fix(commit): stop overwriting working tree after commit
muse commit was calling apply_manifest() after writing the snapshot, restoring every tracked file from the object store and silently destroying any unstaged changes on disk. commit should only write to the object store and advance the branch ref — identical to Git.
Removed apply_manifest call and unused import from commit.py. Replaced TestCommitRestoresFilesToDisk (which asserted the wrong behaviour) with a comment. Added test_commit_workdir_preservation.py with 6-test regression suite covering the data loss path.
sha256:d8ae5a872e6b33e63c3c9d188169fe8f834b2411fcf7d5ca1a0a58faada14082
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sha256:75577aa270f58d62c91d7a7a0e1fd01f906bd0d16a7a1a8de1e3985cf7e6f8cc
snapshot
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