W6: Feat/pull checkout hardening

[Saanvi521]

Summary

• add on a deleted file that is still in the index now stages the deletion, so a merge conflict can be resolved by deleting the file. A never-tracked path still raises "No such file".
• WorkingTree.checkout(tree, conflicted_paths=...) writes conflicted files (with markers) to disk but keeps their pre-merge index entry, so they stay "not staged" until add. Plain checkout(tree) is unchanged. M3 owns refs, HEAD and pending merge state.
• 12 new tests in tests/test_index.py cover fast-forward pull, unsafe-checkout refusals that change nothing, read-only status and diff, and the merge-result flow (markers, add, commit, clean status).

Validation

• scripts/quality-check.sh
• Manual testing, if applicable:

Checklist

• The change is focused and easy to review.
• Tests were added or updated for behavior changes.
• Documentation was updated for user-facing or setup changes.
• No secrets, generated artifacts, or local-only files are included.

Notes for Reviewers