Commit, PR, and Merge

Stage changes, verify quality gates, commit with a descriptive message, create a PR, and merge to main.

Steps

Step 0: Quality Gate (Pre-Commit)

Run before branching. For every changed .qmd, .tex, or .R file that has quality rubrics, run:

python3 scripts/quality_score.py <changed-file-paths>

• If any file scores below 80, halt and report the findings. The user must either fix the issues or explicitly override with phrases like "commit anyway" or "skip quality gate".
• If all files score 80+, continue.

Spawn the verifier agent (via the Agent tool with subagent_type=verifier) to run compilation/render checks on the changed files. Report pass/fail before committing.

Step 0b: Consistency Gate (Pre-Commit)

Runs unconditionally. The full backtest suite — all ten gates (surface-sync count claims like "18 agents, 60 skills, 37 rules, 8 hooks" and marked tables, skill integrity, model currency, links, spec conformance, staleness, repo hygiene, derived counts, ledger coverage, hook battery):

./scripts/backtest.sh

• Exit 0: all gates green — continue.
• Nonzero: at least one gate is red — print its output and halt. Fix, then re-run. Do NOT proceed past this gate on a red result, even with "commit anyway" — count drift alone produced PRs #70, #76, and #78.

Step 0c: Passport Check (Pre-Commit)

If the diff touches a manuscript (.tex/.qmd) that has a passport in quality_reports/passports/, any source_file a passport lists, or any file a claim declares as a display (its location:, or an appears_in path:), read that passport: a load-bearing claim with status: FAIL or STALE is a must-fix — halt, name the claim, and point at /audit-reproducibility (or the stale script) before committing. A touched display triggers the check for the same reason a touched script does: editing one artifact's copy of a number desynchronizes it from that number's other displays — the supplement or deck holding the same value was not necessarily updated in the same commit. Skip silently when no passport exists.

Step 1: Check current state

git status
git diff --stat
git log --oneline -5

Step 2: Create a branch

git checkout -b <short-descriptive-branch-name>

Step 3: Stage files

Add specific files (never use git add -A):

git add <file1> <file2> ...

Do NOT stage .claude/settings.local.json or any files containing secrets.

Step 4: Commit with a descriptive message

If $ARGUMENTS is provided, use it as the commit message. Otherwise, analyze the staged changes and write a message that explains why, not just what.

The subject line states what is TRUE AFTER the commit — a plain sentence about behavior that a reader could go and test. "Fixed review feedback" and "Updated the checker" narrate your afternoon and tell a reader nothing; "The parity gate refuses a fixture whose hash is unregistered" is a claim they can check against the code. Process narration — which review round it came from, who asked, how many attempts it took — belongs in the body if it belongs anywhere. The body still carries the why; the subject carries the claim.

git commit -m "$(cat <<'EOF'
<commit message here>
EOF
)"

Step 5: Push and create PR

git push -u origin <branch-name>
gh pr create --title "<short title>" --body "$(cat <<'EOF'
## Summary
<1-3 bullet points>

## Test plan
<checklist>

🤖 Generated with [Claude Code](https://claude.com/claude-code)
EOF
)"

Step 6: Merge and clean up

gh pr merge <pr-number> --merge --delete-branch
git checkout main
git status --porcelain          # must print nothing before the next line runs
git pull

Expect the tree to be dirty here — that is what Step 3 is for. Staging specific files means
everything the session touched but did not stage, plus every untracked artifact, is still in the
tree when you arrive at this step. The git-guardrails hook this template ships denies
git pull (and merge, and rebase) whenever git status --porcelain is non-empty, because a
pull that resolves on top of uncommitted work cannot be reviewed afterwards — you can no longer
tell which hunk came from the remote. Chaining a stash into the same command line does not help:
the hook reads the tree, it does not predict what the line will do to it.

Clear the tree deliberately, then pull:

git stash push -u -m "post-merge: unstaged leftovers"   # -u, or untracked files stay behind
git pull
git stash pop

git pull --autostash is the one-command alternative, but only on a tree whose dirt is entirely
tracked. git stash does not stash untracked files, so an autostash over a ?? entry starts
the pull on the same dirty tree the check exists to refuse — the hook therefore reads porcelain
and denies --autostash whenever any ?? entry is present. At this step that is the usual
state, so the explicit -u stash above is the default route and --autostash is the shortcut for
the case where git status --porcelain shows no ?? lines at all. Git agrees independently: if
the incoming commits add a file at a path you are holding untracked, it aborts the merge
("untracked working tree files would be overwritten") after the autostash has already been
taken. Either route must be its own command — chaining the stash and the pull onto one line is
denied outright, because an identified history op reaches the tree reading only as a standalone
simple command.

ALLOW_DIRTY_MERGE=1 is the hatch for a dirty state you have looked at and can justify out loud.
It is not the routine remedy, and reaching for it because the block is inconvenient is the
behavior the check exists to prevent.

Step 7: Report

Report the PR URL and what was merged.

Important

• Never skip Step 0. Quality gates catch broken compilation, bad citations, and hardcoded paths before they reach main. If the user insists on skipping, record their override reason in the commit message.
• Always create a NEW branch — never commit directly to main.
• Exclude settings.local.json and sensitive files from staging.
• Use --merge (not --squash or --rebase) unless asked otherwise.
• If the commit message from $ARGUMENTS is provided, use it exactly.