fix(extraction): index independent nested git repos

[sjh9714]

Summary

• Fixes codegraph init -i/scan discovery for top-level workspaces that contain independent nested Git repos.
• Expands untracked nested-repo directory entries from git ls-files -o --exclude-standard by enumerating that repo’s own visible files.
• Adds regression coverage for issue codegraph init -i does not detect source files when run from a top-level CMake workspace containing multiple nested repos #193 while preserving existing Git submodule scan behavior.

Why

Before this change, a parent Git repo saw an unregistered nested repo as a single sub_repo1/ untracked directory. That directory did not match source include patterns, so top-level workspace scans could report no files even though the nested repo contained source files.

Testing

• npx vitest run __tests__/extraction.test.ts -t "independent nested git" — failed before the fix with expected [] to include 'sub_repo1/src/main.cpp'
• npx vitest run __tests__/extraction.test.ts -t "independent nested git|git submodules"
• npx vitest run __tests__/extraction.test.ts
• npm run build
• npm test
• git diff --check

Fixes #193

Note: I used Codex to help inspect the scan path and draft the regression test, then reviewed the final diff and ran the listed verification commands locally.