bm reindex --embeddings silently no-ops on an unsynced project (0 embedded, no warning)

[BigManDrewskii]

Summary

On a fresh project whose files were never indexed, bm reindex --embeddings prints a success-looking 0 entities embedded, 0 skipped, 0 errors while bm status still reports pending changes and read_note returns nothing. The --embeddings path never runs the project index, and there is no hint that a sync must happen first. The docs claim embeddings are "generated automatically on first startup for existing notes" and point at bm reindex --embeddings as the manual rebuild command, which misleads CLI-first users into a silent no-op.

Reproduction (v0.22.1, CLI-only, no MCP server running)

mkdir -p ~/scratch/bm-repro/notes
cat > ~/scratch/bm-repro/notes/note.md <<'EOF'
---
title: Repro Probe Note
type: note
tags: [repro]
---

# Repro Probe Note

## Observations
- [fact] This note was written directly to disk, never via write_note.
EOF

bm project add repro-test ~/scratch/bm-repro --local
bm status --project repro-test            # → notes/ +1 new

bm reindex --embeddings -p repro-test     # → "0 entities embedded, 0 skipped, 0 errors"
bm tool read-note "notes/note" -p repro-test   # → empty

bm reindex -p repro-test                  # → project index runs; "1 entities embedded"
bm tool read-note "notes/note" -p repro-test   # → works
bm tool search-notes "probe note written to disk" -p repro-test  # → finds it

Observed:

• bm reindex --embeddings → 0 entities embedded, 0 skipped, 0 errors (no warning)
• bm status still shows +1 new afterwards
• plain bm reindex (both flags) syncs + embeds and everything works

Root cause

In src/basic_memory/cli/commands/db.py (both v0.22.1 and current main), the embeddings branch calls search_service.reindex_vectors() against DB state only; only the search branch runs the project index (sync_service.sync(...) in v0.22.1, run_local_project_index_for_project(...) on main). The code comment on main makes the ownership split explicit: "the explicit embeddings phase below owns vector (re)builds" — the project index must run first. Nothing warns when reindex_vectors finds 0 entities.

Suggested fix (any subset)

1. When reindex_vectors completes with total_entities == 0 (or embedded == 0 and DB was empty), print a warning: "no entities in DB — run bm reindex (project index) or start the MCP server so files get indexed first."
2. Optionally: auto-run the project index when the DB is empty and the project has files on disk.
3. Docs: on the semantic-search page, clarify that bm reindex --embeddings only re-embeds already-indexed entities, and that first-run indexing for CLI-only setups requires bm reindex (no flags).

Environment

• basic-memory v0.22.1 (CLI), SQLite, semantic_search_enabled: true, FastEmbed bge-small-en-v1.5
• macOS arm64

Related: #959 (CLI-only sync dead end, closed), #1016 (watcher-path writes not embedded until reindex, closed). This is the --embeddings-flag-specific silent no-op variant — #959's repro used plain bm reindex which works.