Instead of blocking checkpoints when nested git repos are detected,
now excludes them from staging to prevent submodule-related errors.

Changes:
- Removed initialization-time nested repo check that blocked feature
- Added findNestedRepos() to detect repos from multiple sources:
  * .gitmodules (declared submodules)
  * git index (gitlinks with mode 160000)
  * filesystem (.git directories and worktrees)
- Modified stageAll() to exclude nested repos using pathspec
- Added safety check to prevent submodule changes in staging
- Updated tests to verify nested repos are excluded from checkpoints

This allows checkpoints to work in monorepos and projects with
submodules while preventing git errors from nested repo changes.

Improvements based on reviewer bot feedback:

1. Enhanced safety check (HIGH priority):
   - Now uses 'git ls-files -s --cached' to detect mode 160000 entries
   - Catches newly added/removed gitlinks, not just pointer changes
   - Added check for .gitmodules changes with warning log

2. Improved pathspec exclusion (MEDIUM priority):
   - Added 'git rm --cached' to remove existing gitlinks before staging
   - Prevents staging of gitlink entries already in the index
   - Ensures complete exclusion of nested repo changes

3. Better error logging (LOW priority):
   - Added warning logs for git command failures in findNestedRepos()
   - Helps debugging while avoiding feature breakage
   - Distinguishes expected errors (no .gitmodules) from real issues

All tests continue to pass with these enhancements.

…gitmodules absolute path; add tests; verify no gitlinks staged and log .gitmodules changes

…(mode 160000)