`git ls-files -co --exclude-standard` only sees the submodule pointer in the main repo's index, so projects using submodules indexed 0 files. Now the tracked list runs with `-c --recurse-submodules` so submodule contents are included; untracked files are gathered with a separate `-o --exclude-standard` call (the two flags can't be combined — git only supports --recurse-submodules with --cached/--stage). Fixes #147. Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>