ✅ Automatic commit with proper message
+- ✅ Tag creation and pushing to GitHub
 - ✅ Release workflow trigger (automatic on tag push)
 
 The GitHub Actions workflow (`.github/workflows/release.yml`) then:
@@ -96,7 +89,7 @@ After PyPI release is published, update the MCP registry:
 
 2. **Publish to MCP Registry**
    ```bash
-   # from the basic-memory repo root
+   cd /Users/drew/code/basic-memory
    mcp-publisher publish
    ```
 
@@ -116,7 +109,7 @@ After PyPI release is published, update the MCP registry:
 
 #### Website Updates
 
-**1. basicmachines.co** (sibling `basicmachines.co` repo)
+**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**:
@@ -133,31 +126,26 @@ After PyPI release is published, update the MCP registry:
      7. Push branch: `git push origin release/v{VERSION}`
    - **Deploy**: Follow deployment process for basicmachines.co
 
-**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".
+**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`
    - **What to do**:
      1. Pull latest from GitHub: `git pull origin main`
      2. Create release branch: `git checkout -b release/v{VERSION}`
-     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
+     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
 
 **4. Announce Release**
    - Post to Discord community if significant changes

AGENTS.md

@@ -300,9 +300,7 @@ 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, 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).
+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.
 
 **Stable release:**
 
@@ -310,7 +308,7 @@ 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` 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.
+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.
 
 **Beta release:** `just beta v0.21.3b1` — same flow with a beta-suffixed tag. PyPI consumers install with `pip install basic-memory --pre`.
 
@@ -321,7 +319,7 @@ 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 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)
+- `docs.basicmemory.com` — add notes to `src/pages/latest-releases.mdx`
 - `basicmachines.co` — bump version in `src/components/sections/hero.tsx`
 - MCP Registry — `mcp-publisher publish` from the repo root
 

CHANGELOG.md

@@ -1,49 +1,5 @@
 # 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

@@ -590,7 +590,7 @@ retention).
 | `BASIC_MEMORY_IMPORT_UPLOAD_MAX_BYTES` | `104857600` | Max uploaded import size |
 
 ```bash
-BASIC_MEMORY_LOG_LEVEL=DEBUG basic-memory reindex
+BASIC_MEMORY_LOG_LEVEL=DEBUG basic-memory sync
 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 reindex
+docker exec basic-memory-server basic-memory sync
 
 # 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 reindex
+   docker exec basic-memory-server basic-memory sync
    ```
 
 ### 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 reindex
+docker exec basic-memory-server basic-memory sync
 ```
 
 ### Environment Variables

docs/character-handling.md

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

docs/manual-pages.md

@@ -1,183 +0,0 @@
-# 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__ = "0.22.1"
+__version__ = "0.22.0"
 
 logger = logging.getLogger("hermes.memory.basic-memory")
 

integrations/hermes/plugin.yaml

@@ -1,5 +1,5 @@
 name: basic-memory
-version: 0.22.1
+version: 0.22.0
 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": "0.22.1",
+  "version": "0.22.0",
   "type": "module",
   "main": "./dist/index.js",
   "types": "./dist/index.d.ts",

justfile

@@ -383,31 +383,17 @@ 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}}"
 
-    # 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 $VERSION_NUM for {{version}} release"
-    git checkout -b "release/{{version}}"
+    # Commit version update
     git add \
         src/basic_memory/__init__.py \
         server.json \
@@ -418,56 +404,22 @@ release version:
         integrations/hermes/plugin.yaml \
         integrations/hermes/__init__.py \
         integrations/openclaw/package.json
-    git commit -s -m "$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 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 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 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 "   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 "   3. MCP Registry - Run: mcp-publisher publish"
     echo "   See: .claude/commands/release/release.md for detailed instructions"
@@ -515,15 +467,7 @@ beta version:
     echo "📝 Updating consolidated package versions..."
     just set-version "{{version}}"
 
-    # 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 $VERSION_NUM for {{version}} beta release"
-    git checkout -b "release/{{version}}"
+    # Commit version update
     git add \
         src/basic_memory/__init__.py \
         server.json \
@@ -534,57 +478,23 @@ beta version:
         integrations/hermes/plugin.yaml \
         integrations/hermes/__init__.py \
         integrations/openclaw/package.json
-    git commit -s -m "$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 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 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 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 "   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 "   See: .claude/commands/release/release.md for detailed instructions"
 

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": "0.22.1"
+    "version": "0.22.0"
   },
   "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": "0.22.1",
+      "version": "0.22.0",
       "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": "0.22.1",
+  "version": "0.22.0",
   "author": {
     "name": "Basic Machines"
   },

plugins/claude-code/schemas/manpage.md

@@ -1,55 +0,0 @@
----
-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": "0.22.1",
+  "version": "0.22.0",
   "description": "A Codex-native bridge to Basic Memory for durable engineering context, decisions, and resumable checkpoints.",
   "author": {
     "name": "Basic Machines",

scripts/generate_tool_docs.py

@@ -0,0 +1,726 @@
+#!/usr/bin/env python3
+"""Generate MCP tool reference documentation from tool docstrings.
+
+Introspects all MCP tool definitions in src/basic_memory/mcp/tools/,
+extracts names, descriptions, parameters, and docstrings, then emits
+a single deterministic markdown reference to docs/mcp-tools.md.
+
+Usage:
+    uv run scripts/generate_tool_docs.py
+
+    # Verify idempotency (diff should be empty):
+    uv run scripts/generate_tool_docs.py && uv run scripts/generate_tool_docs.py
+    git diff docs/mcp-tools.md
+"""
+
+from __future__ import annotations
+
+import ast
+import inspect
+import re
+import sys
+from pathlib import Path
+
+# ---------------------------------------------------------------------------
+# Paths
+# ---------------------------------------------------------------------------
+
+ROOT = Path(__file__).resolve().parents[1]
+TOOLS_DIR = ROOT / "src" / "basic_memory" / "mcp" / "tools"
+OUT_FILE = ROOT / "docs" / "mcp-tools.md"
+
+# Only files that contain public MCP tools (skip helpers/internals).
+# NOTE: ui_sdk.py is intentionally omitted — its two tools are commented out
+# in src/basic_memory/mcp/__init__.py and therefore not public.
+TOOL_FILES = [
+    "build_context.py",
+    "canvas.py",
+    "chatgpt_tools.py",
+    "cloud_info.py",
+    "delete_note.py",
+    "edit_note.py",
+    "list_directory.py",
+    "move_note.py",
+    "project_management.py",
+    "read_content.py",
+    "read_note.py",
+    "recent_activity.py",
+    "release_notes.py",
+    "schema.py",
+    "search.py",
+    "view_note.py",
+    "workspaces.py",
+    "write_note.py",
+]
+
+
+# ---------------------------------------------------------------------------
+# AST-based extraction (no import side-effects)
+# ---------------------------------------------------------------------------
+
+
+def _clean_docstring(raw: str | None) -> str:
+    """Dedent and strip a raw docstring."""
+    if not raw:
+        return ""
+    return inspect.cleandoc(raw)
+
+
+def _get_default_repr(node: ast.expr | None) -> str:
+    """Return a short string representation for a default-value AST node."""
+    if node is None:
+        return ""
+    try:
+        return ast.unparse(node)
+    except Exception:
+        return "..."
+
+
+def _unwrap_annotated(text: str) -> str:
+    """Bracket-aware unwrap of ``Annotated[X, ...]`` → ``X``.
+
+    The naïve regex ``Annotated\\[([^,\\]]+),.*?\\]`` breaks on types whose
+    first argument itself contains brackets or commas, e.g.
+    ``Annotated[Dict[str, Any] | None, ...]`` or
+    ``Annotated[List[str] | None, BeforeValidator(...), ...]``.
+    This function scans character-by-character to find the first
+    *top-level* comma that separates the type from the metadata args,
+    then discards everything from that comma to the matching closing ``]``.
+    """
+    prefix = "Annotated["
+    result = []
+    i = 0
+    while i < len(text):
+        if text[i:].startswith(prefix):
+            # Walk past "Annotated[" and collect the first top-level argument.
+            j = i + len(prefix)
+            depth = 0
+            start = j
+            while j < len(text):
+                ch = text[j]
+                if ch in "([{":
+                    depth += 1
+                elif ch in ")]}":
+                    if depth == 0:
+                        # Closing bracket of Annotated[...] with no comma found
+                        # (shouldn't happen in valid annotations, but be safe).
+                        break
+                    depth -= 1
+                elif ch == "," and depth == 0:
+                    # Found the separator between the type arg and metadata.
+                    break
+                j += 1
+            inner_type = text[start:j]
+            result.append(inner_type)
+            # Skip past the rest of the Annotated[...] construct.
+            # We need to find the matching ']' for the original 'Annotated['.
+            depth = 0
+            while j < len(text):
+                ch = text[j]
+                if ch in "([{":
+                    depth += 1
+                elif ch == "]" and depth == 0:
+                    j += 1  # consume the closing ']'
+                    break
+                elif ch in ")]}":
+                    depth -= 1
+                j += 1
+            i = j
+        else:
+            result.append(text[i])
+            i += 1
+    return "".join(result)
+
+
+def _annotation_repr(node: ast.expr | None) -> str:
+    """Return a readable string for a type-annotation AST node."""
+    if node is None:
+        return ""
+    try:
+        text = ast.unparse(node)
+    except Exception:
+        return ""
+    # Unwrap Annotated[X, ...] → X  (keeps output readable).
+    # Use a bracket-aware unwrap so types like Dict[str, Any] | None are
+    # preserved correctly instead of being truncated at the first comma.
+    text = _unwrap_annotated(text)
+    return text
+
+
+_SENTINEL = object()  # returned when decorator IS @mcp.tool but has no description string
+
+
+def _mcp_tool_description(decorator: ast.expr) -> str | None | object:
+    """Extract the ``description=`` keyword from an ``@mcp.tool(...)`` decorator call.
+
+    Returns:
+        - A string when the decorator carries ``description="..."``
+        - ``_SENTINEL`` when the decorator IS an mcp.tool call but has no description
+        - ``None`` when the decorator is not an mcp.tool call at all
+
+    This distinction lets callers treat mcp.tool-decorated functions without a
+    decorator description string as still valid tools (description comes from the
+    docstring in that case).
+    """
+    if not isinstance(decorator, ast.Call):
+        return None
+
+    func = decorator.func
+    # Accept both ``mcp.tool(...)`` and ``tool(...)``
+    if not (
+        (isinstance(func, ast.Attribute) and func.attr == "tool")
+        or (isinstance(func, ast.Name) and func.id == "tool")
+    ):
+        return None
+
+    for kw in decorator.keywords:
+        if kw.arg == "description" and isinstance(kw.value, ast.Constant):
+            return kw.value.value
+
+    # Also accept a positional string as the tool name (no description)
+    # e.g. @mcp.tool("list_memory_projects", annotations={...})
+    # In this case, the description is not in the decorator; fall through to docstring.
+    return _SENTINEL
+
+
+class ToolInfo:
+    """Holds extracted metadata for a single MCP tool."""
+
+    __slots__ = (
+        "name",
+        "decorator_description",
+        "docstring",
+        "params",
+        "source_file",
+    )
+
+    def __init__(
+        self,
+        name: str,
+        decorator_description: str,
+        docstring: str,
+        params: list[dict[str, str]],
+        source_file: str,
+    ) -> None:
+        self.name = name
+        self.decorator_description = decorator_description
+        self.docstring = docstring
+        self.params = params
+        self.source_file = source_file
+
+
+# Parameters that are MCP/framework plumbing — not useful to document.
+_SKIP_PARAMS = frozenset({"context", "self", "cls"})
+
+
+def extract_tools_from_file(path: Path) -> list[ToolInfo]:
+    """Parse *path* with AST and return a list of ToolInfo for every @mcp.tool function."""
+    source = path.read_text(encoding="utf-8")
+    try:
+        tree = ast.parse(source, filename=str(path))
+    except SyntaxError as exc:
+        print(f"WARNING: could not parse {path}: {exc}", file=sys.stderr)
+        return []
+
+    tools: list[ToolInfo] = []
+
+    for node in ast.walk(tree):
+        if not isinstance(node, (ast.FunctionDef, ast.AsyncFunctionDef)):
+            continue
+
+        # Only process functions that have an @mcp.tool (or @tool) decorator.
+        # decorator_desc is:
+        #   - a non-empty string when found in the decorator
+        #   - _SENTINEL when the decorator is mcp.tool but carries no description
+        #   - None when no mcp.tool decorator is present
+        decorator_desc: str | object | None = None
+        for dec in node.decorator_list:
+            result = _mcp_tool_description(dec)
+            if result is not None:
+                decorator_desc = result
+                break
+
+        if decorator_desc is None:
+            continue
+
+        # When the decorator doesn't carry a description string, fall back to
+        # the first sentence of the docstring (populated below).
+        decorator_has_description = isinstance(decorator_desc, str)
+
+        docstring = _clean_docstring(ast.get_docstring(node))
+
+        # --- Parameters ---
+        params: list[dict[str, str]] = []
+        args = node.args
+        # Defaults are right-aligned against the arg list
+        n_defaults = len(args.defaults)
+        n_args = len(args.args)
+        defaults_padded = [None] * (n_args - n_defaults) + list(args.defaults)  # type: ignore[list-item]
+        kw_defaults = args.kw_defaults  # may contain None for "no default"
+
+        for i, arg in enumerate(args.args):
+            if arg.arg in _SKIP_PARAMS:
+                continue
+            default = defaults_padded[i]
+            params.append(
+                {
+                    "name": arg.arg,
+                    "type": _annotation_repr(arg.annotation),
+                    "default": _get_default_repr(default) if default is not None else "",
+                }
+            )
+
+        for i, arg in enumerate(args.kwonlyargs):
+            if arg.arg in _SKIP_PARAMS:
+                continue
+            default = kw_defaults[i] if i < len(kw_defaults) else None
+            params.append(
+                {
+                    "name": arg.arg,
+                    "type": _annotation_repr(arg.annotation),
+                    "default": _get_default_repr(default) if default is not None else "",
+                }
+            )
+
+        # Build the short one-liner description:
+        # - prefer the explicit decorator description=
+        # - fall back to the first non-blank line of the docstring
+        if decorator_has_description:
+            short_desc = decorator_desc.strip()  # type: ignore[union-attr]
+        else:
+            first_line = next((ln.strip() for ln in docstring.splitlines() if ln.strip()), "")
+            short_desc = first_line
+
+        tools.append(
+            ToolInfo(
+                name=node.name,
+                decorator_description=short_desc,
+                docstring=docstring,
+                params=params,
+                source_file=path.name,
+            )
+        )
+
+    return tools
+
+
+# ---------------------------------------------------------------------------
+# Markdown rendering
+# ---------------------------------------------------------------------------
+
+
+def _escape_table_cell(text: str) -> str:
+    """Escape ``|`` characters so they do not break GitHub-flavoured markdown tables."""
+    return text.replace("|", "\\|")
+
+
+def _params_table(
+    params: list[dict[str, str]], arg_descriptions: dict[str, str] | None = None
+) -> str:
+    """Render parameters as a markdown table.
+
+    ``arg_descriptions`` maps parameter name → one-line description extracted
+    from the docstring ``Args:`` block.
+    """
+    if not params:
+        return ""
+    arg_descriptions = arg_descriptions or {}
+    rows = [
+        "| Parameter | Type | Default | Description |",
+        "|-----------|------|---------|-------------|",
+    ]
+    for p in params:
+        name = f"`{p['name']}`"
+        # Pipe characters inside a table cell break GitHub's renderer; escape them.
+        raw_type = p["type"]
+        typ = f"`{_escape_table_cell(raw_type)}`" if raw_type else ""
+        default_val = p["default"]
+        default = f"`{_escape_table_cell(default_val)}`" if default_val else "*(required)*"
+        desc = _escape_table_cell(arg_descriptions.get(p["name"], ""))
+        rows.append(f"| {name} | {typ} | {default} | {desc} |")
+    return "\n".join(rows)
+
+
+def _extract_examples_section(docstring: str) -> tuple[str, str]:
+    """Split docstring into (body_without_examples, examples_block).
+
+    Looks for an 'Examples:' section (with or without leading '#') and
+    returns everything before it as the body, and everything from the
+    Examples header to the next top-level section (e.g. 'Raises:',
+    'Returns:') as examples.  Trailing sections after Examples are
+    re-appended to the body so they are not silently dropped.
+    """
+    # Match headings like "Examples:", "# Examples", "## Examples", etc.
+    example_pattern = re.compile(r"^(#{1,3}\s*)?Examples:?\s*$", re.MULTILINE | re.IGNORECASE)
+    match = example_pattern.search(docstring)
+    if not match:
+        return docstring.strip(), ""
+
+    body_before = docstring[: match.start()].strip()
+    after_header = docstring[match.end() :]
+
+    # Find the next top-level section that is NOT indented (Raises:, Returns:, etc.)
+    # so we do not swallow it into the examples block.
+    next_section = re.search(r"\n(?=[A-Z][^\n]*:$)", after_header, re.MULTILINE)
+    if next_section:
+        examples_raw = after_header[: next_section.start()].strip()
+        trailing = after_header[next_section.start() :].strip()
+        # Re-attach the trailing section to the body.
+        body = (body_before + "\n\n" + trailing).strip() if trailing else body_before
+    else:
+        examples_raw = after_header.strip()
+        body = body_before
+
+    return body, examples_raw
+
+
+def _parse_args_block(args_text: str) -> dict[str, str]:
+    """Parse a docstring ``Args:`` block into a ``{param_name: description}`` dict.
+
+    Handles the standard Google-style format with optional leading indentation::
+
+        param_name: First line of description.
+            Continuation lines are more deeply indented.
+
+    Works with both un-indented and uniformly-indented blocks (e.g. when the
+    raw docstring is already cleandoc'd but the Args entries still have a
+    consistent leading indent from the original source indentation).
+
+    Returns a dict mapping each parameter name to its single-line summary
+    (first line only, stripped) for use in the parameters table.
+    """
+    result: dict[str, str] = {}
+
+    # Determine the base indent level: the minimum indent of non-empty lines.
+    # Parameter entries sit at this level; continuation lines are deeper.
+    non_empty = [ln for ln in args_text.splitlines() if ln.strip()]
+    if not non_empty:
+        return result
+    base_indent = min(len(ln) - len(ln.lstrip()) for ln in non_empty)
+
+    current_name: str | None = None
+    current_lines: list[str] = []
+
+    for line in args_text.splitlines():
+        if not line.strip():
+            continue
+        indent = len(line) - len(line.lstrip())
+        stripped = line.strip()
+        # A new parameter entry sits at the base indent level with "name: ..."
+        if indent == base_indent:
+            top_level = re.match(r"(\w+)\s*:(.*)", stripped)
+            if top_level:
+                if current_name is not None:
+                    result[current_name] = " ".join(current_lines).strip()
+                current_name = top_level.group(1)
+                rest = top_level.group(2).strip()
+                current_lines = [rest] if rest else []
+                continue
+        # Continuation line — only capture the first continuation line to
+        # keep descriptions terse enough for a table cell.
+        if current_name is not None and not current_lines:
+            current_lines.append(stripped)
+
+    if current_name is not None:
+        result[current_name] = " ".join(current_lines).strip()
+
+    return result
+
+
+def _format_args_section(docstring: str) -> tuple[str, dict[str, str]]:
+    """Remove the 'Args:' block from a docstring and return (cleaned_body, arg_descriptions).
+
+    ``arg_descriptions`` maps each parameter name to its one-line description
+    so callers can populate the Description column of the params table.
+    """
+    pattern = re.compile(r"^Args:\s*$", re.MULTILINE)
+    match = pattern.search(docstring)
+    if not match:
+        return docstring.strip(), {}
+
+    before = docstring[: match.start()].strip()
+    after_start = match.end()
+
+    # The Args block ends at the next top-level section (line that starts
+    # without indentation and ends with ':'), or at end-of-string.
+    next_section = re.search(r"\n(?=[A-Z][^\n:]*:$)", docstring[after_start:], re.MULTILINE)
+    if next_section:
+        # Use lstrip("\n") not strip() so that leading spaces (indent) on the
+        # first arg line are preserved for _parse_args_block's indent detection.
+        args_text = docstring[after_start : after_start + next_section.start()].lstrip("\n")
+        remainder = docstring[after_start + next_section.start() :].strip()
+        body = (before + "\n\n" + remainder).strip()
+    else:
+        args_text = docstring[after_start:].lstrip("\n")
+        body = before.strip()
+
+    return body, _parse_args_block(args_text)
+
+
+def render_tool_section(tool: ToolInfo, anchor_suffix: str = "") -> str:
+    """Return a markdown section for a single tool.
+
+    ``anchor_suffix`` is appended to the HTML id anchor injected before the
+    heading when the tool name would collide with a group-section anchor
+    (e.g. the ``search`` tool inside the ``## Search`` group).
+    """
+    lines: list[str] = []
+    if anchor_suffix:
+        # Inject an explicit anchor so the TOC link resolves to the tool
+        # section rather than the same-named group header.
+        lines.append(f'<a id="{tool.name.replace("_", "-")}{anchor_suffix}"></a>')
+        lines.append("")
+    lines.append(f"### `{tool.name}`")
+    lines.append("")
+
+    # One-liner description from the decorator (most concise)
+    lines.append(tool.decorator_description)
+    lines.append("")
+
+    # Full docstring body (strip Args: and Examples: sub-sections which get
+    # their own formatting below)
+    doc = tool.docstring
+    doc, arg_descriptions = _format_args_section(doc)
+    doc, examples_text = _extract_examples_section(doc)
+
+    # Avoid duplicating the decorator description: if the docstring's first
+    # non-blank line is essentially the same sentence, drop it.
+    if doc:
+        doc_lines = doc.splitlines()
+        first_nonempty_idx = next(
+            (i for i, ln in enumerate(doc_lines) if ln.strip()),
+            None,
+        )
+        if first_nonempty_idx is not None:
+            first_line = doc_lines[first_nonempty_idx].strip()
+            # Normalise both sides for comparison (lowercase, strip punctuation)
+            norm = lambda s: re.sub(r"[^a-z0-9]", "", s.lower())  # noqa: E731
+            if norm(first_line) == norm(tool.decorator_description):
+                doc_lines.pop(first_nonempty_idx)
+                doc = "\n".join(doc_lines).strip()
+
+    # Demote any `###` sub-headers in the body to `####` so they do not
+    # collide with tool-name headers in GitHub's outline sidebar.
+    doc = re.sub(r"^### ", "#### ", doc, flags=re.MULTILINE)
+
+    if doc:
+        lines.append(doc)
+        lines.append("")
+
+    # Parameters table
+    if tool.params:
+        lines.append("**Parameters**")
+        lines.append("")
+        lines.append(_params_table(tool.params, arg_descriptions))
+        lines.append("")
+
+    # Examples block
+    if examples_text:
+        lines.append("**Examples**")
+        lines.append("")
+        # Wrap in a python code fence if not already fenced
+        if "```" not in examples_text:
+            lines.append("```python")
+            lines.append(examples_text)
+            lines.append("```")
+        else:
+            lines.append(examples_text)
+        lines.append("")
+
+    lines.append(f"*Source: `src/basic_memory/mcp/tools/{tool.source_file}`*")
+    lines.append("")
+
+    return "\n".join(lines)
+
+
+# ---------------------------------------------------------------------------
+# Grouping
+# ---------------------------------------------------------------------------
+
+# Stable, hand-curated grouping of tools into logical categories.
+# Tools not listed here fall into "Other Tools".
+TOOL_GROUPS: dict[str, list[str]] = {
+    "Note Management": [
+        "write_note",
+        "read_note",
+        "view_note",
+        "edit_note",
+        "move_note",
+        "delete_note",
+    ],
+    "Reading & Navigation": [
+        "read_content",
+        "build_context",
+        "recent_activity",
+        "list_directory",
+    ],
+    "Search": [
+        "search_notes",
+        "search",
+        "fetch",
+    ],
+    "Project & Workspace Management": [
+        "list_memory_projects",
+        "create_memory_project",
+        "delete_project",
+        "list_workspaces",
+    ],
+    "Schema Tools": [
+        "schema_validate",
+        "schema_infer",
+        "schema_diff",
+    ],
+    "Visualization": [
+        "canvas",
+    ],
+    "Info & Utilities": [
+        "cloud_info",
+        "release_notes",
+    ],
+}
+
+
+def group_tools(tools: list[ToolInfo]) -> dict[str, list[ToolInfo]]:
+    """Return an ordered dict mapping group name → list of ToolInfo."""
+    by_name: dict[str, ToolInfo] = {t.name: t for t in tools}
+    result: dict[str, list[ToolInfo]] = {}
+
+    placed: set[str] = set()
+    for group, names in TOOL_GROUPS.items():
+        members = [by_name[n] for n in names if n in by_name]
+        if members:
+            result[group] = members
+            placed.update(n for n in names if n in by_name)
+
+    # Anything not in TOOL_GROUPS goes to "Other Tools", sorted alphabetically
+    other = sorted([t for t in tools if t.name not in placed], key=lambda t: t.name)
+    if other:
+        result["Other Tools"] = other
+
+    return result
+
+
+# ---------------------------------------------------------------------------
+# Top-level document builder
+# ---------------------------------------------------------------------------
+
+HEADER = """\
+<!--
+  This file is AUTO-GENERATED. Do not edit it by hand.
+
+  To regenerate:
+      uv run scripts/generate_tool_docs.py
+
+  Source: scripts/generate_tool_docs.py
+-->
+
+# Basic Memory MCP Tool Reference
+
+Complete reference for all MCP tools exposed by the Basic Memory server.
+Tools are grouped by function. Parameters marked *(required)* have no default value.
+
+> **Regenerating this file**: run `uv run scripts/generate_tool_docs.py` from the
+> repository root. The output is deterministic; running it twice should produce
+> an identical file (zero diff).
+
+## Table of Contents
+
+"""
+
+
+def _tool_anchor(tool_name: str, group_anchors: set[str]) -> str:
+    """Return a stable GitHub anchor for a tool heading.
+
+    If the plain ``tool_name`` (with ``_`` → ``-``) would collide with a
+    group-section anchor (e.g. the ``search`` tool inside the ``## Search``
+    group), append ``-tool`` to disambiguate.
+    """
+    base = tool_name.replace("_", "-")
+    if base in group_anchors:
+        return base + "-tool"
+    return base
+
+
+def build_toc(groups: dict[str, list[ToolInfo]]) -> str:
+    lines: list[str] = []
+
+    # Collect all group anchors first so tool anchors can avoid collisions.
+    group_anchors: set[str] = set()
+    for group in groups:
+        anchor = re.sub(r"[^\w\s-]", "", group.lower())
+        anchor = re.sub(r"\s+", "-", anchor.strip())
+        group_anchors.add(anchor)
+
+    for group, members in groups.items():
+        # GitHub-style anchor: lowercase, spaces → hyphens, drop punctuation
+        anchor = re.sub(r"[^\w\s-]", "", group.lower())
+        anchor = re.sub(r"\s+", "-", anchor.strip())
+        lines.append(f"- [{group}](#{anchor})")
+        for tool in members:
+            t_anchor = _tool_anchor(tool.name, group_anchors)
+            lines.append(f"  - [`{tool.name}`](#{t_anchor})")
+    return "\n".join(lines)
+
+
+def build_document(groups: dict[str, list[ToolInfo]]) -> str:
+    # Pre-compute group anchors so tool-section rendering can inject explicit
+    # HTML id attributes where tool names would collide with group headers.
+    group_anchors: set[str] = set()
+    for group in groups:
+        anchor = re.sub(r"[^\w\s-]", "", group.lower())
+        anchor = re.sub(r"\s+", "-", anchor.strip())
+        group_anchors.add(anchor)
+
+    parts: list[str] = [HEADER]
+    parts.append(build_toc(groups))
+    parts.append("\n\n---\n")
+
+    for group, members in groups.items():
+        parts.append(f"\n## {group}\n")
+        for tool in members:
+            base = tool.name.replace("_", "-")
+            suffix = "-tool" if base in group_anchors else ""
+            parts.append(render_tool_section(tool, anchor_suffix=suffix))
+            parts.append("---\n")
+
+    # Trailing newline
+    return "\n".join(parts) + "\n"
+
+
+# ---------------------------------------------------------------------------
+# Main
+# ---------------------------------------------------------------------------
+
+
+def main() -> int:
+    all_tools: list[ToolInfo] = []
+    for filename in TOOL_FILES:
+        path = TOOLS_DIR / filename
+        if not path.exists():
+            print(f"WARNING: {path} does not exist — skipping", file=sys.stderr)
+            continue
+        file_tools = extract_tools_from_file(path)
+        all_tools.extend(file_tools)
+
+    if not all_tools:
+        print("ERROR: no tools found — check TOOLS_DIR path", file=sys.stderr)
+        return 1
+
+    # Stable sort: group order is defined by TOOL_GROUPS; within groups, order
+    # is defined by TOOL_GROUPS list. Global sort here is just for determinism
+    # of "Other Tools".
+    groups = group_tools(all_tools)
+    document = build_document(groups)
+
+    OUT_FILE.parent.mkdir(parents=True, exist_ok=True)
+    OUT_FILE.write_text(document, encoding="utf-8")
+
+    total = sum(len(m) for m in groups.values())
+    print(
+        f"Generated {OUT_FILE.relative_to(ROOT)} ({total} tools, {len(OUT_FILE.read_text().splitlines())} lines)"
+    )
+    return 0
+
+
+if __name__ == "__main__":
+    sys.exit(main())

server.json

@@ -6,12 +6,12 @@
     "url": "https://github.com/basicmachines-co/basic-memory.git",
     "source": "github"
   },
-  "version": "0.22.1",
+  "version": "0.22.0",
   "packages": [
     {
       "registryType": "pypi",
       "identifier": "basic-memory",
-      "version": "0.22.1",
+      "version": "0.22.0",
       "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__ = "0.22.1"
+__version__ = "0.22.0"
 
 # API version for FastAPI - independent of package version
 __api_version__ = "v0"

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

@@ -193,7 +193,7 @@ async def add_project(
         return ProjectStatusResponse(  # pyright: ignore [reportCallIssue]
             message=f"Project '{new_project.name}' added successfully",
             status="success",
-            default=new_project.is_default or False,
+            default=project_data.set_default,
             new_project=ProjectItem(
                 id=new_project.id,
                 external_id=new_project.external_id,
@@ -320,20 +320,7 @@ async def resolve_project_identifier(
     )
 
     if not project:
-        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(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)
+        raise HTTPException(status_code=404, detail=f"Project not found: '{data.identifier}'")
 
     return ProjectResolveResponse(
         external_id=project.external_id,
@@ -572,10 +559,12 @@ 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. 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.
+        # 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 new default project by external_id
         new_default_project = await project_repository.get_by_external_id(project_id)
@@ -587,27 +576,17 @@ 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)
 
-        # 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(
+        return ProjectStatusResponse(
+            message=f"Project '{new_default_project.name}' set as default successfully",
+            status="success",
+            default=True,
+            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/utils.py

@@ -147,7 +147,6 @@ 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

@@ -83,11 +83,8 @@ 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

@@ -168,20 +168,6 @@ 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()
@@ -302,7 +288,6 @@ 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

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

src/basic_memory/cli/commands/ci.py

@@ -34,10 +34,8 @@ 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
-
-# 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).
+from basic_memory.mcp.tools import search_notes as mcp_search_notes
+from basic_memory.mcp.tools import write_note as mcp_write_note
 
 
 console = Console()
@@ -254,10 +252,6 @@ 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():
@@ -301,10 +295,6 @@ 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

@@ -3,10 +3,12 @@
 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
@@ -29,9 +31,6 @@ 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:
@@ -54,8 +53,6 @@ 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
@@ -89,9 +86,6 @@ 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

@@ -1,27 +1,24 @@
 """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
-
-if TYPE_CHECKING:
-    from basic_memory.indexing import IndexProgress
+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
 
 console = Console()
 
@@ -162,13 +159,6 @@ 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)
 
@@ -207,12 +197,6 @@ 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"
@@ -336,15 +320,10 @@ async def _reindex(
     project: str | None,
 ):
     """Run reindex operations."""
-    # 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 import EntityRepository
     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
 

src/basic_memory/cli/commands/doctor.py

@@ -7,12 +7,16 @@ 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
@@ -25,12 +29,6 @@ console = Console()
 
 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]}"
@@ -142,9 +140,6 @@ 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

@@ -1,34 +1,25 @@
 """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 TYPE_CHECKING, Annotated, Tuple
+from typing import 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)
@@ -69,9 +60,6 @@ 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

@@ -1,34 +1,25 @@
 """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 TYPE_CHECKING, Annotated, Tuple
+from typing import 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)
@@ -66,9 +57,6 @@ 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

@@ -1,34 +1,25 @@
 """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 TYPE_CHECKING, Annotated, Tuple
+from typing import 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)
@@ -65,9 +56,6 @@ 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

@@ -1,34 +1,25 @@
 """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 TYPE_CHECKING, Annotated, Tuple
+from typing import 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)
@@ -64,9 +55,6 @@ 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

@@ -1,76 +0,0 @@
-"""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

@@ -5,6 +5,7 @@ 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
 
@@ -49,9 +50,6 @@ 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/schema.py

@@ -20,10 +20,9 @@ from basic_memory.cli.app import app
 from basic_memory.cli.commands.command_utils import run_with_cleanup
 from basic_memory.cli.commands.routing import force_routing, validate_routing_flags
 from basic_memory.config import ConfigManager
-
-# 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).
+from basic_memory.mcp.tools import schema_diff as mcp_schema_diff
+from basic_memory.mcp.tools import schema_infer as mcp_schema_infer
+from basic_memory.mcp.tools import schema_validate as mcp_schema_validate
 
 console = Console()
 
@@ -190,9 +189,6 @@ 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)
@@ -276,9 +272,6 @@ 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)
@@ -359,9 +352,6 @@ 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

@@ -5,6 +5,7 @@ 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
@@ -189,16 +190,9 @@ 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"If no Basic Memory server is running, pending changes are never "
-                    f"indexed — run 'bm reindex --project {project_item.name}' instead."
+                    f"to finish indexing ({sync_report.total} pending change(s) remaining)."
                 )
             await asyncio.sleep(poll_interval)
 
@@ -230,9 +224,6 @@ 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

@@ -14,10 +14,18 @@ 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
-
-# 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).
+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
 
 tool_app = typer.Typer()
 app.add_typer(tool_app, name="tool", help="Access to MCP tools via CLI")
@@ -112,9 +120,6 @@ 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)
 
@@ -201,9 +206,6 @@ 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)
 
@@ -270,9 +272,6 @@ 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)
 
@@ -347,9 +346,6 @@ 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)
 
@@ -417,9 +413,6 @@ 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)
 
@@ -483,9 +476,6 @@ 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)
 
@@ -592,9 +582,6 @@ 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)
 
@@ -700,9 +687,6 @@ 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)
 
@@ -736,9 +720,6 @@ 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)
 
@@ -791,9 +772,6 @@ 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)
 
@@ -862,9 +840,6 @@ 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)
 
@@ -921,9 +896,6 @@ 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

@@ -24,7 +24,6 @@ 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

@@ -4,7 +4,6 @@ import importlib.util
 import json
 import os
 import shutil
-import threading
 from dataclasses import dataclass
 from datetime import datetime
 from enum import Enum
@@ -658,26 +657,6 @@ 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.
 
@@ -1120,21 +1099,8 @@ 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")
-        # 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)
+        file_path.write_text(json.dumps(config_dict, indent=2))
+        _secure_config_file(file_path)
     except Exception as e:  # pragma: no cover
         logger.error(f"Failed to save config: {e}")
 

src/basic_memory/db.py

@@ -19,7 +19,7 @@ from sqlalchemy.ext.asyncio import (
     AsyncEngine,
     async_scoped_session,
 )
-from sqlalchemy.pool import AsyncAdaptedQueuePool, NullPool
+from sqlalchemy.pool import NullPool
 
 from basic_memory.repository.postgres_search_repository import PostgresSearchRepository
 from basic_memory.repository.sqlite_search_repository import SQLiteSearchRepository
@@ -216,31 +216,19 @@ def _create_sqlite_engine(db_url: str, db_type: DatabaseType) -> AsyncEngine:
                 "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
-        engine = create_async_engine(
-            db_url,
-            connect_args=connect_args,
-            poolclass=NullPool,  # Disable connection pooling on Windows
-            echo=False,
-        )
+        # 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)
     else:
         engine = create_async_engine(db_url, connect_args=connect_args)
 

src/basic_memory/file_utils.py

@@ -302,76 +302,26 @@ 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 line-anchored frontmatter fences, False otherwise
+        True if content has valid frontmatter markers (---), False otherwise
     """
     if not content:
         return False
 
     # Strip BOM before checking for frontmatter markers
-    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.
+    content = strip_bom(content).strip()
+    if not content.startswith("---"):
         return False
 
+    return "---" in content[3:]
+
 
 def parse_frontmatter(content: str) -> Dict[str, Any]:
     """
@@ -389,14 +339,17 @@ def parse_frontmatter(content: str) -> Dict[str, Any]:
     try:
         # Strip BOM before parsing frontmatter
         content = strip_bom(content)
-        split = _split_frontmatter(content)
-        if split is None:
+        if not content.strip().startswith("---"):
             raise ParseError("Content has no frontmatter")
-        yaml_block, _ = split
+
+        # Split on first two occurrences of ---
+        parts = content.split("---", 2)
+        if len(parts) < 3:
+            raise ParseError("Invalid frontmatter format")
 
         # Parse YAML
         try:
-            frontmatter = yaml.safe_load(yaml_block)
+            frontmatter = yaml.safe_load(parts[1])
             # Handle empty frontmatter (None from yaml.safe_load)
             if frontmatter is None:
                 return {}
@@ -428,17 +381,18 @@ def remove_frontmatter(content: str) -> str:
         ParseError: If content starts with frontmatter marker but is malformed
     """
     # Strip BOM before processing
-    content = strip_bom(content)
+    content = strip_bom(content).strip()
 
-    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()
+    # Return as-is if no frontmatter marker
+    if not content.startswith("---"):
+        return content
 
-    _, body = split
-    return body.strip()
+    # Split on first two occurrences of ---
+    parts = content.split("---", 2)
+    if len(parts) < 3:
+        raise ParseError("Invalid frontmatter format")
+
+    return parts[2].strip()
 
 
 def dump_frontmatter(post: frontmatter.Post) -> str:

src/basic_memory/man/basic-memory.1

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

src/basic_memory/man/bm.1

@@ -1,134 +0,0 @@
-.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

@@ -5,16 +5,14 @@ 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, has_cloud_credentials
+from basic_memory.config import ConfigManager, ProjectMode
 
 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]"]
@@ -30,8 +28,8 @@ 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:
@@ -59,7 +57,7 @@ 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
 
@@ -73,7 +71,7 @@ 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)
@@ -84,10 +82,8 @@ 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
@@ -131,7 +127,7 @@ async def _resolve_local_asgi_database(app: "FastAPI") -> AsyncIterator[LocalDat
         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)
@@ -143,7 +139,7 @@ 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:
@@ -167,7 +163,7 @@ 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):
@@ -177,7 +173,7 @@ def _restore_local_asgi_state_attribute(app: "FastAPI", name: str, previous_valu
 
 
 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:
@@ -200,7 +196,7 @@ 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:
@@ -372,8 +368,7 @@ async def get_client(
     1. Factory injection.
     2. Explicit routing flags (--local/--cloud).
     3. Per-project mode routing when project_name is provided.
-    4. Cloud routing when a workspace selector is provided.
-    5. Local ASGI transport by default.
+    4. Local ASGI transport by default.
     """
     if _client_factory:
         async with _client_factory(workspace=workspace) as client:
@@ -433,26 +428,6 @@ 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

@@ -7,9 +7,7 @@ from typing import Optional, Any
 
 from httpx import AsyncClient
 
-# 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.mcp.tools.utils import call_get
 
 
 class DirectoryClient:
@@ -57,8 +55,6 @@ 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

@@ -8,10 +8,7 @@ from typing import Any
 from httpx import AsyncClient
 
 import logfire
-
-# 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.mcp.tools.utils import call_get, call_post, call_put, call_patch, call_delete
 from basic_memory.schemas.response import (
     EntityResponse,
     DeleteEntitiesResponse,
@@ -60,8 +57,6 @@ 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",
@@ -94,8 +89,6 @@ 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",
@@ -123,8 +116,6 @@ 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",
@@ -156,8 +147,6 @@ 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",
@@ -185,8 +174,6 @@ 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",
@@ -214,8 +201,6 @@ 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",
@@ -246,8 +231,6 @@ 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",
@@ -278,8 +261,6 @@ 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",
@@ -309,8 +290,6 @@ 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",
@@ -330,8 +309,6 @@ 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",
@@ -361,8 +338,6 @@ 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

@@ -8,10 +8,7 @@ from typing import Optional
 from httpx import AsyncClient
 
 import logfire
-
-# 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.mcp.tools.utils import call_get
 from basic_memory.schemas.memory import GraphContext
 
 
@@ -66,8 +63,6 @@ class MemoryClient:
         Raises:
             ToolError: If the request fails
         """
-        from basic_memory.mcp.tools.utils import call_get
-
         params: dict = {
             "depth": depth,
             "page": page,
@@ -118,8 +113,6 @@ 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

@@ -7,9 +7,13 @@ from typing import Any
 
 from httpx import AsyncClient
 
-# 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.mcp.tools.utils import (
+    call_delete,
+    call_get,
+    call_patch,
+    call_post,
+    call_put,
+)
 from basic_memory.schemas import ProjectInfoResponse, SyncReportResponse
 from basic_memory.schemas.project_info import ProjectList, ProjectStatusResponse
 from basic_memory.schemas.v2 import ProjectResolveResponse
@@ -49,8 +53,6 @@ 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/",
@@ -69,8 +71,6 @@ 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/",
@@ -93,8 +93,6 @@ 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"
@@ -116,8 +114,6 @@ 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",
@@ -137,8 +133,6 @@ 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",
@@ -160,8 +154,6 @@ 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}",
@@ -189,8 +181,6 @@ 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:
@@ -214,8 +204,6 @@ 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",
@@ -234,8 +222,6 @@ 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

@@ -6,9 +6,7 @@ Encapsulates all /v2/projects/{project_id}/resource/* endpoints.
 from httpx import AsyncClient, Response
 
 import logfire
-# 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.mcp.tools.utils import call_get
 
 
 class ResourceClient:
@@ -51,8 +49,6 @@ 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

@@ -5,9 +5,7 @@ Encapsulates all /v2/projects/{project_id}/schema/* endpoints.
 
 from httpx import AsyncClient
 
-# 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.mcp.tools.utils import call_post, call_get
 from basic_memory.schemas.schema import (
     ValidationReport,
     InferenceReport,
@@ -58,8 +56,6 @@ 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
@@ -91,8 +87,6 @@ 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",
@@ -112,8 +106,6 @@ 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

@@ -8,10 +8,7 @@ from typing import Any
 from httpx import AsyncClient
 
 import logfire
-
-# 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.mcp.tools.utils import call_post
 from basic_memory.schemas.search import SearchResponse
 
 
@@ -60,8 +57,6 @@ 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

@@ -8,24 +8,10 @@ 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
@@ -33,6 +19,8 @@ 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
@@ -58,9 +46,6 @@ 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,
@@ -69,14 +54,6 @@ _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."""
@@ -483,17 +460,6 @@ 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,
@@ -511,24 +477,6 @@ 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
@@ -774,15 +722,9 @@ 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.
-
-    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:
+    """Build or load the session-local workspace/project lookup index."""
+    if context:
         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:
@@ -856,99 +798,13 @@ 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.
@@ -960,14 +816,23 @@ async def _resolve_workspace_project_from_index(
     except ValueError:
         pass
 
-    workspace_identifier, project_identifier = _split_qualified_project_identifier(project)
+    workspace_slug, project_identifier = _split_qualified_project_identifier(project)
     project_permalink = generate_permalink(project_identifier)
 
-    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)
+    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]
         matches = [
             entry
             for entry in index.entries_by_permalink.get(project_permalink, ())
@@ -978,7 +843,7 @@ async def _resolve_workspace_project_from_index(
                 failed_workspace.tenant_id == workspace.tenant_id
                 for failed_workspace in index.failed_workspaces
             ):
-                raise WorkspaceProjectLookupMiss(
+                raise ValueError(
                     f"Projects for workspace '{workspace.name}' ({workspace.slug}) "
                     "could not be loaded. Retry after workspace discovery recovers."
                 )
@@ -987,7 +852,7 @@ async def _resolve_workspace_project_from_index(
                 for entry in index.entries
                 if entry.workspace.tenant_id == workspace.tenant_id
             )
-            raise WorkspaceProjectLookupMiss(
+            raise ValueError(
                 f"Project '{project_identifier}' was not found in workspace "
                 f"'{workspace.name}' ({workspace.slug}). Available projects: {available}"
             )
@@ -1012,7 +877,7 @@ async def _resolve_workspace_project_from_index(
                 "retry or use a qualified project from an indexed workspace."
             )
         available = ", ".join(entry.qualified_name for entry in index.entries)
-        raise WorkspaceProjectLookupMiss(
+        raise ValueError(
             f"Project '{project}' was not found in indexed cloud workspaces. "
             f"Available projects: {available}.{failed_note}"
         )
@@ -1347,9 +1212,6 @@ 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(
@@ -1576,9 +1438,6 @@ 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

@@ -1,17 +0,0 @@
-"""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

@@ -54,10 +54,7 @@ def _format_entity_block(result: ContextResult) -> str:
         lines.append("")
         lines.append("### Relations")
         for rel in relation_items:
-            # 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}]]")
+            lines.append(f"- {rel.relation_type} [[{rel.to_entity}]]")
 
     # --- Related entities (non-relation related results) ---
     related_entities: list[EntitySummary | ObservationSummary] = [
@@ -115,7 +112,6 @@ 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.
@@ -135,7 +131,6 @@ 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

@@ -17,9 +17,7 @@ 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

@@ -105,9 +105,7 @@ 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(
@@ -169,9 +167,7 @@ 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 basic_memory.mcp.resources.discovery import load_discovery_resource
+from pathlib import Path
+
 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."""
-    return load_discovery_resource("cloud_info.md")
+    content_path = Path(__file__).parent.parent / "resources" / "cloud_info.md"
+    return content_path.read_text(encoding="utf-8")

src/basic_memory/mcp/tools/delete_note.py

@@ -182,9 +182,7 @@ 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

@@ -304,9 +304,7 @@ 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

@@ -11,9 +11,7 @@ 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

@@ -357,9 +357,7 @@ 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

@@ -357,8 +357,6 @@ 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(
@@ -477,14 +475,10 @@ async def _resolve_workspace_routing(
     if workspace is None:
         return None
 
-    forced_local = _explicit_routing() and _force_local_mode()
+    explicit_cloud_routing = _explicit_routing() and not _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 (
-        has_cloud_credentials(config) and not forced_local
+        explicit_cloud_routing and has_cloud_credentials(config)
     )
     if not should_resolve_workspace:
         return workspace
@@ -501,8 +495,6 @@ 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(
@@ -525,9 +517,8 @@ async def create_memory_project(
         workspace: Optional cloud workspace selector to create the project in. Slug is
             preferred for AI callers, but tenant_id and unique name are also accepted.
             When omitted, the connection's default workspace is used. Discover values
-            via `list_workspaces`. A workspace selector implies cloud routing:
-            without cloud credentials the call fails fast instead of silently
-            creating a local project (#954).
+            via `list_workspaces`. In local mode the selector is passed through
+            without slug resolution.
         output_format: "text" returns the existing human-readable result text.
             "json" returns structured project creation metadata.
         context: Optional FastMCP context for progress/status logging.
@@ -645,8 +636,6 @@ async def create_memory_project(
 
 
 @mcp.tool(
-    title="Delete Project",
-    tags={"projects"},
     annotations={"destructiveHint": True, "openWorldHint": False},
 )
 async def delete_project(
@@ -665,9 +654,8 @@ 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. A workspace selector implies cloud routing: without cloud
-            credentials the call fails fast, matching create_memory_project
-            behavior (#954).
+            used. In local mode the selector is passed through without slug
+            resolution, matching create_memory_project behavior.
 
     Returns:
         Confirmation message about project deletion

src/basic_memory/mcp/tools/read_content.py

@@ -155,9 +155,7 @@ 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

@@ -74,9 +74,7 @@ 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

@@ -26,7 +26,6 @@ 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:
@@ -37,7 +36,6 @@ 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 basic_memory.mcp.resources.discovery import load_discovery_resource
+from pathlib import Path
+
 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."""
-    return load_discovery_resource("release_notes.md")
+    content_path = Path(__file__).parent.parent / "resources" / "release_notes.md"
+    return content_path.read_text(encoding="utf-8")

src/basic_memory/mcp/tools/schema.py

@@ -204,9 +204,7 @@ 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(
@@ -319,9 +317,7 @@ 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(
@@ -442,9 +438,7 @@ 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,
-    parse_str_list,
+    coerce_list,
     parse_tags,
     strict_search_tags,
 )
@@ -612,9 +612,7 @@ 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},
@@ -651,30 +649,24 @@ async def search_notes(
     # Plural-vs-singular trips models constantly. Accept the singular too.
     note_types: Annotated[
         List[str] | None,
-        # 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),
+        BeforeValidator(coerce_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(parse_str_list),
+        BeforeValidator(coerce_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. "
-        "Accepts a list, a comma-separated string (e.g. 'entity,observation'), or a JSON-array string.",
+        "'Chapter' here — use note_types instead.",
     ] = None,
     categories: Annotated[
         List[str] | None,
-        BeforeValidator(parse_str_list),
+        BeforeValidator(coerce_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,
@@ -828,11 +820,6 @@ 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")
@@ -906,17 +893,6 @@ 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

@@ -18,9 +18,7 @@ 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},
 )
@@ -94,9 +92,7 @@ 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

@@ -11,9 +11,7 @@ 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

@@ -45,9 +45,7 @@ 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

@@ -25,39 +25,8 @@ 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(
@@ -69,7 +38,6 @@ 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",
@@ -125,8 +93,6 @@ 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().
@@ -204,11 +170,6 @@ 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/search_index_row.py

@@ -36,7 +36,6 @@ 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)
@@ -95,7 +94,6 @@ 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_base.py

@@ -40,11 +40,6 @@ BULLET_PATTERN = re.compile(r"^[\-\*]\s+")
 OVERSIZED_ENTITY_VECTOR_SHARD_SIZE = 256
 _SQLITE_MAX_PREPARE_WINDOW = 8
 
-# 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:
@@ -1862,7 +1857,7 @@ class SearchRepositoryBase(ABC):
     # ------------------------------------------------------------------
 
     @staticmethod
-    def _parse_chunk_key(chunk_key: str) -> SearchIndexKey:
+    def _parse_chunk_key(chunk_key: str) -> tuple[str, int]:
         """Parse a chunk_key like 'observation:5:0' into (type, search_index_id)."""
         parts = chunk_key.split(":")
         return parts[0], int(parts[1])
@@ -1937,27 +1932,26 @@ 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; keep both as the
-        # key because different row types can share the same numeric id (#982).
+        # Each chunk_key encodes the search_index row type and id.
         # Track the best similarity per row (for ranking) and all chunks (for context).
-        similarity_by_si_key: dict[SearchIndexKey, float] = {}
-        chunks_by_si_key: dict[SearchIndexKey, list[tuple[float, str]]] = {}
+        similarity_by_si_id: dict[int, float] = {}
+        chunks_by_si_id: dict[int, 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_key = self._parse_chunk_key(chunk_key)
+                _, si_id = self._parse_chunk_key(chunk_key)
             except (ValueError, IndexError):
                 # Fallback: group by entity_id for chunks without parseable keys
                 continue
-            current = similarity_by_si_key.get(si_key)
+            current = similarity_by_si_id.get(si_id)
             if current is None or similarity > current:
-                similarity_by_si_key[si_key] = similarity
-            chunks_by_si_key.setdefault(si_key, []).append((similarity, chunk_text))
+                similarity_by_si_id[si_id] = similarity
+            chunks_by_si_id.setdefault(si_id, []).append((similarity, chunk_text))
 
-        if not similarity_by_si_key:
+        if not similarity_by_si_id:
             hydrate_ms = (time.perf_counter() - hydrate_start) * 1000
             _log_vector_summary()
             return []
@@ -1968,17 +1962,16 @@ 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_key = {
-                k: v for k, v in similarity_by_si_key.items() if v >= effective_min_similarity
+            similarity_by_si_id = {
+                k: v for k, v in similarity_by_si_id.items() if v >= effective_min_similarity
             }
-            if not similarity_by_si_key:
+            if not similarity_by_si_id:
                 hydrate_ms = (time.perf_counter() - hydrate_start) * 1000
                 _log_vector_summary()
                 return []
 
-        # 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))
+        # Fetch the actual search_index rows
+        si_ids = list(similarity_by_si_id.keys())
         search_index_rows = await self._fetch_search_index_rows_by_ids(si_ids)
 
         # Apply optional filters if requested
@@ -2010,14 +2003,16 @@ class SearchRepositoryBase(ABC):
                 limit=VECTOR_FILTER_SCAN_LIMIT,
                 offset=0,
             )
-            # Use (type, id) tuples to avoid collisions between different
+            # Use (id, type) tuples to avoid collisions between different
             # search_index row types that share the same auto-increment id.
-            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}
+            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
+            }
 
         ranked_rows: list[SearchIndexRow] = []
-        for si_key, similarity in similarity_by_si_key.items():
-            row = search_index_rows.get(si_key)
+        for si_id, similarity in similarity_by_si_id.items():
+            row = search_index_rows.get(si_id)
             if row is None:
                 continue
 
@@ -2027,7 +2022,7 @@ 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_key.get(si_key, [])
+                si_chunks = chunks_by_si_id.get(si_id, [])
                 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
@@ -2093,12 +2088,8 @@ class SearchRepositoryBase(ABC):
 
     async def _fetch_search_index_rows_by_ids(
         self, row_ids: list[int]
-    ) -> 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.
-        """
+    ) -> dict[int, SearchIndexRow]:
+        """Fetch search_index rows by their primary key (id), any type."""
         if not row_ids:
             return {}
         placeholders = ",".join(f":id_{idx}" for idx in range(len(row_ids)))
@@ -2115,11 +2106,11 @@ class SearchRepositoryBase(ABC):
             WHERE project_id = :project_id
               AND id IN ({placeholders})
         """
-        result: dict[SearchIndexKey, SearchIndexRow] = {}
+        result: dict[int, 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.type, row.id)] = SearchIndexRow(
+                result[row.id] = SearchIndexRow(
                     project_id=self.project_id,
                     id=row.id,
                     title=row.title,
@@ -2165,7 +2156,7 @@ class SearchRepositoryBase(ABC):
     ) -> List[SearchIndexRow]:
         """Fuse FTS and vector results using score-based fusion.
 
-        Uses the search_index (type, id) pair as the fusion key. The formula
+        Uses search_index row id as the fusion key. The formula
         ``max(vec, fts) + FUSION_BONUS * min(vec, fts)`` preserves
         the dominant signal and rewards dual-source agreement.
         """
@@ -2208,19 +2199,17 @@ class SearchRepositoryBase(ABC):
         vector_ms = (time.perf_counter() - vector_start) * 1000
         fusion_start = time.perf_counter()
 
-        # --- 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).
+        # --- Score-based fusion keyed on search_index row id ---
         # 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_key: dict[SearchIndexKey, SearchIndexRow] = {}
+        rows_by_id: dict[int, 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[SearchIndexKey, float] = {}
+        fts_scores: dict[int, float] = {}
         for row in fts_results:
             if row.id is None:
                 continue
@@ -2228,32 +2217,32 @@ class SearchRepositoryBase(ABC):
             # Gate: FTS scores below threshold contribute zero
             if norm < FTS_GATE_THRESHOLD:
                 norm = 0.0
-            fts_scores[(row.type, row.id)] = norm
-            rows_by_key[(row.type, row.id)] = row
+            fts_scores[row.id] = norm
+            rows_by_id[row.id] = row
 
-        vec_scores: dict[SearchIndexKey, float] = {}
+        vec_scores: dict[int, 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.type, row.id)] = row.score or 0.0
-            rows_by_key[(row.type, row.id)] = row
+            vec_scores[row.id] = row.score or 0.0
+            rows_by_id[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[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)
+        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)
 
         ranked = sorted(fused_scores.items(), key=lambda item: item[1], reverse=True)
         output: list[SearchIndexRow] = []
-        for row_key, fused_score in ranked[offset : offset + limit]:
-            row = rows_by_key[row_key]
+        for row_id, fused_score in ranked[offset : offset + limit]:
+            row = rows_by_id[row_id]
             # 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/schemas/base.py

@@ -19,6 +19,7 @@ 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
 
@@ -91,10 +92,6 @@ 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

@@ -155,9 +155,6 @@ 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

@@ -18,7 +18,6 @@ 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
@@ -37,7 +36,6 @@ 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
@@ -145,29 +143,6 @@ 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}'")
@@ -417,7 +392,6 @@ 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,
@@ -452,7 +426,6 @@ 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,
@@ -505,10 +478,6 @@ 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,
@@ -572,7 +541,6 @@ class ContextService:
             from_id,
             to_id,
             relation_type,
-            to_name,
             content,
             category,
             entity_id,
@@ -582,7 +550,7 @@ class ContextService:
         FROM entity_graph
         WHERE depth > 0
         GROUP BY type, id, title, permalink, file_path, from_id, to_id,
-                 relation_type, to_name, content, category, entity_id, root_id, created_at
+                 relation_type, content, category, entity_id, root_id, created_at
         ORDER BY depth, type, id
         LIMIT :max_results
        """)
@@ -611,7 +579,6 @@ 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,
@@ -639,7 +606,6 @@ class ContextService:
                 r.from_id,
                 r.to_id,
                 r.relation_type,
-                r.to_name,
                 NULL as content,
                 NULL as category,
                 NULL as entity_id,
@@ -678,7 +644,6 @@ 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,
@@ -712,7 +677,6 @@ class ContextService:
             from_id,
             to_id,
             relation_type,
-            to_name,
             content,
             category,
             entity_id,
@@ -722,7 +686,7 @@ class ContextService:
         FROM entity_graph
         WHERE depth > 0
         GROUP BY type, id, title, permalink, file_path, from_id, to_id,
-                 relation_type, to_name, content, category, entity_id, root_id, created_at
+                 relation_type, content, category, entity_id, root_id, created_at
         ORDER BY depth, type, id
         LIMIT :max_results
        """)

src/basic_memory/services/initialization.py

@@ -13,7 +13,7 @@ from pathlib import Path
 from loguru import logger
 
 from basic_memory import db
-from basic_memory.config import BasicMemoryConfig, DatabaseBackend
+from basic_memory.config import BasicMemoryConfig, DatabaseBackend, ProjectMode
 from basic_memory.models import Project
 from basic_memory.repository import (
     ProjectRepository,
@@ -120,14 +120,18 @@ async def initialize_file_sync(
         active_projects = [p for p in active_projects if p.name == constrained_project]
         logger.info(f"Background sync constrained to project: {constrained_project}")
 
-    # Only sync projects that are in config (source of truth) and have an
-    # absolute local path; see BasicMemoryConfig.is_locally_syncable. This keeps
-    # background sync from adopting the process cwd as a project root and
-    # mutating unrelated files (issue #949).
-    skip = [p.name for p in active_projects if not app_config.is_locally_syncable(p.name, p.path)]
-    if skip:
-        active_projects = [p for p in active_projects if p.name not in skip]
-        logger.info(f"Skipping projects that are not locally syncable for sync: {skip}")
+    # Skip cloud-mode projects that have no local directory.
+    # Cloud projects with a local bisync copy (absolute path) are kept for local sync.
+    cloud_skip = []
+    for p in active_projects:
+        if app_config.get_project_mode(p.name) == ProjectMode.CLOUD:
+            entry = app_config.projects.get(p.name)
+            if entry and Path(entry.path).is_absolute():
+                continue  # Cloud project with local bisync copy — keep for local sync
+            cloud_skip.append(p.name)
+    if cloud_skip:
+        active_projects = [p for p in active_projects if p.name not in cloud_skip]
+        logger.info(f"Skipping cloud-mode projects for local sync: {cloud_skip}")
 
     # Start sync for all projects as background tasks (non-blocking)
     async def sync_project_background(project: Project):

src/basic_memory/services/project_service.py

@@ -256,41 +256,6 @@ class ProjectService:
             await self.repository.set_as_default(created_project.id)
             self.config_manager.set_default_project(name)
             logger.info(f"Project '{name}' set as default")
-        else:
-            config_default = self.config_manager.default_project
-            if config_default is not None:
-                db_default_project = await self.repository.get_by_name(config_default)
-                if db_default_project is None:
-                    # Trigger: config names a default project that has no database row
-                    #      (the fresh-config wedge from issue #974).
-                    # Why: synchronize_projects treats an existing database default as
-                    #      authoritative, so a surviving default must win over promoting
-                    #      the just-added project. set_default_project raises for names
-                    #      absent from config — and reconciliation deletes such rows —
-                    #      so a database default unknown to config cannot be repointed to.
-                    # Outcome: config is repointed at a usable database default when one
-                    #      exists; otherwise the added project becomes the default.
-                    db_default = await self.repository.get_default_project()
-                    if (
-                        db_default is not None
-                        and self.config_manager.get_project(db_default.name)[0] is not None
-                    ):
-                        self.config_manager.set_default_project(db_default.name)
-                        logger.info(
-                            "Repointed config default from missing '%s' at existing "
-                            "database default '%s'",
-                            config_default,
-                            db_default.name,
-                        )
-                    else:
-                        await self.repository.set_as_default(created_project.id)
-                        self.config_manager.set_default_project(name)
-                        logger.info(
-                            "Promoted project '%s' to default because configured default '%s' "
-                            "is missing from database",
-                            name,
-                            config_default,
-                        )
 
         logger.info(f"Project '{name}' added at {resolved_path}")
 

src/basic_memory/sync/watch_service.py

@@ -10,7 +10,7 @@ from typing import List, Optional, Set, Sequence, Callable, Awaitable, TYPE_CHEC
 if TYPE_CHECKING:
     from basic_memory.sync.sync_service import SyncService
 
-from basic_memory.config import BasicMemoryConfig, WATCH_STATUS_JSON
+from basic_memory.config import BasicMemoryConfig, ProjectMode, WATCH_STATUS_JSON
 from basic_memory.ignore_utils import load_gitignore_patterns, should_ignore_path
 from basic_memory.models import Project
 from basic_memory.repository import ProjectRepository
@@ -184,24 +184,24 @@ class WatchService:
              ``--project``, only that project is watched. This keeps concurrent
              MCP processes from producing duplicate watchers that race on the
              same files.
-          2. Projects that are not locally syncable are skipped — those missing
-             from config (config is the source of truth, so stale DB rows must
-             not be watched) or with a non-absolute path (which would resolve
-             against the process cwd and make the watcher observe and mutate the
-             directory the server was launched from). See
-             ``BasicMemoryConfig.is_locally_syncable`` (issue #949). Cloud
-             projects with a local bisync copy keep their absolute path and are
-             still watched.
+          2. Cloud-only projects without a local bisync copy are skipped so we
+             don't watch a path that does not exist on disk.
         """
         projects = await self.project_repository.get_active_projects()
 
         if self.constrained_project:
             projects = [p for p in projects if p.name == self.constrained_project]
 
-        skip = [p.name for p in projects if not self.app_config.is_locally_syncable(p.name, p.path)]
-        if skip:
-            projects = [p for p in projects if p.name not in skip]
-            logger.debug(f"Skipping projects that are not locally syncable in watch cycle: {skip}")
+        cloud_skip: list[str] = []
+        for p in projects:
+            if self.app_config.get_project_mode(p.name) == ProjectMode.CLOUD:
+                entry = self.app_config.projects.get(p.name)
+                if entry and Path(entry.path).is_absolute():
+                    continue  # Cloud project with local bisync copy — keep watching
+                cloud_skip.append(p.name)
+        if cloud_skip:
+            projects = [p for p in projects if p.name not in cloud_skip]
+            logger.debug(f"Skipping cloud-mode projects in watch cycle: {cloud_skip}")
 
         return list(projects)
 

src/basic_memory/utils.py

@@ -600,62 +600,6 @@ def strict_search_tags(v: Any) -> Any:
     return v
 
 
-def parse_str_list(v: Any) -> List[str]:
-    """Parse a list of plain strings from various input formats.
-
-    Like parse_tags but without stripping '#' — correct for type/category params
-    where the value is a literal identifier, not a hashtag.
-
-    Handles the four input shapes that MCP clients commonly produce:
-    - None → []
-    - "note,task" → ["note", "task"] (comma-split string)
-    - '["note","task"]' → ["note", "task"] (JSON array string)
-    - ["note,task"] → ["note", "task"] (list with comma-string element)
-
-    Non-str/list/None values are returned unchanged so Pydantic can reject them
-    with a clear validation error instead of silently coercing.
-    """
-    if v is None:
-        return []
-
-    if isinstance(v, list):
-        # Trigger: a list element is not a string (e.g. [42] or ["note", 42]).
-        # Why: str(raw) would silently convert 42 → "42" and let invalid caller data pass
-        #   Pydantic validation as a junk filter, producing a silent no-result search.
-        # Outcome: return the list unchanged so Pydantic rejects it with a clear error.
-        if not all(isinstance(raw, str) for raw in v if raw is not None):
-            return v  # type: ignore[return-value]
-
-        # Trigger: a list element may itself be a comma-separated string (e.g. some MCP clients
-        #   serialise `["note,task"]` when the caller passed `note_types="note,task"`).
-        # Outcome: flatten each element by splitting on commas and stripping whitespace.
-        return [
-            item.strip()
-            for raw in v
-            if raw is not None
-            for item in raw.split(",")
-            if item and item.strip()
-        ]
-
-    if isinstance(v, str):
-        # Trigger: MCP clients sometimes send a JSON array string like '["note","task"]'.
-        # Outcome: parse it as JSON first, then recurse to handle the resulting list.
-        stripped = v.strip()
-        if stripped.startswith("[") and stripped.endswith("]"):
-            try:
-                parsed_json = json.loads(stripped)
-                if isinstance(parsed_json, list):
-                    return parse_str_list(parsed_json)
-            except json.JSONDecodeError:
-                pass
-
-        # Plain comma-separated string: "note,task" → ["note", "task"]
-        return [item.strip() for item in v.split(",") if item and item.strip()]
-
-    # Non-str/list/None — return unchanged so Pydantic rejects with a clear error.
-    return v  # type: ignore[return-value]
-
-
 def coerce_list(v: Any) -> Any:
     """Coerce string input to list for MCP clients that serialize lists as strings."""
     if v is None:

test-int/cli/test_routing_integration.py

@@ -89,27 +89,6 @@ class TestRoutingFlagsValidation:
         assert "Cannot specify both --local and --cloud" in result.output
 
 
-def _stub_auto_update(monkeypatch, mcp_mod) -> None:
-    """Keep `bm mcp` stdio tests from running the real background auto-update.
-
-    The command starts a daemon thread before mcp_server.run; unstubbed it hits
-    PyPI and rewrites config.json from a background thread, leaking into later
-    tests in the same process (#940's KeyError flake on test_mcp_sse_forces_local).
-    """
-    from basic_memory.cli.auto_update import AutoUpdateResult, AutoUpdateStatus, InstallSource
-
-    def skipped_auto_update(**kwargs) -> AutoUpdateResult:
-        return AutoUpdateResult(
-            status=AutoUpdateStatus.SKIPPED,
-            source=InstallSource.UNKNOWN,
-            checked=False,
-            update_available=False,
-            updated=False,
-        )
-
-    monkeypatch.setattr(mcp_mod, "run_auto_update", skipped_auto_update)
-
-
 class TestMcpCommandRouting:
     """Tests that MCP routing varies by transport."""
 
@@ -130,10 +109,8 @@ class TestMcpCommandRouting:
 
         monkeypatch.setattr(mcp_mod.mcp_server, "run", mock_run)
         monkeypatch.setattr(mcp_mod, "init_mcp_logging", lambda: None)
-        _stub_auto_update(monkeypatch, mcp_mod)
 
-        result = runner.invoke(cli_app, ["mcp"])  # default transport is stdio
-        assert result.exit_code == 0, result.output
+        runner.invoke(cli_app, ["mcp"])  # default transport is stdio
 
         # Command should not have set these vars
         assert env_at_run["FORCE_LOCAL"] is None
@@ -155,10 +132,8 @@ class TestMcpCommandRouting:
 
         monkeypatch.setattr(mcp_mod.mcp_server, "run", mock_run)
         monkeypatch.setattr(mcp_mod, "init_mcp_logging", lambda: None)
-        _stub_auto_update(monkeypatch, mcp_mod)
 
-        result = runner.invoke(cli_app, ["mcp"])
-        assert result.exit_code == 0, result.output
+        runner.invoke(cli_app, ["mcp"])
 
         # Externally-set vars should be preserved
         assert env_at_run["FORCE_CLOUD"] == "true"
@@ -178,8 +153,7 @@ class TestMcpCommandRouting:
         monkeypatch.setattr(mcp_mod.mcp_server, "run", mock_run)
         monkeypatch.setattr(mcp_mod, "init_mcp_logging", lambda: None)
 
-        result = runner.invoke(cli_app, ["mcp", "--transport", "streamable-http"])
-        assert result.exit_code == 0, result.output
+        runner.invoke(cli_app, ["mcp", "--transport", "streamable-http"])
 
         assert env_at_run["FORCE_LOCAL"] == "true"
         assert env_at_run["EXPLICIT"] == "true"
@@ -198,8 +172,7 @@ class TestMcpCommandRouting:
         monkeypatch.setattr(mcp_mod.mcp_server, "run", mock_run)
         monkeypatch.setattr(mcp_mod, "init_mcp_logging", lambda: None)
 
-        result = runner.invoke(cli_app, ["mcp", "--transport", "sse"])
-        assert result.exit_code == 0, result.output
+        runner.invoke(cli_app, ["mcp", "--transport", "sse"])
 
         assert env_at_run["FORCE_LOCAL"] == "true"
         assert env_at_run["EXPLICIT"] == "true"

test-int/mcp/test_project_management_integration.py

@@ -591,35 +591,36 @@ async def test_nested_project_paths_rejected(mcp_server, app, test_project, tmp_
 
 
 @pytest.mark.asyncio
-async def test_create_project_workspace_without_credentials_fails_fast(
+async def test_create_project_accepts_workspace_in_local_mode(
     mcp_server, app, test_project, tmp_path
 ):
-    """A workspace selector without cloud credentials fails fast — no local create (#954).
+    """Passing workspace via the MCP wire is accepted by the tool schema and
+    does not break the local create path.
 
-    The previous contract treated workspace as a local no-op, which was the bug:
-    a caller asking for a cloud team workspace got a silent local project. The
-    tool schema still accepts the parameter (this test exercises it over the
-    MCP wire), but the create must error with auth guidance and leave no
-    project behind.
+    In local mode there is no cloud factory installed, so workspace is a no-op:
+    the request lands on the ASGI transport which has no workspace concept. This
+    test guards the schema so a future change can't accidentally drop the parameter.
     """
-    from fastmcp.exceptions import ToolError
 
     async with Client(mcp_server) as client:
-        with pytest.raises(ToolError, match="cloud workspace was requested"):
-            await client.call_tool(
-                "create_memory_project",
-                {
-                    "project_name": "ws-local-test",
-                    "project_path": str(
-                        tmp_path.parent / (tmp_path.name + "-projects") / "project-ws-local-test"
-                    ),
-                    "workspace": "team-paul",
-                },
-            )
+        create_result = await client.call_tool(
+            "create_memory_project",
+            {
+                "project_name": "ws-local-test",
+                "project_path": str(
+                    tmp_path.parent / (tmp_path.name + "-projects") / "project-ws-local-test"
+                ),
+                "workspace": "team-paul",
+            },
+        )
+
+        assert len(create_result.content) == 1
+        create_text = create_result.content[0].text  # pyright: ignore [reportAttributeAccessIssue]
+        assert "✓" in create_text
+        assert "ws-local-test" in create_text
 
-        # The failed create must not leave a local project behind
         list_result = await client.call_tool("list_memory_projects", {})
-        assert "ws-local-test" not in list_result.content[0].text  # pyright: ignore [reportAttributeAccessIssue]
+        assert "ws-local-test" in list_result.content[0].text  # pyright: ignore [reportAttributeAccessIssue]
 
 
 @pytest.mark.asyncio

tests/api/v2/test_project_router.py

@@ -6,7 +6,6 @@ from pathlib import Path
 import pytest
 from httpx import AsyncClient
 
-from basic_memory.config import ProjectEntry
 from basic_memory.models import Project
 from basic_memory.schemas.project_info import ProjectItem, ProjectStatusResponse
 from basic_memory.schemas.v2 import ProjectResolveResponse
@@ -55,46 +54,6 @@ async def test_get_project_by_id_not_found(client: AsyncClient, v2_projects_url)
     assert "not found" in response.json()["detail"].lower()
 
 
-@pytest.mark.asyncio
-async def test_add_project_response_reflects_promoted_default(
-    client: AsyncClient,
-    v2_projects_url,
-    app_config,
-    config_manager,
-    config_home,
-    project_repository,
-):
-    """Regression #974/#985: POST response should echo persisted default promotion."""
-    main_home = config_home / "basic-memory"
-    main_home.mkdir(parents=True, exist_ok=True)
-    qa_path = config_home / "qa-notes"
-    qa_path.mkdir(parents=True, exist_ok=True)
-
-    fresh_config = app_config.model_copy(
-        update={
-            "projects": {"main": ProjectEntry(path=str(main_home))},
-            "default_project": "main",
-        }
-    )
-    config_manager.save_config(fresh_config)
-
-    for project in await project_repository.find_all():
-        await project_repository.delete(project.id)
-
-    response = await client.post(
-        f"{v2_projects_url}/",
-        json={"name": "qa", "path": str(qa_path), "set_default": False},
-    )
-
-    assert response.status_code == 201
-    status_response = ProjectStatusResponse.model_validate(response.json())
-    assert status_response.status == "success"
-    assert status_response.default is True
-    new_project = _project_item(status_response.new_project)
-    assert new_project.name == "qa"
-    assert new_project.is_default is True
-
-
 @pytest.mark.asyncio
 async def test_update_project_path_by_id(
     client: AsyncClient, test_project: Project, v2_projects_url
@@ -178,37 +137,6 @@ async def test_set_default_project_by_id(
     assert old_project.is_default is False
 
 
-@pytest.mark.asyncio
-async def test_set_default_project_when_none_is_set(
-    client: AsyncClient, test_project: Project, v2_projects_url, project_repository
-):
-    """Regression for #975: setting a default must succeed when none is set.
-
-    This is the bootstrap/recovery case: `bm project default <name>` is exactly
-    the command reached for when no default exists, so the endpoint must not 404.
-    """
-    # Clear any existing default so no row has is_default set.
-    await project_repository.update(test_project.id, {"is_default": None})
-    assert await project_repository.get_default_project() is None
-
-    response = await client.put(f"{v2_projects_url}/{test_project.external_id}/default")
-
-    assert response.status_code == 200
-    status_response = ProjectStatusResponse.model_validate(response.json())
-    assert status_response.status == "success"
-    assert status_response.default is True
-    # No previous default existed, so old_project must be None.
-    assert status_response.old_project is None
-    new_project = _project_item(status_response.new_project)
-    assert new_project.external_id == test_project.external_id
-    assert new_project.is_default is True
-
-    # A follow-up read-back must now return the newly set default.
-    default_project = await project_repository.get_default_project()
-    assert default_project is not None
-    assert default_project.external_id == test_project.external_id
-
-
 @pytest.mark.asyncio
 async def test_set_default_project_not_found(client: AsyncClient, v2_projects_url):
     """Test setting a non-existent project as default returns 404."""
@@ -445,41 +373,6 @@ async def test_resolve_project_not_found(client: AsyncClient, v2_projects_url):
     assert "not found" in response.json()["detail"].lower()
 
 
-@pytest.mark.asyncio
-async def test_resolve_project_not_found_fresh_install_names_setup_command(
-    client: AsyncClient, v2_projects_url, project_repository
-):
-    """#974 follow-up: a fresh install fails its first read with a bare not-found.
-
-    config.json bootstraps a "main" default before any reconciliation has created
-    database rows (the one-shot CLI never runs the server lifespan), so resolving
-    the configured default 404s. With an empty projects table the error must point
-    at first-run setup instead of reading like a broken install.
-    """
-    for project in await project_repository.find_all():
-        await project_repository.delete(project.id)
-
-    response = await client.post(f"{v2_projects_url}/resolve", json={"identifier": "main"})
-
-    assert response.status_code == 404
-    detail = response.json()["detail"]
-    assert detail.startswith("Project not found: 'main'")
-    assert "basic-memory project add" in detail
-
-
-@pytest.mark.asyncio
-async def test_resolve_project_not_found_with_projects_keeps_plain_message(
-    client: AsyncClient, test_project: Project, v2_projects_url
-):
-    """A miss against a populated projects table stays a plain not-found."""
-    response = await client.post(
-        f"{v2_projects_url}/resolve", json={"identifier": "nonexistent-project"}
-    )
-
-    assert response.status_code == 404
-    assert response.json()["detail"] == "Project not found: 'nonexistent-project'"
-
-
 @pytest.mark.asyncio
 async def test_resolve_project_empty_identifier(client: AsyncClient, v2_projects_url):
     """Test resolving with empty identifier returns 422."""

tests/cli/test_auto_update.py

@@ -3,7 +3,6 @@
 from __future__ import annotations
 
 import subprocess
-import sys
 from datetime import datetime, timedelta, timezone
 from io import StringIO
 from typing import Any, cast
@@ -16,7 +15,6 @@ from basic_memory.cli.auto_update import (
     InstallSource,
     _check_homebrew_update_available,
     _is_interactive_session,
-    _preload_lazy_console_modules,
     detect_install_source,
     maybe_run_periodic_auto_update,
     run_auto_update,
@@ -161,19 +159,6 @@ def test_check_homebrew_update_available_exit_code_0_means_up_to_date(monkeypatc
     assert is_outdated is False
 
 
-def test_preload_lazy_console_modules_imports_deferred_modules(monkeypatch):
-    # Regression: the in-place upgrade deletes the running install's files, so
-    # any module rich/typer defers until print time must already be loaded or
-    # the final status message crashes with ModuleNotFoundError.
-    monkeypatch.delitem(sys.modules, "rich._emoji_codes", raising=False)
-    monkeypatch.delitem(sys.modules, "typer.rich_utils", raising=False)
-
-    _preload_lazy_console_modules()
-
-    assert "rich._emoji_codes" in sys.modules
-    assert "typer.rich_utils" in sys.modules
-
-
 def test_homebrew_outdated_triggers_upgrade(monkeypatch, tmp_path):
     config = _base_config(tmp_path)
     manager = StubConfigManager(config)

tests/cli/test_ci_commands.py

@@ -219,8 +219,8 @@ def test_setup_does_not_partially_write_generated_files_when_target_exists(
     mock_seed.assert_not_awaited()
 
 
-@patch("basic_memory.mcp.tools.search_notes", new_callable=AsyncMock)
-@patch("basic_memory.mcp.tools.write_note", new_callable=AsyncMock)
+@patch("basic_memory.cli.commands.ci.mcp_search_notes", new_callable=AsyncMock)
+@patch("basic_memory.cli.commands.ci.mcp_write_note", new_callable=AsyncMock)
 async def test_seed_project_update_schemas_skips_existing_notes_by_default(
     mock_write: AsyncMock,
     mock_search: AsyncMock,
@@ -235,8 +235,8 @@ async def test_seed_project_update_schemas_skips_existing_notes_by_default(
     mock_write.assert_not_awaited()
 
 
-@patch("basic_memory.mcp.tools.search_notes", new_callable=AsyncMock)
-@patch("basic_memory.mcp.tools.write_note", new_callable=AsyncMock)
+@patch("basic_memory.cli.commands.ci.mcp_search_notes", new_callable=AsyncMock)
+@patch("basic_memory.cli.commands.ci.mcp_write_note", new_callable=AsyncMock)
 async def test_seed_project_update_schemas_refreshes_existing_notes(
     mock_write: AsyncMock,
     mock_search: AsyncMock,
@@ -327,8 +327,8 @@ def test_agent_schema_command_writes_schema(tmp_path: Path) -> None:
     assert schema["title"] == "AgentSynthesis"
 
 
-@patch("basic_memory.mcp.tools.search_notes", new_callable=AsyncMock)
-@patch("basic_memory.mcp.tools.write_note", new_callable=AsyncMock)
+@patch("basic_memory.cli.commands.ci.mcp_search_notes", new_callable=AsyncMock)
+@patch("basic_memory.cli.commands.ci.mcp_write_note", new_callable=AsyncMock)
 def test_publish_command_upserts_project_update_note(
     mock_write: AsyncMock,
     mock_search: AsyncMock,
@@ -401,8 +401,8 @@ def test_publish_command_upserts_project_update_note(
     )
 
 
-@patch("basic_memory.mcp.tools.search_notes", new_callable=AsyncMock)
-@patch("basic_memory.mcp.tools.write_note", new_callable=AsyncMock)
+@patch("basic_memory.cli.commands.ci.mcp_search_notes", new_callable=AsyncMock)
+@patch("basic_memory.cli.commands.ci.mcp_write_note", new_callable=AsyncMock)
 def test_publish_command_preserves_existing_note_path_for_idempotency_match(
     mock_write: AsyncMock,
     mock_search: AsyncMock,
@@ -464,8 +464,8 @@ def test_publish_command_preserves_existing_note_path_for_idempotency_match(
     assert kwargs["directory"] == "custom/project-updates"
 
 
-@patch("basic_memory.mcp.tools.search_notes", new_callable=AsyncMock)
-@patch("basic_memory.mcp.tools.write_note", new_callable=AsyncMock)
+@patch("basic_memory.cli.commands.ci.mcp_search_notes", new_callable=AsyncMock)
+@patch("basic_memory.cli.commands.ci.mcp_write_note", new_callable=AsyncMock)
 def test_publish_command_uses_project_id_without_workspace_qualifying_project(
     mock_write: AsyncMock,
     mock_search: AsyncMock,

tests/cli/test_cli_exit.py

@@ -86,46 +86,6 @@ def test_bm_version_does_not_import_heavy_modules():
     )
 
 
-def test_bm_cli_import_does_not_load_heavy_stack():
-    """Regression test (#886): registering all CLI commands must stay lightweight.
-
-    Importing basic_memory.cli.main with a normal argv registers every command
-    module. None of them may pull FastAPI, the API app, SQLAlchemy/Alembic, the
-    MCP tool stack, or the markdown/services layers in at import time — those
-    must load lazily when a command actually runs.
-    """
-    heavy_modules = (
-        "fastapi",
-        "sqlalchemy",
-        "alembic",
-        "fastmcp",
-        "mcp",
-        "basic_memory.api.app",
-        "basic_memory.db",
-        "basic_memory.markdown",
-        "basic_memory.mcp.tools",
-        "basic_memory.services",
-    )
-    check_script = (
-        "import sys; "
-        "sys.argv = ['bm', 'tool', 'search-notes', '--help']; "
-        "import basic_memory.cli.main; "
-        f"heavy = [m for m in {heavy_modules!r} if m in sys.modules]; "
-        "print(','.join(heavy) if heavy else 'CLEAN')"
-    )
-    result = subprocess.run(
-        ["uv", "run", "python", "-c", check_script],
-        capture_output=True,
-        text=True,
-        timeout=20,
-        cwd=Path(__file__).parent.parent.parent,
-    )
-    assert result.returncode == 0
-    assert "CLEAN" in result.stdout, (
-        f"Heavy modules loaded during CLI import: {result.stdout.strip()}"
-    )
-
-
 def test_bm_help_does_not_import_api_app():
     """Regression test: 'bm --help' must not build the FastAPI app graph."""
     check_script = (

tests/cli/test_cli_schema.py

@@ -87,7 +87,7 @@ def _mock_config_manager():
 
 @patch("basic_memory.cli.commands.schema.ConfigManager")
 @patch(
-    "basic_memory.mcp.tools.schema_validate",
+    "basic_memory.cli.commands.schema.mcp_schema_validate",
     new_callable=AsyncMock,
     return_value=VALIDATE_REPORT,
 )
@@ -108,7 +108,7 @@ def test_validate_renders_table(mock_mcp, mock_config_cls):
 
 @patch("basic_memory.cli.commands.schema.ConfigManager")
 @patch(
-    "basic_memory.mcp.tools.schema_validate",
+    "basic_memory.cli.commands.schema.mcp_schema_validate",
     new_callable=AsyncMock,
     return_value=VALIDATE_REPORT,
 )
@@ -123,7 +123,7 @@ def test_validate_strict_exits_on_errors(mock_mcp, mock_config_cls):
 
 @patch("basic_memory.cli.commands.schema.ConfigManager")
 @patch(
-    "basic_memory.mcp.tools.schema_validate",
+    "basic_memory.cli.commands.schema.mcp_schema_validate",
     new_callable=AsyncMock,
     return_value={"error": "No notes found of type 'person'"},
 )
@@ -139,7 +139,7 @@ def test_validate_error_response(mock_mcp, mock_config_cls):
 
 @patch("basic_memory.cli.commands.schema.ConfigManager")
 @patch(
-    "basic_memory.mcp.tools.schema_validate",
+    "basic_memory.cli.commands.schema.mcp_schema_validate",
     new_callable=AsyncMock,
     return_value=VALIDATE_REPORT,
 )
@@ -159,7 +159,7 @@ def test_validate_identifier_heuristic(mock_mcp, mock_config_cls):
 
 @patch("basic_memory.cli.commands.schema.ConfigManager")
 @patch(
-    "basic_memory.mcp.tools.schema_infer",
+    "basic_memory.cli.commands.schema.mcp_schema_infer",
     new_callable=AsyncMock,
     return_value=INFER_REPORT,
 )
@@ -179,7 +179,7 @@ def test_infer_renders_table(mock_mcp, mock_config_cls):
 
 @patch("basic_memory.cli.commands.schema.ConfigManager")
 @patch(
-    "basic_memory.mcp.tools.schema_infer",
+    "basic_memory.cli.commands.schema.mcp_schema_infer",
     new_callable=AsyncMock,
     return_value=INFER_REPORT,
 )
@@ -195,7 +195,7 @@ def test_infer_threshold_passthrough(mock_mcp, mock_config_cls):
 
 @patch("basic_memory.cli.commands.schema.ConfigManager")
 @patch(
-    "basic_memory.mcp.tools.schema_infer",
+    "basic_memory.cli.commands.schema.mcp_schema_infer",
     new_callable=AsyncMock,
     return_value={"error": "No schema pattern found for 'person' (threshold: 25%)"},
 )
@@ -211,7 +211,7 @@ def test_infer_error_response(mock_mcp, mock_config_cls):
 
 @patch("basic_memory.cli.commands.schema.ConfigManager")
 @patch(
-    "basic_memory.mcp.tools.schema_infer",
+    "basic_memory.cli.commands.schema.mcp_schema_infer",
     new_callable=AsyncMock,
     return_value={
         "note_type": "person",
@@ -238,7 +238,7 @@ def test_infer_zero_notes(mock_mcp, mock_config_cls):
 
 @patch("basic_memory.cli.commands.schema.ConfigManager")
 @patch(
-    "basic_memory.mcp.tools.schema_diff",
+    "basic_memory.cli.commands.schema.mcp_schema_diff",
     new_callable=AsyncMock,
     return_value=DIFF_REPORT_WITH_DRIFT,
 )
@@ -259,7 +259,7 @@ def test_diff_renders_drift(mock_mcp, mock_config_cls):
 
 @patch("basic_memory.cli.commands.schema.ConfigManager")
 @patch(
-    "basic_memory.mcp.tools.schema_diff",
+    "basic_memory.cli.commands.schema.mcp_schema_diff",
     new_callable=AsyncMock,
     return_value=DIFF_REPORT_NO_DRIFT,
 )
@@ -275,7 +275,7 @@ def test_diff_no_drift(mock_mcp, mock_config_cls):
 
 @patch("basic_memory.cli.commands.schema.ConfigManager")
 @patch(
-    "basic_memory.mcp.tools.schema_diff",
+    "basic_memory.cli.commands.schema.mcp_schema_diff",
     new_callable=AsyncMock,
     return_value={"error": "No schema found for type 'person'"},
 )

tests/cli/test_cli_tool_json_output.py

@@ -98,7 +98,7 @@ SEARCH_RESULT = {
 
 
 @patch(
-    "basic_memory.mcp.tools.write_note",
+    "basic_memory.cli.commands.tool.mcp_write_note",
     new_callable=AsyncMock,
     return_value=WRITE_NOTE_RESULT,
 )
@@ -129,7 +129,7 @@ def test_write_note_json_output(mock_mcp_write):
 
 
 @patch(
-    "basic_memory.mcp.tools.write_note",
+    "basic_memory.cli.commands.tool.mcp_write_note",
     new_callable=AsyncMock,
     return_value=WRITE_NOTE_RESULT,
 )
@@ -161,7 +161,7 @@ def test_write_note_project_id_passthrough(mock_mcp_write):
 
 
 @patch(
-    "basic_memory.mcp.tools.write_note",
+    "basic_memory.cli.commands.tool.mcp_write_note",
     new_callable=AsyncMock,
     return_value=WRITE_NOTE_RESULT,
 )
@@ -190,7 +190,7 @@ def test_write_note_with_tags(mock_mcp_write):
 
 
 @patch(
-    "basic_memory.mcp.tools.write_note",
+    "basic_memory.cli.commands.tool.mcp_write_note",
     new_callable=AsyncMock,
     return_value=WRITE_NOTE_RESULT,
 )
@@ -217,7 +217,7 @@ def test_write_note_type_passthrough(mock_mcp_write):
 
 
 @patch(
-    "basic_memory.mcp.tools.write_note",
+    "basic_memory.cli.commands.tool.mcp_write_note",
     new_callable=AsyncMock,
     return_value=WRITE_NOTE_RESULT,
 )
@@ -245,7 +245,7 @@ def test_write_note_type_defaults_to_note(mock_mcp_write):
 
 
 @patch(
-    "basic_memory.mcp.tools.read_note",
+    "basic_memory.cli.commands.tool.mcp_read_note",
     new_callable=AsyncMock,
     return_value=READ_NOTE_RESULT,
 )
@@ -267,7 +267,7 @@ def test_read_note_json_output(mock_mcp_read):
 
 
 @patch(
-    "basic_memory.mcp.tools.read_note",
+    "basic_memory.cli.commands.tool.mcp_read_note",
     new_callable=AsyncMock,
     return_value=READ_NOTE_RESULT,
 )
@@ -286,7 +286,7 @@ def test_read_note_include_frontmatter(mock_mcp_read):
 
 
 @patch(
-    "basic_memory.mcp.tools.delete_note",
+    "basic_memory.cli.commands.tool.mcp_delete_note",
     new_callable=AsyncMock,
     return_value=DELETE_NOTE_RESULT,
 )
@@ -307,7 +307,7 @@ def test_delete_note_json_output(mock_mcp_delete: AsyncMock) -> None:
 
 
 @patch(
-    "basic_memory.mcp.tools.delete_note",
+    "basic_memory.cli.commands.tool.mcp_delete_note",
     new_callable=AsyncMock,
     return_value=DELETE_DIRECTORY_RESULT,
 )
@@ -325,7 +325,7 @@ def test_delete_note_directory_flag(mock_mcp_delete: AsyncMock) -> None:
 
 
 @patch(
-    "basic_memory.mcp.tools.delete_note",
+    "basic_memory.cli.commands.tool.mcp_delete_note",
     new_callable=AsyncMock,
     return_value={
         "deleted": False,
@@ -349,7 +349,7 @@ def test_delete_note_not_found_outputs_json(mock_mcp_delete: AsyncMock) -> None:
 
 
 @patch(
-    "basic_memory.mcp.tools.delete_note",
+    "basic_memory.cli.commands.tool.mcp_delete_note",
     new_callable=AsyncMock,
     return_value={
         "deleted": False,
@@ -371,7 +371,7 @@ def test_delete_note_error_response(mock_mcp_delete: AsyncMock) -> None:
 
 
 @patch(
-    "basic_memory.mcp.tools.delete_note",
+    "basic_memory.cli.commands.tool.mcp_delete_note",
     new_callable=AsyncMock,
     return_value={
         "deleted": False,
@@ -398,7 +398,7 @@ def test_delete_note_directory_partial_failure_exits_nonzero(
 
 
 @patch(
-    "basic_memory.mcp.tools.delete_note",
+    "basic_memory.cli.commands.tool.mcp_delete_note",
     new_callable=AsyncMock,
     return_value=DELETE_NOTE_RESULT,
 )
@@ -418,7 +418,7 @@ def test_delete_note_project_id_passthrough(mock_mcp_delete: AsyncMock) -> None:
 
 
 @patch(
-    "basic_memory.mcp.tools.edit_note",
+    "basic_memory.cli.commands.tool.mcp_edit_note",
     new_callable=AsyncMock,
     return_value=EDIT_NOTE_RESULT,
 )
@@ -446,7 +446,7 @@ def test_edit_note_json_output(mock_mcp_edit):
 
 
 @patch(
-    "basic_memory.mcp.tools.edit_note",
+    "basic_memory.cli.commands.tool.mcp_edit_note",
     new_callable=AsyncMock,
     return_value={"title": "Test", "permalink": "test", "error": "Edit failed: not found"},
 )
@@ -472,7 +472,7 @@ def test_edit_note_error_response(mock_mcp_edit):
 
 
 @patch(
-    "basic_memory.mcp.tools.build_context",
+    "basic_memory.cli.commands.tool.mcp_build_context",
     new_callable=AsyncMock,
     return_value=BUILD_CONTEXT_RESULT,
 )
@@ -491,7 +491,7 @@ def test_build_context_json_output(mock_build_ctx):
 
 
 @patch(
-    "basic_memory.mcp.tools.build_context",
+    "basic_memory.cli.commands.tool.mcp_build_context",
     new_callable=AsyncMock,
     return_value=BUILD_CONTEXT_RESULT,
 )
@@ -526,7 +526,7 @@ def test_build_context_with_options(mock_build_ctx):
 
 
 @patch(
-    "basic_memory.mcp.tools.recent_activity",
+    "basic_memory.cli.commands.tool.mcp_recent_activity",
     new_callable=AsyncMock,
     return_value=RECENT_ACTIVITY_RESULT,
 )
@@ -548,7 +548,7 @@ def test_recent_activity_json_output(mock_mcp_recent):
 
 
 @patch(
-    "basic_memory.mcp.tools.recent_activity",
+    "basic_memory.cli.commands.tool.mcp_recent_activity",
     new_callable=AsyncMock,
     return_value=RECENT_ACTIVITY_RESULT,
 )
@@ -566,7 +566,7 @@ def test_recent_activity_pagination(mock_mcp_recent):
 
 
 @patch(
-    "basic_memory.mcp.tools.recent_activity",
+    "basic_memory.cli.commands.tool.mcp_recent_activity",
     new_callable=AsyncMock,
     return_value=[],
 )
@@ -586,7 +586,7 @@ def test_recent_activity_empty(mock_mcp_recent):
 
 
 @patch(
-    "basic_memory.mcp.tools.search_notes",
+    "basic_memory.cli.commands.tool.mcp_search",
     new_callable=AsyncMock,
     return_value=SEARCH_RESULT,
 )
@@ -606,7 +606,7 @@ def test_search_notes_json_output(mock_mcp_search):
 
 
 @patch(
-    "basic_memory.mcp.tools.search_notes",
+    "basic_memory.cli.commands.tool.mcp_search",
     new_callable=AsyncMock,
     return_value=SEARCH_RESULT,
 )
@@ -622,7 +622,7 @@ def test_search_notes_with_meta_filter(mock_mcp_search):
 
 
 @patch(
-    "basic_memory.mcp.tools.search_notes",
+    "basic_memory.cli.commands.tool.mcp_search",
     new_callable=AsyncMock,
     return_value=SEARCH_RESULT,
 )
@@ -638,7 +638,7 @@ def test_search_notes_permalink_mode(mock_mcp_search):
 
 
 @patch(
-    "basic_memory.mcp.tools.search_notes",
+    "basic_memory.cli.commands.tool.mcp_search",
     new_callable=AsyncMock,
     return_value="Error: search failed",
 )
@@ -699,7 +699,7 @@ SCHEMA_VALIDATE_RESULT = {
 
 
 @patch(
-    "basic_memory.mcp.tools.schema_validate",
+    "basic_memory.cli.commands.tool.mcp_schema_validate",
     new_callable=AsyncMock,
     return_value=SCHEMA_VALIDATE_RESULT,
 )
@@ -719,7 +719,7 @@ def test_schema_validate_json_output(mock_mcp):
 
 
 @patch(
-    "basic_memory.mcp.tools.schema_validate",
+    "basic_memory.cli.commands.tool.mcp_schema_validate",
     new_callable=AsyncMock,
     return_value=SCHEMA_VALIDATE_RESULT,
 )
@@ -736,7 +736,7 @@ def test_schema_validate_identifier_heuristic(mock_mcp):
 
 
 @patch(
-    "basic_memory.mcp.tools.schema_validate",
+    "basic_memory.cli.commands.tool.mcp_schema_validate",
     new_callable=AsyncMock,
     return_value={"error": "No notes found of type 'person'"},
 )
@@ -769,7 +769,7 @@ SCHEMA_INFER_RESULT = {
 
 
 @patch(
-    "basic_memory.mcp.tools.schema_infer",
+    "basic_memory.cli.commands.tool.mcp_schema_infer",
     new_callable=AsyncMock,
     return_value=SCHEMA_INFER_RESULT,
 )
@@ -789,7 +789,7 @@ def test_schema_infer_json_output(mock_mcp):
 
 
 @patch(
-    "basic_memory.mcp.tools.schema_infer",
+    "basic_memory.cli.commands.tool.mcp_schema_infer",
     new_callable=AsyncMock,
     return_value=SCHEMA_INFER_RESULT,
 )
@@ -818,7 +818,7 @@ SCHEMA_DIFF_RESULT = {
 
 
 @patch(
-    "basic_memory.mcp.tools.schema_diff",
+    "basic_memory.cli.commands.tool.mcp_schema_diff",
     new_callable=AsyncMock,
     return_value=SCHEMA_DIFF_RESULT,
 )
@@ -860,7 +860,7 @@ LIST_PROJECTS_RESULT = {
 
 
 @patch(
-    "basic_memory.mcp.tools.list_memory_projects",
+    "basic_memory.cli.commands.tool.mcp_list_projects",
     new_callable=AsyncMock,
     return_value=LIST_PROJECTS_RESULT,
 )
@@ -898,7 +898,7 @@ LIST_WORKSPACES_RESULT = {
 
 
 @patch(
-    "basic_memory.mcp.tools.list_workspaces",
+    "basic_memory.cli.commands.tool.mcp_list_workspaces",
     new_callable=AsyncMock,
     return_value=LIST_WORKSPACES_RESULT,
 )
@@ -919,7 +919,7 @@ def test_list_workspaces_json_output(mock_mcp):
 
 
 @patch(
-    "basic_memory.mcp.tools.list_workspaces",
+    "basic_memory.cli.commands.tool.mcp_list_workspaces",
     new_callable=AsyncMock,
     return_value={"workspaces": [], "count": 0},
 )

tests/cli/test_db_reindex.py

@@ -195,21 +195,15 @@ async def test_reindex_project_full_passes_force_full_to_sync_and_reports_mode(m
             if "total" in kwargs:
                 self.tasks[task_id].total = kwargs["total"]
 
-    # _reindex imports its database/sync dependencies at call time (#886),
-    # so stubs target the source modules instead of db_cmd attributes.
+    monkeypatch.setattr(db_cmd, "reconcile_projects_with_config", AsyncMock())
     monkeypatch.setattr(
-        "basic_memory.services.initialization.reconcile_projects_with_config", AsyncMock()
-    )
-    monkeypatch.setattr(
-        "basic_memory.db.get_or_create_db",
+        db_cmd.db,
+        "get_or_create_db",
         AsyncMock(return_value=(None, session_maker)),
     )
-    monkeypatch.setattr("basic_memory.db.shutdown_db", AsyncMock())
-    monkeypatch.setattr("basic_memory.repository.ProjectRepository", StubProjectRepository)
-    monkeypatch.setattr(
-        "basic_memory.sync.sync_service.get_sync_service",
-        AsyncMock(return_value=sync_service),
-    )
+    monkeypatch.setattr(db_cmd.db, "shutdown_db", AsyncMock())
+    monkeypatch.setattr(db_cmd, "ProjectRepository", StubProjectRepository)
+    monkeypatch.setattr(db_cmd, "get_sync_service", AsyncMock(return_value=sync_service))
     monkeypatch.setattr(db_cmd, "Progress", SilentProgress)
     monkeypatch.setattr(
         db_cmd.console,
@@ -283,17 +277,14 @@ async def test_reindex_embeddings_only_full_passes_force_full_to_vector_reindex(
             if "total" in kwargs:
                 self.tasks[task_id].total = kwargs["total"]
 
-    # _reindex imports its database/sync dependencies at call time (#886),
-    # so stubs target the source modules instead of db_cmd attributes.
+    monkeypatch.setattr(db_cmd, "reconcile_projects_with_config", AsyncMock())
     monkeypatch.setattr(
-        "basic_memory.services.initialization.reconcile_projects_with_config", AsyncMock()
-    )
-    monkeypatch.setattr(
-        "basic_memory.db.get_or_create_db",
+        db_cmd.db,
+        "get_or_create_db",
         AsyncMock(return_value=(None, session_maker)),
     )
-    monkeypatch.setattr("basic_memory.db.shutdown_db", AsyncMock())
-    monkeypatch.setattr("basic_memory.repository.ProjectRepository", StubProjectRepository)
+    monkeypatch.setattr(db_cmd.db, "shutdown_db", AsyncMock())
+    monkeypatch.setattr(db_cmd, "ProjectRepository", StubProjectRepository)
     monkeypatch.setattr(
         "basic_memory.repository.search_repository.create_search_repository",
         lambda *args, **kwargs: object(),

tests/cli/test_json_output.py

@@ -368,7 +368,7 @@ def test_status_wait_json_timeout_emits_error(
 
 @patch("basic_memory.cli.commands.schema.ConfigManager")
 @patch(
-    "basic_memory.mcp.tools.schema_validate",
+    "basic_memory.cli.commands.schema.mcp_schema_validate",
     new_callable=AsyncMock,
     return_value=VALIDATE_REPORT,
 )
@@ -387,7 +387,7 @@ def test_schema_validate_json(mock_mcp, mock_config_cls):
 
 @patch("basic_memory.cli.commands.schema.ConfigManager")
 @patch(
-    "basic_memory.mcp.tools.schema_validate",
+    "basic_memory.cli.commands.schema.mcp_schema_validate",
     new_callable=AsyncMock,
     return_value={"error": "No schema found for type 'person'"},
 )
@@ -404,7 +404,7 @@ def test_schema_validate_json_error(mock_mcp, mock_config_cls):
 
 @patch("basic_memory.cli.commands.schema.ConfigManager")
 @patch(
-    "basic_memory.mcp.tools.schema_validate",
+    "basic_memory.cli.commands.schema.mcp_schema_validate",
     new_callable=AsyncMock,
     return_value=VALIDATE_REPORT,
 )
@@ -427,7 +427,7 @@ def test_schema_validate_json_strict_exit(mock_mcp, mock_config_cls):
 
 @patch("basic_memory.cli.commands.schema.ConfigManager")
 @patch(
-    "basic_memory.mcp.tools.schema_infer",
+    "basic_memory.cli.commands.schema.mcp_schema_infer",
     new_callable=AsyncMock,
     return_value=INFER_REPORT,
 )
@@ -451,7 +451,7 @@ def test_schema_infer_json(mock_mcp, mock_config_cls):
 
 @patch("basic_memory.cli.commands.schema.ConfigManager")
 @patch(
-    "basic_memory.mcp.tools.schema_diff",
+    "basic_memory.cli.commands.schema.mcp_schema_diff",
     new_callable=AsyncMock,
     return_value=DIFF_REPORT_WITH_DRIFT,
 )

tests/cli/test_man_command.py

@@ -1,95 +0,0 @@
-"""Tests for `bm man install` (#952 / #610: make `man bm` work)."""
-
-import subprocess
-
-from typer.testing import CliRunner
-
-from basic_memory.cli.app import app
-
-# Importing the module registers the man command group on the top-level app.
-import basic_memory.cli.commands.man as man_command  # noqa: F401
-
-runner = CliRunner()
-
-
-def _flattened(output: str) -> str:
-    # rich wraps console output at the terminal width, which differs between
-    # local shells and CI — collapse all whitespace so phrase assertions can't
-    # be split by a line break.
-    return " ".join(output.split())
-
-
-def test_man_install_writes_pages_to_target(tmp_path):
-    """Install copies every bundled page into <root>/man1 as valid groff."""
-    result = runner.invoke(app, ["man", "install", "--dir", str(tmp_path)])
-
-    assert result.exit_code == 0, result.output
-
-    bm_page = tmp_path / "man1" / "bm.1"
-    alias_page = tmp_path / "man1" / "basic-memory.1"
-    assert bm_page.exists()
-    assert alias_page.exists()
-    # groff sanity: a real title header and the alias .so include
-    assert bm_page.read_text().startswith(".TH BM 1")
-    assert alias_page.read_text().strip() == ".so man1/bm.1"
-    assert "Try:" in _flattened(result.output)
-
-
-def test_man_install_warns_when_root_not_on_manpath(tmp_path, monkeypatch):
-    """A root provably absent from manpath output gets the MANPATH hint."""
-
-    def fake_run(*args, **kwargs):
-        return subprocess.CompletedProcess(
-            args=["manpath"], returncode=0, stdout="/usr/share/man:/opt/man", stderr=""
-        )
-
-    monkeypatch.setattr(man_command.subprocess, "run", fake_run)
-    result = runner.invoke(app, ["man", "install", "--dir", str(tmp_path)])
-
-    assert result.exit_code == 0, result.output
-    assert "not on your manpath" in _flattened(result.output)
-    assert "MANPATH" in _flattened(result.output)
-
-
-def test_man_install_stays_quiet_when_manpath_unavailable(tmp_path, monkeypatch):
-    """No manpath binary → no false-alarm warning, install still succeeds."""
-
-    def fake_run(*args, **kwargs):
-        raise FileNotFoundError("manpath")
-
-    monkeypatch.setattr(man_command.subprocess, "run", fake_run)
-    result = runner.invoke(app, ["man", "install", "--dir", str(tmp_path)])
-
-    assert result.exit_code == 0, result.output
-    assert "not on your manpath" not in _flattened(result.output)
-
-
-def test_man_install_treats_manpath_failure_as_unknown(tmp_path, monkeypatch):
-    """manpath exiting non-zero → unknown, no warning."""
-
-    def fake_run(*args, **kwargs):
-        return subprocess.CompletedProcess(args=["manpath"], returncode=1, stdout="", stderr="boom")
-
-    monkeypatch.setattr(man_command.subprocess, "run", fake_run)
-    result = runner.invoke(app, ["man", "install", "--dir", str(tmp_path)])
-
-    assert result.exit_code == 0, result.output
-    assert "not on your manpath" not in _flattened(result.output)
-
-
-def test_man_install_skips_app_initialization(tmp_path, monkeypatch):
-    """man install must not touch the database (PR #971 review).
-
-    Installing offline docs only copies packaged files; a locked or broken
-    local database must not block it, so `man` is in skip_init_commands.
-    """
-    import basic_memory.services.initialization as init_module
-
-    def explode(*args, **kwargs):
-        raise AssertionError("ensure_initialization must not run for `bm man`")
-
-    monkeypatch.setattr(init_module, "ensure_initialization", explode)
-    result = runner.invoke(app, ["man", "install", "--dir", str(tmp_path)])
-
-    assert result.exit_code == 0, result.output
-    assert (tmp_path / "man1" / "bm.1").exists()

tests/cli/test_status_wait_timeout.py

@@ -1,55 +0,0 @@
-"""Tests for the `bm status --wait` timeout guidance (#959)."""
-
-import pytest
-
-import basic_memory.cli.commands.status as status_module
-from basic_memory.cli.commands.status import StatusTimeout, run_status
-from basic_memory.schemas import SyncReportResponse
-from basic_memory.schemas.project_info import ProjectItem
-
-
-@pytest.mark.asyncio
-async def test_status_wait_timeout_points_at_reindex(monkeypatch, config_manager):
-    """The timeout error must hand the user the command that actually indexes.
-
-    In CLI-only sessions no sync coordinator runs, so pending changes never
-    drain and --wait always times out; without the hint the dead end looks
-    like a hung indexer (#959).
-    """
-    project_item = ProjectItem(
-        id=1,
-        external_id="11111111-1111-1111-1111-111111111111",
-        name="scratch",
-        path="/tmp/scratch",
-        is_default=True,
-    )
-    pending_report = SyncReportResponse(new={"notes/seed.md"}, total=1)
-
-    class FakeProjectClient:
-        def __init__(self, client):
-            pass
-
-        async def get_status(self, external_id):
-            return pending_report
-
-    class FakeClientContext:
-        async def __aenter__(self):
-            return object()
-
-        async def __aexit__(self, *args):
-            return False
-
-    async def fake_get_active_project(client, project, context):
-        return project_item
-
-    monkeypatch.setattr(status_module, "get_client", lambda **kwargs: FakeClientContext())
-    monkeypatch.setattr(status_module, "get_active_project", fake_get_active_project)
-    monkeypatch.setattr(status_module, "ProjectClient", FakeProjectClient)
-
-    with pytest.raises(StatusTimeout) as exc_info:
-        await run_status(project="scratch", wait=True, timeout=0.01, poll_interval=0.001)
-
-    message = str(exc_info.value)
-    assert "Timed out" in message
-    assert "bm reindex --project scratch" in message
-    assert "no Basic Memory server is running" in message

tests/db/test_memory_db_session_isolation.py

@@ -1,93 +0,0 @@
-"""Regression test for issue #940: lost writes on the in-memory SQLite engine.
-
-The in-memory SQLite URL (``sqlite+aiosqlite://``) used to fall back to
-SQLAlchemy's StaticPool, which hands the same DBAPI connection to every
-concurrently checked-out session. Concurrent asyncio tasks then share one
-transaction scope: a rollback issued by one session — scoped_session's
-exception handling, or the pool's reset-on-return at checkin — silently rolls
-back another session's uncommitted writes. During sync this manifested as a
-freshly inserted relation row vanishing without any error, which is how
-``test_sync_entity_circular_relations`` failed on CI with
-``len(entity_b.outgoing_relations) == 0``.
-
-This test pins the isolation invariant directly: a session that rolls back in
-one task must never destroy an uncommitted write of a session in another task.
-"""
-
-import asyncio
-from pathlib import Path
-
-import pytest
-from sqlalchemy import text
-
-from basic_memory import db
-from basic_memory.models import Base
-
-
-class _SimulatedIndexingFailure(Exception):
-    """Stand-in for any per-file error that _run_bounded swallows during sync."""
-
-
-@pytest.mark.asyncio
-async def test_concurrent_session_rollback_does_not_destroy_uncommitted_writes():
-    """A rolled-back session in one task must not erase another task's writes."""
-    async with db.engine_session_factory(
-        db_path=Path("unused.db"), db_type=db.DatabaseType.MEMORY
-    ) as (engine, session_maker):
-        async with engine.begin() as conn:
-            await conn.run_sync(Base.metadata.create_all)
-
-        # Seed a project and entity so a relation row satisfies its FK constraints.
-        async with db.scoped_session(session_maker) as session:
-            await session.execute(
-                text(
-                    "INSERT INTO project (id, external_id, name, description, path, is_active,"
-                    " is_default, created_at, updated_at, permalink) "
-                    "VALUES (1, 'px', 'p', '', '/tmp', 1, 1, '2024-01-01', '2024-01-01', 'p')"
-                )
-            )
-            await session.execute(
-                text(
-                    "INSERT INTO entity (id, external_id, title, note_type, content_type,"
-                    " project_id, file_path, created_at, updated_at) "
-                    "VALUES (1, 'ex', 'E', 'note', 'text/markdown', 1, 'e.md',"
-                    " '2024-01-01', '2024-01-01')"
-                )
-            )
-
-        write_in_flight = asyncio.Event()
-
-        async def writer() -> None:
-            # Mirrors RelationRepository.add_all_ignore_duplicates: INSERT executed,
-            # commit only happens at scoped_session exit several awaits later.
-            async with db.scoped_session(session_maker) as session:
-                await session.execute(
-                    text(
-                        "INSERT INTO relation (project_id, from_id, to_id, to_name,"
-                        " relation_type) VALUES (1, 1, NULL, 'target', 'depends_on')"
-                    )
-                )
-                write_in_flight.set()
-                # Real DB roundtrips (not sleeps) keep this transaction open across
-                # await points, exactly like the multi-statement sessions in sync.
-                for _ in range(10):
-                    await session.execute(text("SELECT 1"))
-
-        async def failing_reader() -> None:
-            # Mirrors any per-file failure during batch indexing: scoped_session
-            # rolls back on the exception path while sibling tasks are mid-write.
-            await write_in_flight.wait()
-            with pytest.raises(_SimulatedIndexingFailure):
-                async with db.scoped_session(session_maker) as session:
-                    await session.execute(text("SELECT 1"))
-                    raise _SimulatedIndexingFailure()
-
-        await asyncio.gather(writer(), failing_reader())
-
-        async with db.scoped_session(session_maker) as session:
-            count = (await session.execute(text("SELECT count(*) FROM relation"))).scalar()
-
-        assert count == 1, (
-            "writer's committed INSERT was rolled back by a concurrent session — "
-            "the in-memory engine is sharing one transaction scope across sessions"
-        )

tests/mcp/clients/test_clients.py

@@ -27,6 +27,7 @@ class TestKnowledgeClient:
     @pytest.mark.asyncio
     async def test_create_entity(self, monkeypatch):
         """Test create_entity calls correct endpoint."""
+        from basic_memory.mcp.clients import knowledge as knowledge_mod
 
         mock_response = MagicMock()
         mock_response.json.return_value = {
@@ -46,7 +47,7 @@ class TestKnowledgeClient:
             assert kwargs.get("params") is None
             return mock_response
 
-        monkeypatch.setattr("basic_memory.mcp.tools.utils.call_post", mock_call_post)
+        monkeypatch.setattr(knowledge_mod, "call_post", mock_call_post)
 
         mock_http = MagicMock()
         client = KnowledgeClient(mock_http, "proj-123")
@@ -56,6 +57,7 @@ class TestKnowledgeClient:
     @pytest.mark.asyncio
     async def test_update_entity(self, monkeypatch):
         """Test update_entity calls correct endpoint without fast query params."""
+        from basic_memory.mcp.clients import knowledge as knowledge_mod
 
         mock_response = MagicMock()
         mock_response.json.return_value = {
@@ -75,7 +77,7 @@ class TestKnowledgeClient:
             assert kwargs.get("params") is None
             return mock_response
 
-        monkeypatch.setattr("basic_memory.mcp.tools.utils.call_put", mock_call_put)
+        monkeypatch.setattr(knowledge_mod, "call_put", mock_call_put)
 
         mock_http = MagicMock()
         client = KnowledgeClient(mock_http, "proj-123")
@@ -85,6 +87,7 @@ class TestKnowledgeClient:
     @pytest.mark.asyncio
     async def test_patch_entity(self, monkeypatch):
         """Test patch_entity calls correct endpoint without fast query params."""
+        from basic_memory.mcp.clients import knowledge as knowledge_mod
 
         mock_response = MagicMock()
         mock_response.json.return_value = {
@@ -104,7 +107,7 @@ class TestKnowledgeClient:
             assert kwargs.get("params") is None
             return mock_response
 
-        monkeypatch.setattr("basic_memory.mcp.tools.utils.call_patch", mock_call_patch)
+        monkeypatch.setattr(knowledge_mod, "call_patch", mock_call_patch)
 
         mock_http = MagicMock()
         client = KnowledgeClient(mock_http, "proj-123")
@@ -114,6 +117,7 @@ class TestKnowledgeClient:
     @pytest.mark.asyncio
     async def test_resolve_entity(self, monkeypatch):
         """Test resolve_entity returns external_id."""
+        from basic_memory.mcp.clients import knowledge as knowledge_mod
 
         mock_response = MagicMock()
         mock_response.json.return_value = {"external_id": "entity-uuid-123"}
@@ -122,7 +126,7 @@ class TestKnowledgeClient:
             assert "/v2/projects/proj-123/knowledge/resolve" in url
             return mock_response
 
-        monkeypatch.setattr("basic_memory.mcp.tools.utils.call_post", mock_call_post)
+        monkeypatch.setattr(knowledge_mod, "call_post", mock_call_post)
 
         mock_http = MagicMock()
         client = KnowledgeClient(mock_http, "proj-123")
@@ -132,6 +136,7 @@ class TestKnowledgeClient:
     @pytest.mark.asyncio
     async def test_sync_file(self, monkeypatch):
         """Test sync_file posts the file path to the sync-file endpoint."""
+        from basic_memory.mcp.clients import knowledge as knowledge_mod
 
         mock_response = MagicMock()
         mock_response.json.return_value = {
@@ -151,7 +156,7 @@ class TestKnowledgeClient:
             assert kwargs.get("json") == {"file_path": "notes/disk-note.md"}
             return mock_response
 
-        monkeypatch.setattr("basic_memory.mcp.tools.utils.call_post", mock_call_post)
+        monkeypatch.setattr(knowledge_mod, "call_post", mock_call_post)
 
         mock_http = MagicMock()
         client = KnowledgeClient(mock_http, "proj-123")
@@ -161,6 +166,7 @@ class TestKnowledgeClient:
     @pytest.mark.asyncio
     async def test_get_orphans_validates_response(self, monkeypatch):
         """Orphan responses are validated into GraphNode objects."""
+        from basic_memory.mcp.clients import knowledge as knowledge_mod
         from basic_memory.schemas.v2.graph import GraphNode
 
         mock_response = MagicMock()
@@ -180,7 +186,7 @@ class TestKnowledgeClient:
             assert "/v2/projects/proj-123/knowledge/orphans" in url
             return mock_response
 
-        monkeypatch.setattr("basic_memory.mcp.tools.utils.call_get", mock_call_get)
+        monkeypatch.setattr(knowledge_mod, "call_get", mock_call_get)
 
         mock_http = MagicMock()
         client = KnowledgeClient(mock_http, "proj-123")
@@ -205,6 +211,7 @@ class TestSearchClient:
     @pytest.mark.asyncio
     async def test_search(self, monkeypatch):
         """Test search calls correct endpoint."""
+        from basic_memory.mcp.clients import search as search_mod
 
         mock_response = MagicMock()
         mock_response.json.return_value = {
@@ -218,7 +225,7 @@ class TestSearchClient:
             assert kwargs.get("params") == {"page": 1, "page_size": 10}
             return mock_response
 
-        monkeypatch.setattr("basic_memory.mcp.tools.utils.call_post", mock_call_post)
+        monkeypatch.setattr(search_mod, "call_post", mock_call_post)
 
         mock_http = MagicMock()
         client = SearchClient(mock_http, "proj-123")
@@ -241,6 +248,7 @@ class TestMemoryClient:
     @pytest.mark.asyncio
     async def test_build_context(self, monkeypatch):
         """Test build_context calls correct endpoint."""
+        from basic_memory.mcp.clients import memory as memory_mod
         from datetime import datetime
 
         mock_response = MagicMock()
@@ -256,7 +264,7 @@ class TestMemoryClient:
             assert "/v2/projects/proj-123/memory/specs/search" in url
             return mock_response
 
-        monkeypatch.setattr("basic_memory.mcp.tools.utils.call_get", mock_call_get)
+        monkeypatch.setattr(memory_mod, "call_get", mock_call_get)
 
         mock_http = MagicMock()
         client = MemoryClient(mock_http, "proj-123")
@@ -266,6 +274,7 @@ class TestMemoryClient:
     @pytest.mark.asyncio
     async def test_recent(self, monkeypatch):
         """Test recent calls correct endpoint."""
+        from basic_memory.mcp.clients import memory as memory_mod
         from datetime import datetime
 
         mock_response = MagicMock()
@@ -284,7 +293,7 @@ class TestMemoryClient:
             assert params.get("depth") == 2
             return mock_response
 
-        monkeypatch.setattr("basic_memory.mcp.tools.utils.call_get", mock_call_get)
+        monkeypatch.setattr(memory_mod, "call_get", mock_call_get)
 
         mock_http = MagicMock()
         client = MemoryClient(mock_http, "proj-123")
@@ -295,6 +304,7 @@ class TestMemoryClient:
     @pytest.mark.asyncio
     async def test_recent_with_types(self, monkeypatch):
         """Test recent with types filter."""
+        from basic_memory.mcp.clients import memory as memory_mod
         from datetime import datetime
 
         mock_response = MagicMock()
@@ -312,7 +322,7 @@ class TestMemoryClient:
             assert params.get("type") == "note,spec"
             return mock_response
 
-        monkeypatch.setattr("basic_memory.mcp.tools.utils.call_get", mock_call_get)
+        monkeypatch.setattr(memory_mod, "call_get", mock_call_get)
 
         mock_http = MagicMock()
         client = MemoryClient(mock_http, "proj-123")
@@ -334,6 +344,7 @@ class TestDirectoryClient:
     @pytest.mark.asyncio
     async def test_list(self, monkeypatch):
         """Test list calls correct endpoint."""
+        from basic_memory.mcp.clients import directory as directory_mod
 
         mock_response = MagicMock()
         mock_response.json.return_value = [{"name": "folder", "type": "directory"}]
@@ -342,7 +353,7 @@ class TestDirectoryClient:
             assert "/v2/projects/proj-123/directory/list" in url
             return mock_response
 
-        monkeypatch.setattr("basic_memory.mcp.tools.utils.call_get", mock_call_get)
+        monkeypatch.setattr(directory_mod, "call_get", mock_call_get)
 
         mock_http = MagicMock()
         client = DirectoryClient(mock_http, "proj-123")
@@ -365,6 +376,7 @@ class TestResourceClient:
     @pytest.mark.asyncio
     async def test_read(self, monkeypatch):
         """Test read calls correct endpoint."""
+        from basic_memory.mcp.clients import resource as resource_mod
 
         mock_response = MagicMock()
         mock_response.text = "# Note content"
@@ -373,7 +385,7 @@ class TestResourceClient:
             assert "/v2/projects/proj-123/resource/entity-123" in url
             return mock_response
 
-        monkeypatch.setattr("basic_memory.mcp.tools.utils.call_get", mock_call_get)
+        monkeypatch.setattr(resource_mod, "call_get", mock_call_get)
 
         mock_http = MagicMock()
         client = ResourceClient(mock_http, "proj-123")
@@ -393,6 +405,7 @@ class TestProjectClient:
     @pytest.mark.asyncio
     async def test_list_projects(self, monkeypatch):
         """Test list_projects calls correct endpoint."""
+        from basic_memory.mcp.clients import project as project_mod
 
         mock_response = MagicMock()
         mock_response.json.return_value = {
@@ -412,7 +425,7 @@ class TestProjectClient:
             assert "/v2/projects" in url
             return mock_response
 
-        monkeypatch.setattr("basic_memory.mcp.tools.utils.call_get", mock_call_get)
+        monkeypatch.setattr(project_mod, "call_get", mock_call_get)
 
         mock_http = MagicMock()
         client = ProjectClient(mock_http)

tests/mcp/test_async_client_modes.py

@@ -618,42 +618,3 @@ async def test_get_cloud_control_plane_client_raises_without_credentials(config_
     with pytest.raises(RuntimeError, match="Cloud routing requested but no credentials found"):
         async with get_cloud_control_plane_client():
             pass
-
-
-@pytest.mark.asyncio
-async def test_get_client_workspace_selector_routes_to_cloud(config_manager):
-    """A bare workspace selector routes to the cloud proxy, not local ASGI (#954).
-
-    This is the create_memory_project(workspace=...) path on a local MCP
-    server: no factory, no explicit flags, no project_name — the selector
-    alone must imply cloud routing.
-    """
-    cfg = config_manager.load_config()
-    cfg.cloud_host = "https://cloud.example.test"
-    cfg.cloud_api_key = "bmc_test_key_123"
-    config_manager.save_config(cfg)
-
-    async with get_client(workspace="tenant-123") as client:
-        assert str(client.base_url).rstrip("/") == "https://cloud.example.test/proxy"
-        assert client.headers.get("X-Workspace-ID") == "tenant-123"
-
-
-@pytest.mark.asyncio
-async def test_get_client_workspace_selector_without_credentials_fails_fast(
-    config_manager, monkeypatch
-):
-    """No credentials + workspace selector must raise, never fall back to local (#954).
-
-    The silent local fallback was the bug: a cloud project create either
-    failed on a cloud-style path or silently created a local project.
-    """
-    cfg = config_manager.load_config()
-    cfg.cloud_host = "https://cloud.example.test"
-    cfg.cloud_api_key = None
-    cfg.cloud_client_id = "cid"
-    cfg.cloud_domain = "https://auth.example.test"
-    config_manager.save_config(cfg)
-
-    with pytest.raises(RuntimeError, match="cloud workspace was requested"):
-        async with get_client(workspace="team-slug"):
-            pass

tests/mcp/test_client_schema.py

@@ -63,7 +63,7 @@ class TestSchemaClientValidate:
             assert kwargs.get("params") == {}
             return mock_response
 
-        monkeypatch.setattr("basic_memory.mcp.tools.utils.call_post", mock_call_post)
+        monkeypatch.setattr("basic_memory.mcp.clients.schema.call_post", mock_call_post)
 
         result = await schema_client.validate()
         assert isinstance(result, ValidationReport)
@@ -88,7 +88,7 @@ class TestSchemaClientValidate:
             assert kwargs["params"]["note_type"] == "person"
             return mock_response
 
-        monkeypatch.setattr("basic_memory.mcp.tools.utils.call_post", mock_call_post)
+        monkeypatch.setattr("basic_memory.mcp.clients.schema.call_post", mock_call_post)
 
         result = await schema_client.validate(note_type="person")
         assert result.note_type == "person"
@@ -113,7 +113,7 @@ class TestSchemaClientValidate:
             assert kwargs["params"]["identifier"] == "people/alice"
             return mock_response
 
-        monkeypatch.setattr("basic_memory.mcp.tools.utils.call_post", mock_call_post)
+        monkeypatch.setattr("basic_memory.mcp.clients.schema.call_post", mock_call_post)
 
         result = await schema_client.validate(identifier="people/alice")
         assert result.total_notes == 1
@@ -144,7 +144,7 @@ class TestSchemaClientInfer:
             assert kwargs["params"]["threshold"] == 0.25
             return mock_response
 
-        monkeypatch.setattr("basic_memory.mcp.tools.utils.call_post", mock_call_post)
+        monkeypatch.setattr("basic_memory.mcp.clients.schema.call_post", mock_call_post)
 
         result = await schema_client.infer("person")
         assert isinstance(result, InferenceReport)
@@ -171,7 +171,7 @@ class TestSchemaClientInfer:
             assert kwargs["params"]["threshold"] == 0.5
             return mock_response
 
-        monkeypatch.setattr("basic_memory.mcp.tools.utils.call_post", mock_call_post)
+        monkeypatch.setattr("basic_memory.mcp.clients.schema.call_post", mock_call_post)
 
         result = await schema_client.infer("meeting", threshold=0.5)
         assert result.note_type == "meeting"
@@ -197,7 +197,7 @@ class TestSchemaClientDiff:
             assert url == "/v2/projects/test-project-id/schema/diff/person"
             return mock_response
 
-        monkeypatch.setattr("basic_memory.mcp.tools.utils.call_get", mock_call_get)
+        monkeypatch.setattr("basic_memory.mcp.clients.schema.call_get", mock_call_get)
 
         result = await schema_client.diff("person")
         assert isinstance(result, DriftReport)
@@ -235,7 +235,7 @@ class TestSchemaClientDiff:
         async def mock_call_get(client, url, **kwargs):
             return mock_response
 
-        monkeypatch.setattr("basic_memory.mcp.tools.utils.call_get", mock_call_get)
+        monkeypatch.setattr("basic_memory.mcp.clients.schema.call_get", mock_call_get)
 
         result = await schema_client.diff("person")
         assert len(result.new_fields) == 1

tests/mcp/test_project_context.py

@@ -679,7 +679,7 @@ async def test_resolve_workspace_project_identifier_handles_qualified_and_collis
     )
     index = _build_workspace_project_index((personal, acme), entries)
 
-    async def fake_index(context=None, force_refresh=False):
+    async def fake_index(context=None):
         return index
 
     monkeypatch.setattr(project_context, "_ensure_workspace_project_index", fake_index)
@@ -694,170 +694,6 @@ async def test_resolve_workspace_project_identifier_handles_qualified_and_collis
     assert resolved.project.external_id == "personal-project-id"
 
 
-def _patch_index(monkeypatch, workspaces, entries):
-    """Install a fake workspace/project index for resolver tests."""
-    import basic_memory.mcp.project_context as project_context
-    from basic_memory.mcp.project_context import _build_workspace_project_index
-
-    index = _build_workspace_project_index(workspaces, entries)
-
-    async def fake_index(context=None, force_refresh=False):
-        return index
-
-    monkeypatch.setattr(project_context, "_ensure_workspace_project_index", fake_index)
-
-
-@pytest.mark.asyncio
-async def test_resolve_workspace_identifier_by_slug_tenant_id_and_name(monkeypatch):
-    """Qualified routes resolve the workspace segment by slug, tenant_id, or display name."""
-    from basic_memory.mcp.project_context import (
-        WorkspaceProjectEntry,
-        resolve_workspace_project_identifier,
-    )
-
-    acme = _workspace(
-        tenant_id="acme-tenant-uuid",
-        workspace_type="organization",
-        slug="acme-slug",
-        name="Acme Corp",
-        role="editor",
-    )
-    entries = (
-        WorkspaceProjectEntry(
-            workspace=acme,
-            project=_project("Meeting Notes", id=1, external_id="acme-project-id"),
-        ),
-    )
-    _patch_index(monkeypatch, (acme,), entries)
-
-    # slug (existing behavior, stays green)
-    by_slug = await resolve_workspace_project_identifier("acme-slug/meeting-notes")
-    assert by_slug.project.external_id == "acme-project-id"
-
-    # tenant_id (exact, opaque id)
-    by_tenant = await resolve_workspace_project_identifier("acme-tenant-uuid/meeting-notes")
-    assert by_tenant.project.external_id == "acme-project-id"
-
-    # display name, case-insensitive
-    by_name = await resolve_workspace_project_identifier("ACME corp/meeting-notes")
-    assert by_name.project.external_id == "acme-project-id"
-
-
-@pytest.mark.asyncio
-async def test_resolve_workspace_identifier_ambiguous_name_lists_candidates(monkeypatch):
-    """A display name shared by multiple workspaces fails fast naming the candidate slugs."""
-    from basic_memory.mcp.project_context import (
-        WorkspaceProjectEntry,
-        resolve_workspace_project_identifier,
-    )
-
-    alpha = _workspace(
-        tenant_id="alpha-tenant",
-        workspace_type="organization",
-        slug="research-alpha",
-        name="Research",
-        role="editor",
-    )
-    beta = _workspace(
-        tenant_id="beta-tenant",
-        workspace_type="organization",
-        slug="research-beta",
-        name="Research",
-        role="editor",
-    )
-    entries = (
-        WorkspaceProjectEntry(
-            workspace=alpha,
-            project=_project("Notes", id=1, external_id="alpha-project-id"),
-        ),
-        WorkspaceProjectEntry(
-            workspace=beta,
-            project=_project("Notes", id=2, external_id="beta-project-id"),
-        ),
-    )
-    _patch_index(monkeypatch, (alpha, beta), entries)
-
-    with pytest.raises(ValueError) as exc_info:
-        await resolve_workspace_project_identifier("Research/notes")
-
-    message = str(exc_info.value)
-    assert "matched multiple workspaces" in message
-    assert "research-alpha" in message
-    assert "research-beta" in message
-    assert "slug or tenant_id" in message
-
-
-@pytest.mark.asyncio
-async def test_resolve_workspace_identifier_unknown_lists_tried_forms(monkeypatch):
-    """An unknown workspace identifier reports the slug/tenant_id/name forms that were tried."""
-    from basic_memory.mcp.project_context import (
-        WorkspaceProjectEntry,
-        resolve_workspace_project_identifier,
-    )
-
-    acme = _workspace(
-        tenant_id="acme-tenant",
-        workspace_type="organization",
-        slug="acme",
-        name="Acme",
-        role="editor",
-    )
-    entries = (
-        WorkspaceProjectEntry(
-            workspace=acme,
-            project=_project("Notes", id=1, external_id="acme-project-id"),
-        ),
-    )
-    _patch_index(monkeypatch, (acme,), entries)
-
-    with pytest.raises(ValueError) as exc_info:
-        await resolve_workspace_project_identifier("nonexistent/notes")
-
-    message = str(exc_info.value)
-    assert "was not found by slug, tenant_id, or name" in message
-    assert "acme" in message
-
-
-@pytest.mark.asyncio
-async def test_resolve_workspace_identifier_slug_wins_over_name_collision(monkeypatch):
-    """A name that equals another workspace's slug resolves to the slug owner."""
-    from basic_memory.mcp.project_context import (
-        WorkspaceProjectEntry,
-        resolve_workspace_project_identifier,
-    )
-
-    # slug_owner.slug == "shared"; name_owner.name == "shared" — the slug owner must win.
-    slug_owner = _workspace(
-        tenant_id="slug-owner-tenant",
-        workspace_type="organization",
-        slug="shared",
-        name="Slug Owner",
-        role="editor",
-    )
-    name_owner = _workspace(
-        tenant_id="name-owner-tenant",
-        workspace_type="organization",
-        slug="name-owner-slug",
-        name="shared",
-        role="editor",
-    )
-    entries = (
-        WorkspaceProjectEntry(
-            workspace=slug_owner,
-            project=_project("Notes", id=1, external_id="slug-owner-project-id"),
-        ),
-        WorkspaceProjectEntry(
-            workspace=name_owner,
-            project=_project("Notes", id=2, external_id="name-owner-project-id"),
-        ),
-    )
-    _patch_index(monkeypatch, (slug_owner, name_owner), entries)
-
-    resolved = await resolve_workspace_project_identifier("shared/notes")
-    assert resolved.workspace.slug == "shared"
-    assert resolved.project.external_id == "slug-owner-project-id"
-
-
 @pytest.mark.asyncio
 async def test_detect_project_from_memory_url_prefix_resolves_workspace_slug(monkeypatch):
     import basic_memory.mcp.project_context as project_context
@@ -895,7 +731,7 @@ async def test_detect_project_from_memory_url_prefix_resolves_workspace_slug(mon
     )
     index = _build_workspace_project_index((personal, team), entries)
 
-    async def fake_index(context=None, force_refresh=False):
+    async def fake_index(context=None):
         return index
 
     monkeypatch.setattr(project_context, "_ensure_workspace_project_index", fake_index)
@@ -1026,7 +862,7 @@ async def test_detect_project_from_identifier_prefix_resolves_workspace_with_loc
         ),
     )
 
-    async def fake_index(context=None, force_refresh=False):
+    async def fake_index(context=None):
         return index
 
     monkeypatch.setattr(project_context, "_ensure_workspace_project_index", fake_index)
@@ -1081,7 +917,7 @@ async def test_resolve_workspace_qualified_memory_url_ignores_workspace_project_
     )
     index = _build_workspace_project_index((workspace,), entries)
 
-    async def fake_index(context=None, force_refresh=False):
+    async def fake_index(context=None):
         return index
 
     monkeypatch.setattr(project_context, "_ensure_workspace_project_index", fake_index)
@@ -1121,7 +957,7 @@ async def test_resolve_workspace_qualified_memory_url_fails_on_duplicate_project
     )
     index = _build_workspace_project_index((team,), entries)
 
-    async def fake_index(context=None, force_refresh=False):
+    async def fake_index(context=None):
         return index
 
     monkeypatch.setattr(project_context, "_ensure_workspace_project_index", fake_index)
@@ -1162,7 +998,7 @@ async def test_resolve_workspace_qualified_memory_url_uses_personal_canonical_pa
     )
     index = _build_workspace_project_index((personal,), entries)
 
-    async def fake_index(context=None, force_refresh=False):
+    async def fake_index(context=None):
         return index
 
     monkeypatch.setattr(project_context, "_ensure_workspace_project_index", fake_index)
@@ -1204,7 +1040,7 @@ async def test_resolve_workspace_qualified_memory_url_keeps_org_canonical_path_w
     )
     index = _build_workspace_project_index((team,), entries)
 
-    async def fake_index(context=None, force_refresh=False):
+    async def fake_index(context=None):
         return index
 
     monkeypatch.setattr(project_context, "_ensure_workspace_project_index", fake_index)
@@ -1318,7 +1154,7 @@ async def test_resolve_workspace_project_identifier_uses_active_workspace_for_du
     )
     index = _build_workspace_project_index((personal, acme), entries)
 
-    async def fake_index(context=None, force_refresh=False):
+    async def fake_index(context=None):
         return index
 
     monkeypatch.setattr(project_context, "_ensure_workspace_project_index", fake_index)
@@ -1374,7 +1210,7 @@ async def test_resolve_workspace_project_identifier_resolves_by_external_id(monk
     )
     index = _build_workspace_project_index((personal, acme), entries)
 
-    async def fake_index(context=None, force_refresh=False):
+    async def fake_index(context=None):
         return index
 
     monkeypatch.setattr(project_context, "_ensure_workspace_project_index", fake_index)
@@ -1411,7 +1247,7 @@ async def test_resolve_workspace_project_identifier_normalizes_uuid_forms(monkey
     )
     index = _build_workspace_project_index((workspace,), entries)
 
-    async def fake_index(context=None, force_refresh=False):
+    async def fake_index(context=None):
         return index
 
     monkeypatch.setattr(project_context, "_ensure_workspace_project_index", fake_index)
@@ -1666,7 +1502,7 @@ async def test_get_project_client_with_cloud_project_id_routes_to_workspace_with
         (WorkspaceProjectEntry(workspace=personal, project=cloud_project),),
     )
 
-    async def fake_index(context=None, force_refresh=False):
+    async def fake_index(context=None):
         return index
 
     get_client_calls: list[dict[str, str | None]] = []
@@ -3153,142 +2989,3 @@ class TestGetProjectClientRoutingOrder:
         finally:
             # Restore original factory to avoid polluting other tests
             async_client._client_factory = original_factory
-
-
-@pytest.mark.asyncio
-async def test_resolver_refreshes_index_on_miss(monkeypatch):
-    """A stale index miss triggers one rebuild and the retry resolves (#956).
-
-    Mirrors the field failure: a teammate (or the CLI) creates a project after
-    the session index was built; project_id routing must find it without a
-    session restart.
-    """
-    import basic_memory.mcp.project_context as project_context
-    from basic_memory.mcp.project_context import (
-        WorkspaceProjectEntry,
-        WorkspaceProjectLookupMiss,
-        _build_workspace_project_index,
-        resolve_workspace_project_identifier,
-    )
-
-    team = _workspace(
-        tenant_id="team-tenant",
-        workspace_type="organization",
-        slug="team",
-        name="Team",
-        role="owner",
-        is_default=True,
-    )
-    old_entry = WorkspaceProjectEntry(
-        workspace=team,
-        project=_project("Existing", id=1, external_id="11111111-1111-4111-8111-111111111111"),
-    )
-    new_entry = WorkspaceProjectEntry(
-        workspace=team,
-        project=_project("Manual", id=2, external_id="22222222-2222-4222-8222-222222222222"),
-    )
-    stale = _build_workspace_project_index((team,), (old_entry,))
-    fresh = _build_workspace_project_index((team,), (old_entry, new_entry))
-
-    calls = []
-
-    async def fake_index(context=None, force_refresh=False):
-        calls.append(force_refresh)
-        return fresh if force_refresh else stale
-
-    monkeypatch.setattr(project_context, "_ensure_workspace_project_index", fake_index)
-
-    # By external_id (the project_id routing path that failed in the field)
-    resolved = await resolve_workspace_project_identifier(
-        "22222222-2222-4222-8222-222222222222"
-    )
-    assert resolved.project.permalink == "manual"
-    assert calls == [False, True]
-
-    # By name, same refresh-and-retry
-    calls.clear()
-    resolved = await resolve_workspace_project_identifier("manual")
-    assert resolved.project.permalink == "manual"
-    assert calls == [False, True]
-
-    # A project absent from the fresh index too: exactly one refresh, then the
-    # authoritative miss propagates
-    calls.clear()
-    with pytest.raises(WorkspaceProjectLookupMiss):
-        await resolve_workspace_project_identifier("never-existed")
-    assert calls == [False, True]
-
-    # A hit on the cached index never triggers a rebuild
-    calls.clear()
-    resolved = await resolve_workspace_project_identifier("existing")
-    assert resolved.project.permalink == "existing"
-    assert calls == [False]
-
-
-@pytest.mark.asyncio
-async def test_resolve_project_and_path_keeps_patterns_project_qualified(
-    config_manager,
-    monkeypatch,
-):
-    """Glob patterns are qualified with the project prefix only, never the workspace (#957).
-
-    The search index stores project-qualified permalinks (manual/man3/...), so a
-    workspace-qualified pattern (<ws>/manual/man3*) can never match anything.
-    Direct URLs keep workspace qualification (the link resolver handles them);
-    patterns have no resolver fallback and must match the index form.
-    """
-    from mcp.server.fastmcp.exceptions import ToolError
-
-    from basic_memory.mcp.project_context import resolve_project_and_path
-    from basic_memory.schemas.project_info import ProjectItem
-
-    config = config_manager.load_config()
-    config.permalinks_include_project = True
-    config_manager.save_config(config)
-
-    context = ContextState()
-    cached_project = ProjectItem(
-        id=1,
-        external_id="11111111-1111-1111-1111-111111111111",
-        name="manual",
-        path="/tmp/manual",
-        is_default=False,
-    )
-    team_workspace = _workspace(
-        tenant_id="team-tenant",
-        workspace_type="organization",
-        slug="team-paul",
-        name="Team Paul",
-        role="editor",
-    )
-    await context.set_state("active_project", cached_project.model_dump())
-    await context.set_state("active_workspace", team_workspace.model_dump())
-
-    async def fake_call_post(*args, **kwargs):
-        raise ToolError("project not found")
-
-    monkeypatch.setattr("basic_memory.mcp.tools.utils.call_post", fake_call_post)
-
-    # Bare pattern: project prefix only — no workspace slug
-    _, resolved_path, _ = await resolve_project_and_path(
-        client=cast(Any, None),
-        identifier="memory://man3/*",
-        context=ctx(context),
-    )
-    assert resolved_path == "manual/man3/*"
-
-    # Workspace-qualified pattern URL: workspace stripped down to index form
-    _, resolved_path, _ = await resolve_project_and_path(
-        client=cast(Any, None),
-        identifier="memory://team-paul/manual/man3/*",
-        context=ctx(context),
-    )
-    assert resolved_path == "manual/man3/*"
-
-    # Direct URLs keep the full workspace-qualified canonical path
-    _, resolved_path, _ = await resolve_project_and_path(
-        client=cast(Any, None),
-        identifier="memory://man3/write-note-3",
-        context=ctx(context),
-    )
-    assert resolved_path == "team-paul/manual/man3/write-note-3"

tests/mcp/test_tool_build_context.py

@@ -254,53 +254,3 @@ async def test_build_context_markdown_not_found(client, test_project):
     assert isinstance(result, str)
     assert "No results found" in result
     assert test_project.name in result
-
-
-def test_format_entity_block_renders_unresolved_relations_by_name():
-    """Unresolved forward references render their target text, not [[None]] (#955)."""
-    from datetime import UTC, datetime
-
-    from basic_memory.mcp.tools.build_context import _format_entity_block
-    from basic_memory.schemas.memory import (
-        ContextResult,
-        EntitySummary,
-        RelationSummary,
-    )
-
-    now = datetime.now(UTC)
-    page = EntitySummary(
-        external_id="entity-1",
-        entity_id=1,
-        title="write-note(3)",
-        permalink="man3/write-note-3",
-        content="# write-note(3)",
-        file_path="man3/write-note-3.md",
-        created_at=now,
-    )
-    unresolved = RelationSummary(
-        title="see_also: edit-note(3)",
-        file_path="man3/write-note-3.md",
-        permalink="man3/write-note-3/see-also/edit-note-3",
-        relation_type="see_also",
-        from_entity="write-note(3)",
-        to_entity=None,
-        to_name="edit-note(3)",
-        created_at=now,
-    )
-    resolved = RelationSummary(
-        title="see_also: bm-note(5)",
-        file_path="man3/write-note-3.md",
-        permalink="man3/write-note-3/see-also/bm-note-5",
-        relation_type="see_also",
-        from_entity="write-note(3)",
-        to_entity="bm-note(5)",
-        to_name="bm-note(5)",
-        created_at=now,
-    )
-    block = _format_entity_block(
-        ContextResult(primary_result=page, observations=[], related_results=[unresolved, resolved])
-    )
-
-    assert "- see_also [[edit-note(3)]]" in block
-    assert "- see_also [[bm-note(5)]]" in block
-    assert "[[None]]" not in block