feat(store): enhance repository handling and corruption recovery logic

- Added safeguards against repository corruption with improved recovery mechanisms, including remote re-cloning and worktree restoration.
- Introduced fine-grained repository integrity checks and missing file restoration logic.
- Centralized repository locking with `ensureRepositoryLocked` to standardize synchronization.
- Enhanced conflict resolution during pulls with automated reconciliation of remote and local changes.
- Improved worktree and index reset workflows to handle dirty and missing paths gracefully.
- Increased robustness for garbage collection with extended grace period and recovery paths.

Closes: #4629