fix(checkpoints): remove files added after restore target

[visualfox-ch]

Summary

• remove files added after the selected checkpoint when restoring
• derive removals from Hermes' pre-rollback snapshot instead of using destructive git clean
• preserve ignored, excluded, oversized, and pre-existing untracked user files
• prune only empty directories created by removed checkpoint additions

Test plan

• python -m pytest tests/tools/test_checkpoint_manager.py tests/test_batch_runner_checkpoint.py tests/integration/test_checkpoint_resumption.py -q -o 'addopts='
• ruff check tools/checkpoint_manager.py tests/tools/test_checkpoint_manager.py

Safety

The restore path never recursively cleans the repository. It only removes paths recorded as additions between the target checkpoint and Hermes' pre-rollback snapshot.

[tonydwb]

Code Review Summary

Verdict: Approved

Fix for checkpoint restoration removing files added after the restore target. Clean (95 additions, 0 deletions). No security concerns.

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Reviewed by Hermes Agent

[teknium1]

Thanks for addressing the full-directory restore gap; current main still uses git checkout <commit> -- . in tools/checkpoint_manager.py:826-830, so post-checkpoint additions are indeed left behind.

Problems

• The new reconciliation runs after the existing pre-rollback _take() at tools/checkpoint_manager.py:820. _take() can cross max_snapshots, then _prune() rewrites history and runs git gc --prune=now (tools/checkpoint_manager.py:1053-1118). If the requested target is the oldest retained checkpoint, it can become unreachable before the new diff/checkout code uses it. The added tests do not exercise that retention boundary.

Suggested changes

• Resolve and pin the target tree before _take(), use the temporary ref for restore, and delete it in finally.
• Add small-retention regression coverage for full and file-scoped restores. The timeline-linked #64966 independently covers this target-pinning case.

Automated hermes-sweeper review.

[teknium1]

This diff runs after the existing pre-rollback _take() call. _take() can exceed max_snapshots, after which _prune() rewrites the ref and runs gc --prune=now; an oldest retained commit_hash can be unreachable here. Resolve and pin the target tree before _take(), then diff/restore through that temporary ref and delete it in finally.