fix(cli): remove F-09 spillover from F-12 branch, keep only wiki group
cli.py and config.py were accidentally contaminated with uncommitted F-09
changes (search_app restructure, rich ingest, mathpix/figures settings).
This restores both files to main-baseline + F-12-only additions:
- cli.py: wiki_app group (compile/list/check), restore @app.command search
- config.py: wiki_dir, wiki_llm_model, wiki_llm_url, wiki_top_k only
All 127 tests green, ruff+mypy clean.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>