fix: handle nested git repos gracefully in checkpoints

[daniel-lxs]

Fixes #8433

Summary

Instead of blocking the checkpoints feature when nested git repositories are detected, this PR modifies the behavior to exclude nested repos from staging, allowing checkpoints to work in monorepos and projects with submodules.

Changes

• Removed initialization-time check: No longer throws an error when nested git repos are detected during
• Added method: Detects nested repositories from multiple sources:
  • (declared submodules)
  • Git index (gitlinks with mode 160000)
  • Filesystem ( directories and worktrees)
• Modified method: Uses pathspec excludes to prevent staging files from nested repos
• Added safety check: Verifies no submodule changes are staged after the add operation
• Updated tests: Modified test expectations to verify nested repos are properly excluded from checkpoints

Benefits

• Checkpoints now work in monorepos and projects with submodules
• Prevents git errors related to nested repository changes
• Maintains checkpoint functionality for the main workspace files
• Provides clear logging when nested repos are detected and excluded

Testing

All existing tests pass, including the updated test that now verifies:

• Initialization succeeds with nested repos present
• Only main workspace files are included in checkpoints
• Nested repo changes are properly excluded
• Logging confirms exclusion behavior

---

Important

Modifies checkpoints to exclude nested git repos from staging, allowing functionality in monorepos and submodules.

• Behavior:
  • Removes initialization-time error for nested git repos in ShadowCheckpointService.ts.
  • Excludes nested repos from staging using pathspec excludes in stageAll().
  • Adds safety check to ensure no submodule changes are staged.
• Detection:
  • findNestedRepos() detects nested repos from .gitmodules, git index, and filesystem.
  • Normalizes Windows-style paths to POSIX format.
• Testing:
  • Updates tests in ShadowCheckpointService.spec.ts to verify nested repos are excluded.
  • Adds tests for handling .gitmodules, path normalization, and gitlink entries with spaces.

^{This description was created by for c98980d. You can customize this summary. It will automatically update as commits are pushed.}

[roomote]

Rooviewer   See task on Roo Cloud

Reviewed commit c98980d. All previously flagged issues have been resolved.

• Incomplete pathspec exclusion: Fixed by adding explicit gitlink removal before staging using git rm --cached --ignore-unmatch -r
• Limited safety check coverage: Enhanced to use git ls-files -s --cached for comprehensive verification of mode 160000 entries, plus additional check for .gitmodules changes
• Silent error handling: All git operations now log warnings when failures occur, improving debuggability
• Redundant variable declaration in HEAD file processing: Fixed in commit 05fb2a3
• Redundant variable declaration in worktree processing: Fixed in commit 05fb2a3
• Path parsing fails for nested repos with spaces: Fixed in commit c98980d by using regex pattern to properly capture filenames with spaces

Previous reviews

• 05fb2a3: Review #1
• fd22d0f: Review #2
• 0d089b1: Review #3
• b02bf48: Review #4

_{Mention @roomote in a comment to request specific changes to this pull request or fix all unresolved issues.}

[roomote]

Review complete. Found 3 issues that should be addressed before approval. Please see the inline comments for details.

[roomote]

Posted 2 inline review comments focusing on correctness across platforms and config resolution. Both are minor and straightforward to address.

• Normalize nested repo pathspecs to POSIX when building excludes in TypeScript.stageAll() so Windows backslashes do not break git pathspec matching
• Read .gitmodules via absolute path from workspaceDir in TypeScript.findNestedRepos() to ensure submodules are detected from the main workspace instead of shadow repo cwd

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[mrubens]

@daniel-lxs do you buy the Oroocle's comments?

[daniel-lxs]

Moving back to Changes Requested

[hannesrudolph]

stale