chore: update version to 0.21.1 for v0.21.1 release

CI-only point release to validate #833's inline Homebrew bump end-to-end
on a real tag push.

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

.github/workflows/release.yml

@@ -63,25 +63,63 @@ jobs:
     # Only run for stable releases (not dev, beta, or rc versions)
     if: ${{ !contains(github.ref_name, 'dev') && !contains(github.ref_name, 'b') && !contains(github.ref_name, 'rc') }}
     permissions:
-      contents: write
-      actions: read
+      contents: read
     steps:
+      # Inline bump replaces mislav/bump-homebrew-formula-action@v4.x.
+      # The action does a HEAD request to api.github.com /repos/.../tarball/<ref>
+      # with the bearer token and expects a 302 redirect. GitHub now returns
+      # 303 on that endpoint when authenticated, which the action treats as a
+      # fatal error. Re-implementing the bump as plain git+sed keeps the same
+      # contract (update url + sha256, commit, push) with no third-party action.
       - name: Update Homebrew formula
-        uses: mislav/bump-homebrew-formula-action@v4.1
-        with:
-          # Formula name in homebrew-basic-memory repo
-          formula-name: basic-memory
-          # The tap repository
-          homebrew-tap: basicmachines-co/homebrew-basic-memory
-          # Base branch of the tap repository
-          base-branch: main
-          # Download URL will be automatically constructed from the tag
-          download-url: https://github.com/basicmachines-co/basic-memory/archive/refs/tags/${{ github.ref_name }}.tar.gz
-          # Commit message for the formula update
-          commit-message: |
-            {{formulaName}} {{version}}
-
-            Created by https://github.com/basicmachines-co/basic-memory/actions/runs/${{ github.run_id }}
         env:
-          # Personal Access Token with repo scope for homebrew-basic-memory repo
-          COMMITTER_TOKEN: ${{ secrets.HOMEBREW_TOKEN }}
+          HOMEBREW_TOKEN: ${{ secrets.HOMEBREW_TOKEN }}
+          REF: ${{ github.ref_name }}
+          REPO: ${{ github.repository }}
+          RUN_URL: https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}
+        run: |
+          set -euo pipefail
+
+          VERSION="${REF#v}"
+          ARCHIVE_URL="https://github.com/${REPO}/archive/refs/tags/${REF}.tar.gz"
+
+          echo "::group::Compute tarball sha256"
+          SHA256="$(curl --fail --silent --location "$ARCHIVE_URL" | sha256sum | awk '{print $1}')"
+          test -n "$SHA256"
+          echo "sha256: $SHA256"
+          echo "::endgroup::"
+
+          echo "::group::Clone tap"
+          git clone \
+            --depth 1 \
+            "https://x-access-token:${HOMEBREW_TOKEN}@github.com/basicmachines-co/homebrew-basic-memory.git" \
+            tap
+          cd tap
+          git config user.name "github-actions[bot]"
+          git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          echo "::endgroup::"
+
+          echo "::group::Patch Formula/basic-memory.rb"
+          # Pipe-delimited sed because the URL contains slashes. The Formula
+          # only has one `url` and one `sha256` directive, so a first-match
+          # replacement is unambiguous. POSIX character classes ([[:space:]])
+          # keep this portable across BSD and GNU sed.
+          sed -i -E \
+            -e "s|^([[:space:]]*url[[:space:]]+)\"[^\"]+\"|\1\"${ARCHIVE_URL}\"|" \
+            -e "s|^([[:space:]]*sha256[[:space:]]+)\"[^\"]+\"|\1\"${SHA256}\"|" \
+            Formula/basic-memory.rb
+          git --no-pager diff Formula/basic-memory.rb
+          echo "::endgroup::"
+
+          if git diff --quiet Formula/basic-memory.rb; then
+            echo "Formula already at ${REF}; nothing to do."
+            exit 0
+          fi
+
+          echo "::group::Commit & push"
+          git add Formula/basic-memory.rb
+          git commit -m "basic-memory ${VERSION}
+
+          Created by ${RUN_URL}"
+          git push origin HEAD:main
+          echo "::endgroup::"

CHANGELOG.md

@@ -1,6 +1,24 @@
 # CHANGELOG
 
-## Unreleased
+## v0.21.1 (2026-05-16)
+
+CI-only release. No user-facing changes.
+
+### Maintenance
+
+- **#833**: Replace `mislav/bump-homebrew-formula-action` with an inline
+  bash bump step. The action's `resolveRedirect` HEAD-requests
+  `api.github.com /repos/.../tarball/<ref>` expecting HTTP 302; GitHub now
+  returns 303 for authenticated requests on that endpoint, which broke
+  the v0.21.0 Homebrew job and required a manual tap bump. The inline
+  step does the same work (curl + sha256sum, clone tap, sed-bump
+  `url`/`sha256`, commit, push) without any third-party dependency.
+
+## v0.21.0 (2026-05-16)
+
+Workspace-aware everywhere: every MCP tool and CLI command now routes through the
+same workspace/project model, the search and sync paths are noticeably faster,
+and a handful of long-standing parsing and routing footguns are gone.
 
 ### Breaking Changes
 
@@ -11,6 +29,109 @@
   - Bare list wikilinks like `- [[Target]]` now index as `links_to`.
   - Prose list items like `- some other thing [[Target]]` now index as `links_to`.
   - To preserve existing multi-word relation types on re-sync, quote them before upgrading.
+  - See **#824**.
+
+### Features
+
+- **#816**: `bm orphan` CLI command surfaces entities whose underlying markdown
+  files are gone, with a flag to clean them out.
+- **#789**: Create projects directly by cloud workspace slug from MCP
+  (`create_memory_project(workspace=...)`).
+- **#757**: Discover projects across every accessible cloud workspace in MCP's
+  project list — no more per-workspace blind spots.
+- **#766**: MCP tools accept training-data-friendly parameter aliases
+  (`q`/`search`/`text` for `query`, etc.) so models reach for them naturally.
+- **#776**: `bm db reset` refuses to run while a `basic-memory mcp` process is
+  alive, so resets can no longer corrupt an open session.
+- **#791**: Search responses include result totals so pagers can stop guessing.
+- **#719**: Cloud `note_content` tenant schema primitive lands on the backend.
+- **#715**: `bm project add` accepts a `--visibility` flag for cloud projects.
+
+### Bug Fixes
+
+#### Search and recent activity
+- **#832**: SQLite project deletion now sweeps `search_index`,
+  `search_vector_chunks`, and `search_vector_embeddings`, so a project that
+  reuses a recycled auto-increment id can't inherit the previous tenant's content.
+- **#812**: `recent_activity` orders and filters by `updated_at`, so edits bubble
+  to the top instead of staying pinned to creation time.
+- **#807**: Multi-project `search_notes` is opt-in (`search_all_projects=True`);
+  default search stays scoped to the resolved project.
+- **#785**: `recent_activity` caps responses and emits an explicit truncation
+  footer instead of silently dropping rows.
+- **#713**: Eliminated an N+1 query in search result hydration.
+
+#### Workspace / project routing
+- **#822**: `bm project list` now includes projects from every workspace, not
+  just the current one.
+- **#813**, **#808**, **#806**, **#803**, **#801**, **#795**, **#790**, **#778**,
+  **#777**, **#722**, **#712**, **#704**: Workspace-qualified permalink routing
+  is centralized and applied consistently across `edit_note`, `delete_project`,
+  `build_context`, `memory://` URLs, factory-mode project listing, cloud uploads,
+  and the API client.
+
+#### Sync
+- **#827**: `rclone bisync` filters from `.bmignore` are preserved across syncs.
+- **#815**: Watch service ignores hidden paths relative to the watched project,
+  not just relative to `$HOME`.
+- **#814**: `scan` subprocesses no longer go through the shell, avoiding quoting
+  issues with paths that contain special characters.
+- **#759**: Watch service stays inside `--project` scope.
+- **#746**: Canonical markdown is preserved during single-file sync.
+
+#### Parsing
+- **#796**: Picoschema modifier descriptions (`field?(modifier, description)`)
+  parse correctly.
+- **#769**: Obsidian callout blocks are skipped by the observation parser
+  instead of being mis-extracted as observations.
+
+#### CLI
+- **#775**: `bm project set-cloud` / `set-local` cleans up local DB state for
+  the affected project.
+- **#773**: `bm cloud logout` clears `default_workspace`.
+- **#780**: `bm cloud setup` hint points at `bm cloud sync-setup`.
+- **#734**: `bm project info` shows cloud index freshness.
+- **#718**: Private cloud projects display under their `display_name` instead of
+  raw UUID.
+- **#768**: `read_note` / `view_note` drop no-op pagination params from their
+  signatures.
+
+#### Stability
+- **#774**: `sqlite-vec` failures during init degrade gracefully to keyword-only
+  search instead of crashing startup.
+- **#733**: Delete-vector and cloud-sync cleanup is now consistent.
+- **#702**: Race conditions in concurrent `delete_entity` are resolved.
+- **#724**: `external_id` is preserved when entities are re-upserted during a
+  re-index.
+- **#728**: Vector init no longer issues runtime `ALTER TABLE`.
+- **#744**: `BASIC_MEMORY_CONFIG_DIR` is honored across remaining call sites.
+- **#743**: FastEmbed cache lives under the data dir instead of `/tmp`.
+- **#752**: Cloud projects report `source=cloud` in factory mode.
+- Stripped null bytes from markdown content before DB insert.
+- Allowed long `relation_type` values in API responses.
+
+#### Installer
+- **#772**: Docker-compose config volume mounts under the `appuser` home.
+- **#695**: Bumped `brew outdated` timeout from 15s to 60s.
+
+### Performance
+
+- **#828**: CLI startup no longer pulls in the local ASGI FastAPI app when it
+  isn't needed.
+- **#751**, **#726**, **#717**, **#714**, single-file/batch indexing: marked
+  speedups on the sync hot path; unchanged markdown is skipped entirely.
+- **#731**, **#723**: Vector sync is faster on both backends, with tuned
+  fastembed defaults.
+
+### Maintenance
+
+- **#825**: Dependency refresh + security hardening.
+- Updated to `fastmcp` 3.3.1.
+- **#754**: Removed in-house telemetry wrappers in favor of direct `logfire`
+  usage.
+- **#736**: `ty` is now the default typechecker.
+- **#771**, **#770**, **#716**: New regression guards for vector-row cleanup,
+  long relation types, and recent activity hydration.
 
 ## v0.20.3 (2026-03-26)
 

server.json

@@ -6,12 +6,12 @@
     "url": "https://github.com/basicmachines-co/basic-memory.git",
     "source": "github"
   },
-  "version": "0.20.3",
+  "version": "0.21.1",
   "packages": [
     {
       "registryType": "pypi",
       "identifier": "basic-memory",
-      "version": "0.20.3",
+      "version": "0.21.1",
       "runtimeHint": "uvx",
       "runtimeArguments": [
         {"type": "positional", "value": "basic-memory"},

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__ = "0.20.3"
+__version__ = "0.21.1"
 
 # API version for FastAPI - independent of package version
 __api_version__ = "v0"

src/basic_memory/alembic/versions/n7i8j9k0l1m2_cleanup_sqlite_search_orphans.py

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

src/basic_memory/mcp/tools/search.py

@@ -10,8 +10,13 @@ from loguru import logger
 from fastmcp import Context
 from pydantic import AliasChoices, BeforeValidator, Field
 
-from basic_memory.config import ConfigManager
+from basic_memory.config import ConfigManager, has_cloud_credentials
 from basic_memory.utils import build_canonical_permalink, coerce_dict, coerce_list
+from basic_memory.mcp.async_client import (
+    _explicit_routing,
+    _force_local_mode,
+    is_factory_mode,
+)
 from basic_memory.mcp.container import get_container
 from basic_memory.mcp.project_context import (
     detect_project_from_identifier_prefix,
@@ -479,12 +484,30 @@ async def _search_all_projects(
     total = 0
     any_project_has_more = False
 
+    # Trigger: caller asked for an account-wide search.
+    # Why: project_id (external UUID) routes through the cloud v2 API path,
+    #      which 401s on local installs because there's no JWT to present.
+    #      Project names route through the local-ASGI path and work for both
+    #      backends — cloud disambiguates names via the workspace/project
+    #      qualified_name already baked into project_ref["project"].
+    # Outcome: forward project_id only when the same signals get_project_client
+    #          uses to pick a cloud route are present. Mirrors the cloud_available
+    #          composite in project_context.get_project_client (single source of
+    #          truth for "can we route to cloud?").
+    config = ConfigManager().config
+    use_cloud_routing = (
+        is_factory_mode()
+        or (_explicit_routing() and not _force_local_mode())
+        or has_cloud_credentials(config)
+    )
+
     for project_ref in project_refs:
+        recursive_project_id = project_ref["project_id"] if use_cloud_routing else None
         try:
             results = await search_notes(
                 query=query,
                 project=project_ref["project"],
-                project_id=project_ref["project_id"],
+                project_id=recursive_project_id,
                 page=1,
                 page_size=per_project_page_size,
                 search_type=search_type,

src/basic_memory/repository/project_repository.py

@@ -4,7 +4,9 @@ from pathlib import Path
 from typing import Optional, Sequence, Union
 
 
-from sqlalchemy import text
+from loguru import logger
+from sqlalchemy import inspect as sa_inspect, select, text
+from sqlalchemy.exc import NoResultFound, OperationalError
 from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker
 
 from basic_memory import db
@@ -12,6 +14,65 @@ from basic_memory.models.project import Project
 from basic_memory.repository.repository import Repository
 
 
+async def _load_sqlite_vec_on_session(session) -> bool:
+    """Ensure the sqlite-vec extension is loaded on this session's connection.
+
+    Returns True when vec0 is available after the call. Returns False when the
+    extension can't be loaded on this Python build (e.g., python.org macOS or
+    Windows interpreters without `enable_load_extension`) — every connection in
+    the pool shares the same interpreter, so a False here also means no
+    embedding row could ever have been written, and skipping the embeddings
+    purge is safe.
+
+    Mirrors SQLiteSearchRepository._ensure_sqlite_vec_loaded but as a free
+    function: we don't have a SearchRepository instance during project delete,
+    and the per-connection nature of extension loading means a pooled connection
+    routed to this session might not have vec loaded even when other
+    connections wrote embeddings.
+    """
+    try:
+        await session.execute(text("SELECT vec_version()"))
+        return True
+    except OperationalError:
+        pass
+
+    try:
+        import sqlite_vec  # type: ignore[import-not-found]
+    except ImportError:
+        logger.debug("sqlite-vec package not installed; skipping vec purge")
+        return False
+
+    async_connection = await session.connection()
+    raw_connection = await async_connection.get_raw_connection()
+    driver_connection = raw_connection.driver_connection
+
+    if not hasattr(driver_connection, "enable_load_extension"):
+        # Trigger: CPython build without sqlite extension support (#711).
+        # Why: load_extension is unavailable, so no connection in this pool
+        #      can host vec0. No embeddings exist anywhere.
+        # Outcome: skip the embeddings purge entirely.
+        logger.debug(
+            "Skipping search_vector_embeddings purge: this Python build does "
+            "not support SQLite extension loading"
+        )
+        return False
+
+    try:
+        await driver_connection.enable_load_extension(True)
+        await driver_connection.load_extension(sqlite_vec.loadable_path())
+        await driver_connection.enable_load_extension(False)
+        await session.execute(text("SELECT vec_version()"))
+    except Exception as exc:
+        logger.warning(
+            "Failed to load sqlite-vec for project delete cleanup; "
+            "skipping embeddings purge: {}",
+            exc,
+        )
+        return False
+
+    return True
+
+
 class ProjectRepository(Repository[Project]):
     """Repository for Project model.
 
@@ -121,6 +182,83 @@ class ProjectRepository(Repository[Project]):
                 return target_project
             return None  # pragma: no cover
 
+    async def delete(self, entity_id: int) -> bool:
+        """Delete a project and its derived search rows in one transaction.
+
+        The cascade picture differs by backend:
+
+        - search_index → project: Postgres has ON DELETE CASCADE FK; SQLite
+          stores search_index as an FTS5 virtual table and can't carry FKs,
+          so it needs explicit cleanup.
+        - search_vector_chunks → project: neither backend has an FK here, so
+          both need an explicit DELETE.
+        - search_vector_embeddings → search_vector_chunks: Postgres has an FK
+          (chunk_id REFERENCES … ON DELETE CASCADE); SQLite stores embeddings
+          in a vec0 virtual table keyed by rowid with no cascade. On SQLite
+          the embeddings must be purged before the chunk rows, otherwise
+          `_run_vector_query` keeps returning stale vectors that crowd out
+          live results.
+
+        Each derived table is created lazily (search_index by
+        SearchRepository.init_search_index, the vector tables once semantic
+        search initializes), so any of them may be absent on minimal test DBs.
+        Inspect the connection once and skip whichever is missing.
+        """
+        logger.debug(f"Deleting Project and search rows for project_id: {entity_id}")
+        async with db.scoped_session(self.session_maker) as session:
+            try:
+                result = await session.execute(
+                    select(self.Model).filter(self.primary_key == entity_id)
+                )
+                project = result.scalars().one()
+            except NoResultFound:
+                logger.debug(f"No Project found to delete: {entity_id}")
+                return False
+
+            dialect_name = session.bind.dialect.name if session.bind else "sqlite"
+            is_sqlite = dialect_name == "sqlite"
+
+            existing_tables = await session.run_sync(
+                lambda sync_session: set(sa_inspect(sync_session.connection()).get_table_names())
+            )
+
+            # search_index: SQLite has no FK on the FTS5 virtual table; Postgres
+            # cascades from the project FK, so the explicit DELETE is redundant.
+            if is_sqlite and "search_index" in existing_tables:
+                await session.execute(
+                    text("DELETE FROM search_index WHERE project_id = :project_id"),
+                    {"project_id": entity_id},
+                )
+
+            # search_vector_chunks: no FK to project on either backend, so both
+            # backends need this. SQLite must purge vec0 embeddings first
+            # (rowid pseudocolumn — Postgres uses chunk_id and would 500 here);
+            # Postgres' chunk_id FK CASCADE handles its embeddings cleanup when
+            # we delete the chunk rows below.
+            if "search_vector_chunks" in existing_tables:
+                if is_sqlite and "search_vector_embeddings" in existing_tables:
+                    # Extension loading is per-connection. We must load vec0 on
+                    # *this* session before the DELETE; otherwise a different
+                    # pooled connection might have written embeddings that we'd
+                    # silently leave behind.
+                    if await _load_sqlite_vec_on_session(session):
+                        await session.execute(
+                            text(
+                                "DELETE FROM search_vector_embeddings WHERE rowid IN ("
+                                "SELECT id FROM search_vector_chunks "
+                                "WHERE project_id = :project_id)"
+                            ),
+                            {"project_id": entity_id},
+                        )
+                await session.execute(
+                    text("DELETE FROM search_vector_chunks WHERE project_id = :project_id"),
+                    {"project_id": entity_id},
+                )
+
+            await session.delete(project)
+            logger.debug(f"Deleted Project and search rows for project_id: {entity_id}")
+            return True
+
     async def update_path(self, project_id: int, new_path: str) -> Optional[Project]:
         """Update project path.
 

tests/mcp/tools/test_search_notes_multi_project.py

@@ -8,8 +8,38 @@ import pytest
 from basic_memory.schemas.search import SearchItemType, SearchResponse, SearchResult
 
 
+def _stub_routing_mode(monkeypatch, *, cloud: bool) -> None:
+    """Pin the three cloud-route signals search.py reads.
+
+    `_search_all_projects` only forwards project_id (external UUID) when a
+    cloud route is available. The composite mirrors get_project_client:
+    factory mode OR explicit --cloud OR has_cloud_credentials. Tests stub
+    all three so a dev box with OAuth tokens on disk can't bleed into the
+    local-mode case.
+    """
+    search_mod = importlib.import_module("basic_memory.mcp.tools.search")
+    monkeypatch.setattr(search_mod, "is_factory_mode", lambda: False)
+    monkeypatch.setattr(search_mod, "_explicit_routing", lambda: cloud)
+    monkeypatch.setattr(search_mod, "_force_local_mode", lambda: False)
+    monkeypatch.setattr(search_mod, "has_cloud_credentials", lambda config: cloud)
+
+
+@pytest.fixture
+def cloud_routing(monkeypatch):
+    """Force the cloud-routing path for multi-project search tests."""
+    _stub_routing_mode(monkeypatch, cloud=True)
+
+
+@pytest.fixture
+def local_routing(monkeypatch):
+    """Force the local-routing path for multi-project search tests."""
+    _stub_routing_mode(monkeypatch, cloud=False)
+
+
 @pytest.mark.asyncio
-async def test_search_notes_search_all_projects_qualifies_result_permalinks(monkeypatch):
+async def test_search_notes_search_all_projects_qualifies_result_permalinks(
+    monkeypatch, cloud_routing
+):
     """Multi-project search belongs to search_notes and keeps result ids routable."""
     clients_mod = importlib.import_module("basic_memory.mcp.clients")
     search_mod = importlib.import_module("basic_memory.mcp.tools.search")
@@ -169,7 +199,7 @@ async def test_search_notes_search_all_projects_with_no_refs_returns_empty_all_p
 
 @pytest.mark.asyncio
 async def test_search_notes_search_all_projects_continues_after_project_failure(
-    monkeypatch,
+    monkeypatch, cloud_routing
 ):
     """One failing project should not discard successful all-project search results."""
     clients_mod = importlib.import_module("basic_memory.mcp.clients")
@@ -254,3 +284,85 @@ async def test_search_notes_search_all_projects_continues_after_project_failure(
     assert result["total"] == 1
     assert any("team-paul/main" in warning for warning in warnings)
     assert any("team index unavailable" in warning for warning in warnings)
+
+
+@pytest.mark.asyncio
+async def test_search_notes_search_all_projects_local_omits_project_id(
+    monkeypatch, local_routing
+):
+    """Without a cloud route, fan-out must address each project by name only.
+
+    project_id (external UUID) routes through the cloud v2 API path, which
+    returns 401 on local installs because there's no JWT to present. Local
+    fan-out has to fall back to the name-routed path so each per-project
+    search actually returns results instead of silently failing.
+    """
+    clients_mod = importlib.import_module("basic_memory.mcp.clients")
+    search_mod = importlib.import_module("basic_memory.mcp.tools.search")
+
+    project_refs = [
+        {
+            "project": "alpha",
+            "project_id": "11111111-1111-1111-1111-111111111111",
+        },
+        {
+            "project": "beta",
+            "project_id": "22222222-2222-2222-2222-222222222222",
+        },
+    ]
+    searched_projects: list[tuple[str | None, str | None]] = []
+
+    async def fake_load_search_project_refs(context=None):
+        return project_refs
+
+    class StubProject:
+        def __init__(self, name: str | None, external_id: str | None):
+            self.name = name or "main"
+            self.external_id = external_id or "local-main"
+
+    @asynccontextmanager
+    async def fake_get_project_client(project=None, context=None, project_id=None):
+        searched_projects.append((project, project_id))
+        yield object(), StubProject(project, project_id)
+
+    async def fake_resolve_project_and_path(client, identifier, project=None, context=None):
+        return StubProject(project, None), identifier, False
+
+    class MockSearchClient:
+        def __init__(self, client, project_id):
+            self.project_id = project_id
+
+        async def search(self, payload, page, page_size):
+            return SearchResponse(
+                results=[
+                    SearchResult(
+                        title=f"Note in {self.project_id or 'local'}",
+                        permalink="notes/example",
+                        content="",
+                        type=SearchItemType.ENTITY,
+                        score=0.5,
+                        file_path="/notes/example.md",
+                    )
+                ],
+                current_page=page,
+                page_size=page_size,
+                total=1,
+            )
+
+    monkeypatch.setattr(search_mod, "_load_search_project_refs", fake_load_search_project_refs)
+    monkeypatch.setattr(search_mod, "get_project_client", fake_get_project_client)
+    monkeypatch.setattr(search_mod, "resolve_project_and_path", fake_resolve_project_and_path)
+    monkeypatch.setattr(clients_mod, "SearchClient", MockSearchClient)
+
+    result = await search_mod.search_notes(
+        query="anything",
+        search_all_projects=True,
+        output_format="json",
+    )
+
+    assert isinstance(result, dict)
+    assert searched_projects == [("alpha", None), ("beta", None)], (
+        "Local fan-out must omit project_id so the recursive search_notes calls "
+        "take the name-routed path."
+    )
+    assert result["total"] == 2

tests/services/test_project_removal_bug.py

@@ -6,7 +6,9 @@ from datetime import timezone, datetime
 from pathlib import Path
 
 import pytest
+from sqlalchemy import text
 
+from basic_memory import db
 from basic_memory.services.project_service import ProjectService
 
 
@@ -136,3 +138,215 @@ async def test_remove_project_with_related_entities(project_service: ProjectServ
                     project = await project_service.get_project(test_project_name)
                     if project:
                         await project_service.repository.delete(project.id)
+
+
+async def _table_exists(session_maker, table: str) -> bool:
+    """Return True if the named table is present on the current connection."""
+    from sqlalchemy import inspect as sa_inspect
+
+    async with db.scoped_session(session_maker) as session:
+        return await session.run_sync(
+            lambda sync_session: table in sa_inspect(sync_session.connection()).get_table_names()
+        )
+
+
+@pytest.mark.asyncio
+async def test_remove_project_purges_search_rows(project_service: ProjectService):
+    """Project deletion must sweep the derived search tables.
+
+    SQLite stores search_index as an FTS5 virtual table, which cannot carry a
+    foreign key, so without an explicit purge the FTS rows survive the project
+    and leak into the next project that reuses the same auto-increment id.
+    Postgres has the cascade FK, but we expect the same end-state on either
+    backend. This test fails on the pre-fix code: search_index still holds the
+    project's rows after remove_project completes.
+    """
+    test_project_name = f"test-search-cleanup-{os.urandom(4).hex()}"
+    with tempfile.TemporaryDirectory() as temp_dir:
+        test_project_path = str(Path(temp_dir) / "test-search-cleanup")
+        os.makedirs(test_project_path, exist_ok=True)
+
+        await project_service.add_project(test_project_name, test_project_path)
+        project = await project_service.get_project(test_project_name)
+        assert project is not None
+        project_id = project.id
+
+        # Seed both derived tables directly. The bug is in the cleanup path,
+        # not the indexer, so a synthetic row is enough to prove the sweep.
+        async with db.scoped_session(project_service.repository.session_maker) as session:
+            await session.execute(
+                text(
+                    "INSERT INTO search_index "
+                    "(id, title, content_stems, content_snippet, permalink, "
+                    " file_path, type, project_id) "
+                    "VALUES (:id, :title, :stems, :snippet, :permalink, "
+                    " :file_path, :type, :project_id)"
+                ),
+                {
+                    "id": 999_001,
+                    "title": "leak canary",
+                    "stems": "leak canary",
+                    "snippet": "leak canary",
+                    "permalink": f"leak-canary-{project_id}",
+                    "file_path": "leak-canary.md",
+                    "type": "entity",
+                    "project_id": project_id,
+                },
+            )
+            await session.execute(
+                text(
+                    "INSERT INTO search_vector_chunks "
+                    "(entity_id, project_id, chunk_key, chunk_text, source_hash, "
+                    " entity_fingerprint, embedding_model) "
+                    "VALUES (:entity_id, :project_id, :chunk_key, :chunk_text, "
+                    " :source_hash, :entity_fingerprint, :embedding_model)"
+                ),
+                {
+                    "entity_id": 999_001,
+                    "project_id": project_id,
+                    "chunk_key": "canary",
+                    "chunk_text": "leak canary",
+                    "source_hash": "abc",
+                    "entity_fingerprint": "",
+                    "embedding_model": "",
+                },
+            )
+
+        async with db.scoped_session(project_service.repository.session_maker) as session:
+            pre_index = (
+                await session.execute(
+                    text("SELECT COUNT(*) FROM search_index WHERE project_id = :pid"),
+                    {"pid": project_id},
+                )
+            ).scalar_one()
+            pre_chunks = (
+                await session.execute(
+                    text("SELECT COUNT(*) FROM search_vector_chunks WHERE project_id = :pid"),
+                    {"pid": project_id},
+                )
+            ).scalar_one()
+        assert pre_index >= 1, "seed row should exist before removal"
+        assert pre_chunks >= 1, "seed chunk should exist before removal"
+
+        await project_service.remove_project(test_project_name)
+
+        async with db.scoped_session(project_service.repository.session_maker) as session:
+            post_index = (
+                await session.execute(
+                    text("SELECT COUNT(*) FROM search_index WHERE project_id = :pid"),
+                    {"pid": project_id},
+                )
+            ).scalar_one()
+            post_chunks = (
+                await session.execute(
+                    text("SELECT COUNT(*) FROM search_vector_chunks WHERE project_id = :pid"),
+                    {"pid": project_id},
+                )
+            ).scalar_one()
+
+        assert post_index == 0, (
+            f"search_index still has {post_index} rows for deleted project_id={project_id} "
+            "— project deletion did not sweep the FTS table."
+        )
+        assert post_chunks == 0, (
+            f"search_vector_chunks still has {post_chunks} rows for deleted "
+            f"project_id={project_id}."
+        )
+
+
+@pytest.mark.asyncio
+async def test_delete_returns_false_for_missing_project_id(project_service: ProjectService):
+    """ProjectRepository.delete must return False when the project id is gone.
+
+    The override loses the base Repository.delete contract if the NoResultFound
+    branch isn't covered — a silent True would mislead callers into thinking
+    a non-existent project was removed.
+    """
+    result = await project_service.repository.delete(9_999_999)
+    assert result is False
+
+
+@pytest.mark.asyncio
+async def test_remove_project_purges_vector_embeddings(project_service: ProjectService):
+    """Project deletion must also drop sqlite-vec embeddings keyed by chunk rowid.
+
+    sqlite-vec stores vectors in a vec0 virtual table that has no cascade
+    behavior. If embeddings linger after the chunks they reference are gone,
+    `_run_vector_query` pulls them as top-k candidates and crowds out live
+    results. The test only runs when the embeddings table is present, which
+    matches the install path that exercises semantic search.
+    """
+    test_project_name = f"test-vec-cleanup-{os.urandom(4).hex()}"
+    session_maker = project_service.repository.session_maker
+
+    # The embeddings table only exists once semantic search has initialized.
+    # Skipping when it's absent keeps this test honest on minimal CI DBs.
+    if not await _table_exists(session_maker, "search_vector_embeddings"):
+        pytest.skip("search_vector_embeddings is not present on this connection")
+
+    with tempfile.TemporaryDirectory() as temp_dir:
+        test_project_path = str(Path(temp_dir) / "test-vec-cleanup")
+        os.makedirs(test_project_path, exist_ok=True)
+
+        await project_service.add_project(test_project_name, test_project_path)
+        project = await project_service.get_project(test_project_name)
+        assert project is not None
+        project_id = project.id
+
+        async with db.scoped_session(session_maker) as session:
+            await session.execute(
+                text(
+                    "INSERT INTO search_vector_chunks "
+                    "(id, entity_id, project_id, chunk_key, chunk_text, source_hash, "
+                    " entity_fingerprint, embedding_model) "
+                    "VALUES (:id, :entity_id, :project_id, :chunk_key, :chunk_text, "
+                    " :source_hash, :entity_fingerprint, :embedding_model)"
+                ),
+                {
+                    "id": 999_201,
+                    "entity_id": 999_201,
+                    "project_id": project_id,
+                    "chunk_key": "vec-canary",
+                    "chunk_text": "vec canary",
+                    "source_hash": "abc",
+                    "entity_fingerprint": "",
+                    "embedding_model": "",
+                },
+            )
+            # vec0 requires a vector matching the configured dimensions, but the
+            # delete path filters by rowid; a non-existing dimension would block
+            # this seed step. Skip the insert if the embeddings DDL hasn't run.
+            try:
+                await session.execute(
+                    text(
+                        "INSERT INTO search_vector_embeddings (rowid, embedding) "
+                        "VALUES (:rowid, :embedding)"
+                    ),
+                    {"rowid": 999_201, "embedding": "[" + ",".join(["0.0"] * 384) + "]"},
+                )
+            except Exception:
+                pytest.skip("search_vector_embeddings rejected the synthetic seed row")
+
+        async with db.scoped_session(session_maker) as session:
+            pre = (
+                await session.execute(
+                    text("SELECT COUNT(*) FROM search_vector_embeddings WHERE rowid = :rowid"),
+                    {"rowid": 999_201},
+                )
+            ).scalar_one()
+        assert pre >= 1, "seed embedding should exist before removal"
+
+        await project_service.remove_project(test_project_name)
+
+        async with db.scoped_session(session_maker) as session:
+            post = (
+                await session.execute(
+                    text("SELECT COUNT(*) FROM search_vector_embeddings WHERE rowid = :rowid"),
+                    {"rowid": 999_201},
+                )
+            ).scalar_one()
+
+        assert post == 0, (
+            f"search_vector_embeddings still has {post} rows for rowid 999_201 "
+            "— project deletion did not sweep the sqlite-vec embeddings table."
+        )