gabriel / muse public
fix BREAKING task/commit-id-v2 #2 / 2
AI Agent gabriel · 149 days ago · Apr 24, 2026 · Diff

fix: apply_manifest only deletes tracked files; _walk_tree stages dotfiles

Two data-safety bugs fixed:

1. apply_manifest(root, prev_manifest, target_manifest) — new 3-arg signature. Deletion candidates come from prev_manifest.keys() instead of walk_workdir(), so untracked files (Write tool docs, local scripts) are never deleted.

2. _walk_tree in code_stage.py — removed dotfile skip. muse code add . now stages .museattributes, .museignore, and other dotfiles just as git add . stages .gitattributes and .gitignore.

All callers updated. 196 tests pass.

sha256:55a8bbec0d35d504592b28a75462e1010cfed70023c31283d5057e577347cd8f sha
sha256:148e92dd21404e63cd40f8f12e45aec1cf401c111eb02a5c2bd3f4eebbed9d43 parent
+11 ~57 −2 symbols
sha256:acdbb52fcb78d43ef8dc7380c61e8e21613d35603481cb6ce620617893afd404 snapshot
+11
symbols added
~57
symbols modified
−2
symbols removed
0
dead code introduced
Semantic Changes 70 symbols
~ muse/cli/commands/cherry_pick.py .py 1 symbol modified
~ run
~ muse/cli/commands/clone.py .py 1 symbol modified
~ _restore_working_tree
~ muse/cli/commands/code_stage.py .py 1 symbol modified
~ _walk_tree
~ muse/cli/commands/commit.py .py 1 symbol modified
~ run
~ muse/cli/commands/merge.py .py 2 symbols modified
~ _run_abort
~ _run_merge
~ muse/cli/commands/pull.py .py 1 symbol added, 12 symbols modified
+ get_commit_snapshot_manifest import import get_commit_snapshot_manifest L60–60
~ CommitRecord
~ SnapshotRecord
~ get_all_commits
~ get_head_commit_id
~ get_head_snapshot_manifest
~ read_commit
~ read_current_branch
~ read_snapshot
~ write_branch_ref
~ write_commit
~ write_snapshot
~ run
~ muse/cli/commands/reset.py .py 1 symbol added, 6 symbols modified
+ get_commit_snapshot_manifest import import get_commit_snapshot_manifest L45–45
~ get_head_commit_id
~ read_current_branch
~ read_snapshot
~ resolve_commit_ref
~ write_branch_ref
~ run
~ muse/cli/commands/revert.py .py 2 symbols modified
~ _apply_manifest_safe
~ run
~ muse/cli/commands/shelf.py .py 2 symbols modified
~ _shelf_push_programmatic
~ run_save
~ muse/core/rebase.py .py 1 symbol modified
~ replay_one
~ muse/core/workdir.py .py 1 symbol modified
~ apply_manifest
~ tests/test_cmd_sparse_checkout.py .py 3 symbols modified
~ TestApplyManifestSparse
~ test_apply_manifest_no_sparse_config_writes_all
~ test_apply_manifest_respects_sparse_config
~ tests/test_code_stage.py .py 2 symbols added
+ test_add_dot_stages_museattributes function function test_add_dot_stages_museattributes L739–755
+ test_add_dot_stages_museignore function function test_add_dot_stages_museignore L758–774
~ tests/test_commit_object_store_completeness.py .py 3 symbols modified
~ TestApplyManifestAfterCommit
~ test_apply_manifest_does_not_raise_after_commit
~ test_apply_manifest_does_not_raise_when_parent_objects_were_missing
~ tests/test_merge_data_integrity.py .py 1 symbol added, 1 symbol removed, 6 symbols modified
− test_I3_apply_manifest_with_empty_target_deletes_all_tracked_files method method test_I3_apply_manifest_with_empty_target_deletes_all_tracked_files L202–243
+ test_I3_apply_manifest_with_empty_target_raises_when_prev_non_empty method method test_I3_apply_manifest_with_empty_target_raises_when_prev_non_empty L202–224
~ TestApplyManifestSafetyV
~ test_V1_apply_manifest_writes_target_files
~ test_V2_apply_manifest_removes_files_not_in_target
~ test_V3_apply_manifest_does_not_delete_muse_dir
~ test_V4_apply_manifest_does_not_follow_symlinks
~ TestSentinelValuesI
~ tests/test_workdir_integrity.py .py 6 symbols added, 1 symbol removed, 15 symbols modified
− test_II7_empty_manifest_non_empty_workdir_raises_value_error method method test_II7_empty_manifest_non_empty_workdir_raises_value_error L363–370
+ test_II7_empty_manifest_non_empty_prev_raises_value_error method method test_II7_empty_manifest_non_empty_prev_raises_value_error L368–375
+ TestApplyManifestUntrackedFilesIX class class TestApplyManifestUntrackedFilesIX L1117–1206
+ test_IX1_untracked_file_not_deleted_by_apply_manifest method method test_IX1_untracked_file_not_deleted_by_apply_manifest L1126–1146
+ test_IX2_untracked_dotfile_not_deleted method method test_IX2_untracked_dotfile_not_deleted L1148–1164
+ test_IX3_tracked_file_removed_from_target_gets_deleted method method test_IX3_tracked_file_removed_from_target_gets_deleted L1166–1178
+ test_IX4_commit_does_not_delete_untracked_file method method test_IX4_commit_does_not_delete_untracked_file L1180–1206
~ TestApplyManifestMissingObjectII
~ test_II1_missing_single_object_raises_runtime_error
~ test_II2_error_message_names_the_missing_path
~ test_II3_partial_manifest_some_missing_raises
~ test_II4_all_objects_present_succeeds
~ test_II5_multiple_missing_reported_in_error
~ test_II6_apply_manifest_removes_files_not_in_target
~ TestCheckoutMissingObjectVI
~ test_VI2_apply_manifest_raises_on_missing_object_not_silent
~ TestEditorCacheSimulationVII
~ test_VII3_correct_state_after_reapplying_manifest
~ TestStressWorkdirVIII
~ test_VIII5_stress_apply_manifest_100_times_deterministic
~ TestVerifyWorkdirIntegrityIII
~ test_III7_correct_content_after_apply_manifest
← Older Oldest on task/commit-id-v2
All commits Newer fix: migrate tests to commit-id-v2 (branch→created_on_branch, co… sha256:6b6e63d804f829df8580591dc85e98ac540b9dfcac10529a291c97c1c04a6dbc

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