Edge case hardening (renames, binary files, submodules)

Handle git edge cases that may break conflict detection on real repos:

- File renames (one worktree renames, another modifies)
- Binary files
- Deleted vs modified conflicts
- Submodules
- Bare repositories
- Detached HEAD state
- Symbolic links
- File permission changes

Each edge case can be tackled independently - good for contributors to pick off one at a time.