fix(cli): warn when embedding reindex has no entities

[phernandez]

Why

bm reindex --embeddings only rebuilds vectors for entities already present in the database. On a fresh CLI-only project it could therefore report 0 entities embedded and finish successfully while files still had not been indexed, with no explanation of the prerequisite.

Fixes #1184.

What Changed

• warn when embeddings-only mode finds zero indexed entities
• explain that --embeddings does not discover project files
• direct users to plain bm reindex or the MCP server's initial index
• update the semantic-search quick start and reindex reference to distinguish the two commands
• add a CLI regression for the zero-entity output

Implementation Details

The lifecycle boundary is unchanged. Embeddings-only mode still operates exclusively on database entities and does not implicitly run the project-index coordinator. The warning is emitted only when --embeddings runs without the search/index phase and reindex_vectors() reports zero total entities.

That keeps existing incremental and provider-rebuild behavior predictable while making the unsynced-project no-op explicit.

Testing

Automated

• uv run pytest -q tests/cli/test_db_reindex.py --no-cov: 9 passed
• just fast-check: Ruff fix/check, formatting, and ty type checking passed
• git diff --check: passed

Manual

• No live embedding provider was needed; the CLI regression captures the rendered zero-entity summary and warning.

Risks / Follow-ups

• The command still exits successfully because an empty indexed project is not itself an operational failure. The user-visible warning supplies the missing next action.
• This PR deliberately does not auto-index files from --embeddings; plain bm reindex remains the command that owns project discovery and indexing.