fix(deps): anchor index resolution to target path; add fresh deps exraction

[VioletCranberry]

Summary

Two related dependency-extraction safety fixes, discovered while diagnosing why another repository index had thin
dependency data (only workflow-YAML edges, no Python).

1. CLI index-resolution data-loss bug 🐛

cocosearch deps extract resolved the index name from the caller's cwd, not the target path. All three
resolution steps — config discovery (find_config_file), git derivation (derive_index_from_git), and the derived-name
fallback — ignored the path argument.

Impact: run from a project directory, deps extract /other/repo --fresh resolves to this project's index and wipes its
edges while re-extracting against the wrong files. (index had the same latent bug; fallback_path only masked
it when no cwd config existed.)

Fix:

• find_config_file(start_dir=None) — anchor config + git-root discovery to a given directory (git-root lookup now
  uses git -C)
• derive_index_from_git(path=None) — forward the path to get_main_repo_root
• _resolve_index_name — pass fallback_path into the git step
• deps_extract_command / index_command — anchor config + index-name resolution to the target codebase path

Backward compatible (new params default to cwd behavior). The read-only deps show/tree/impact/stats commands are
intentionally untouched — they take a relative file arg and are meant to run in-project.

2. Dashboard "Fresh Extract Deps" ✨

The dashboard "Extract Deps" button only ran incremental extraction, so files unchanged since a stale/broken index
were never re-extracted (the button reported success but did nothing for them). Added a fresh path end to end:

• /api/extract-deps now accepts a fresh flag, forwarded to extract_dependencies
• A red "Fresh Extract Deps" button mirrors the existing Reindex / Fresh Index two-button pattern

Testing

• New unit tests: find_config_file start_dir anchoring (+ git-root variant), derive_index_from_git path forwarding,
  deps_extract_command regression (resolves from target path, not cwd), /api/extract-deps fresh-flag forwarding
  (default + explicit)
• Full suite green (1257 passing across affected areas), ruff clean
• E2E: re-ran the exact command that corrupted an index pre-fix (deps extract --fresh, no --name, from a
  different project dir) — now correctly targets the right index and leaves the cwd project's edges untouched