fix: remove git clean and reset --hard from checkpoint restore

[roomote]

This PR addresses the critical data loss issue reported in #6209 by removing the dangerous git clean and git reset --hard commands from the checkpoint restoration process.

Changes Made

• Removed git clean -d -f command that was forcefully deleting all untracked files
• Removed git reset --hard command that could cause data loss
• Implemented a safer restoration approach that:
  • Only restores tracked files from the checkpoint
  • Preserves untracked files in the working directory
  • Properly handles edge cases like when all files have been deleted

Technical Details

The new implementation uses:

• git ls-tree to get the list of files in the target commit
• git checkout with specific file paths to restore only tracked files
• git rm to remove files that exist in the working directory but not in the target commit

This approach ensures that user data in untracked files is never lost during checkpoint restoration.

Testing

All existing tests pass, including the specific test case for handling file deletions.

Fixes #6209

---

Important

Removes git clean and git reset --hard from checkpoint restoration in ShadowCheckpointService.ts to prevent data loss, using a safer method to restore tracked files.

• Behavior:
  • Removed git clean -d -f and git reset --hard from checkpoint restoration in ShadowCheckpointService.ts.
  • New method restores only tracked files, preserving untracked files.
  • Handles edge cases like all files being deleted.
• Implementation:
  • Uses git ls-tree to list files in target commit.
  • Uses git checkout to restore tracked files.
  • Uses git rm to remove files not in target commit.
• Testing:
  • All existing tests pass, including file deletion handling.
• Fixes:
  • Fixes Critical Issue with Checkpoint restore #6209.

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[daniel-lxs]

This implementation seems incomplete, and could have a high impact in performance when using git checkout [commitHash] -- ...files, closing for now