git-resolve-conflicts

Resolve every unmerged path in the current worktree, continue whatever git operation is pending, and commit the result.

Workflow

1. Inspect state:

   git status
   git ls-files -u
   

   Identify the pending operation:

   • MERGE_HEAD / rebase-merge / rebase-apply / CHERRY_PICK_HEAD / REVERT_HEAD present -> merge/rebase/cherry-pick/revert.
   • Otherwise (unmerged paths but no HEAD pointer) -> likely a stash pop conflict or manual merge; resolve in place.

   List the conflicted files: git diff --name-only --diff-filter=U.

2. For each conflicted file, inspect the three stages:

   git show :1:<path>   # base
   git show :2:<path>   # ours (HEAD / current branch)
   git show :3:<path>   # theirs (incoming / stashed)
   

   And the working-tree conflict markers.

3. Resolve per file using these rules:

   • Machine-generated / filtered state files (e.g. .codex/*.config.toml trust hashes, lockfiles): keep ours (git checkout --ours <path>); the clean filter re-normalizes on git add.
   • Dependency / version bumps: keep the higher version; if already upstream, --skip the commit.
   • Deliberate config updates (incoming value intended): take theirs (git checkout --theirs <path>).
   • Generated artifacts: regenerate from source, then stage.
   • Stash-pop conflicts where the stash is stale (its changes already present in HEAD): keep ours for every file; the stash adds nothing.
   • Hand-written source with a genuine semantic collision: pause and ask the user before choosing; never guess.
   • JSON / JSONL / TOML data files with duplicate or contradictory rows: drop duplicates and obviously bogus rows (downgrades, empty values, format-only changes), keeping one clean copy of each legitimate entry.

   When a file has conflict markers, remove the markers and keep the chosen side's content. For 3-way markers (<<<<<<< / ||||||| / ======= / >>>>>>>), select the intended side and delete the marker lines.

4. Stage every resolved file:

   git add <path> ...
   

5. Verify no conflict markers remain:

   git diff --check
   

   If any remain, fix before continuing.

6. Continue the pending operation:

   • Merge: git commit (use the prepared MERGE_MSG).
   • Rebase/cherry-pick: git rebase --continue (or --skip if the commit became empty) / git cherry-pick --continue.
   • Revert: git revert --continue.
   • Stash pop / manual: nothing to continue; proceed to commit.

7. If the working tree now has changes relative to HEAD, commit them using the project's commit convention (see git-commit skill). If the tree is clean, report that there was nothing to commit.

8. Report: which files conflicted, how each was resolved, and the resulting commit (or "nothing to commit").

Notes

• Never run git stash (push/pop/apply/drop) in a shared workspace; resolve conflicts in place and leave the stash list untouched if dropping is blocked.
• Do not force-resolve hand-written source collisions without user confirmation.
• Prefer the version already in HEAD when the incoming change is a stale duplicate.