feat(init): make the generated cocosearch.yaml a complete config reference

[VioletCranberry]

Summary

cocosearch init generated a config that documented only indexing, search, and embedding (model only). Several supported config sections were missing, so they were effectively
undiscoverable to anyone who didn't read the README:

• the optional query-rewrite controller
• embedding providers (provider / baseUrl for ollama/openai/openrouter)
• file logging (logging.file)

This PR fills those gaps so the generated cocosearch.yaml doubles as a full, accurate config reference — and brings it in line with the README and the Pydantic schema.

What changed

CONFIG_TEMPLATE (generator.py) — added commented-out blocks for:

• embedding: provider, per-provider model defaults, baseUrl (custom/OpenAI-compatible endpoints), outputDimension, plus COCOSEARCH_EMBEDDING_API_KEY / --fresh reindex notes
• controller: enabled / provider / model / baseUrl / timeout
• logging: the file toggle → ~/.cocosearch/logs/

Everything is commented out, so the generated config is byte-for-byte inert — no behavior change, no generative model ever called by default. The style matches the existing linkedIndexes
example.

Docs:

• docs/cli-reference.md — the init section listed only 5 of the 7 interactive prompts/flags. Added the missing --no-claude-settings and --no-claude-hook (pre-existing debt from the merged
  nudge-hook work), plus a note that the generated config documents every section.
• README.md — added a logging: block to the hand-written cocosearch.yaml example so it mirrors the complete template.

Why commented-out

The template's convention is "documented but inert" — every field is a commented example (see linkedIndexes). A user opts in by uncommenting. This keeps init as the single source of truth
for what's configurable without changing any defaults.

Testing

• uv run pytest tests/unit/config/ tests/unit/test_cli_init.py — 295 passed
• uv run ruff check / ruff format — clean
• New tests:
  • presence checks for the controller, embedding-provider, and logging docs
  • two schema-validation guards that uncomment the controller and logging examples and load them through ControllerSection / LoggingSection, so the documented examples can't silently
    drift from the schema (shared, block-bounded _uncomment_block helper)
• Manual smoke: real init renders all sections and the result loads as a valid config (embedding.provider=ollama, controller.enabled=False, logging.file=False)