Merge Pull Request

Merge Pull Request

Prepare PR for human merge via GitHub web UI (<30 seconds prep).

Purpose

Final step in V3 workflow: commit → create PR → fix PR → merge PR

Philosophy: AI prepares, human executes merge (trust + safety)

Handles:

• Verify CI passing (all checks green)
• Verify approvals (recommended but not required)
• Check working tree clean
• Verify Beads issue already closed (NOT close it - that happens at PR creation)
• Provide merge instructions for web UI
• Post-merge cleanup (switch to master, sync Beads, cache docs)

Human responsibility:

• Execute merge via GitHub web UI
• Delete remote branch (via web UI)

When to Use This Skill

Trigger phrases:

• "merge the PR"
• "merge it"
• "merge this"
• "prepare to merge"
• "ready to merge"

Automatically invoked when:

• User asks to merge current branch's PR
• User says "merge" in context of an open PR

Workflow

1. Get PR Context

# Get current branch
BRANCH=$(git branch --show-current)

# Extract FEATURE_KEY from feature-<KEY>
FEATURE_KEY=$(echo $BRANCH | sed 's/^feature-//')

# Get PR number and URL
gh pr view --json number,url -q '{number, url}'

2. Verify PR Status

A. Check CI Status

gh pr view --json statusCheckRollup -q '.statusCheckRollup[] | select(.status == "COMPLETED") | {name, conclusion}'

Criteria:

• ✅ All required checks passed → Proceed
• ⚠️ Some checks pending → Warn user, let them decide
• ❌ Failing checks → Block prep, suggest "fix the PR" first

B. Check Approvals (Recommended)

gh pr view --json reviewDecision -q '.reviewDecision'

Criteria:

• ✅ APPROVED → Ideal, proceed
• ⚠️ Empty (no reviews) → Warn but allow (solo dev OK)
• ❌ CHANGES_REQUESTED → Block prep, suggest addressing feedback first

C. Check Merge Conflicts

gh pr view --json mergeable -q '.mergeable'

Criteria:

• ✅ MERGEABLE → Proceed
• ❌ CONFLICTING → Block prep, suggest rebasing first

3. Check Working Tree

CRITICAL: Must be clean before closing Beads

git status --porcelain

If dirty:

• Ask user: "Working tree has uncommitted changes. Commit them first?"
• Options:
  • a) Commit changes now (with Feature-Key trailer)
  • b) Stash changes
  • c) Abort merge prep

If clean:

• Proceed to Beads verification

4. Verify Beads Issue Already Closed

CRITICAL: Issue must be closed BEFORE merge (happens at PR creation)

# Get current issue status
STATUS=$(bd show $FEATURE_KEY --json | jq -r '.status')

if [ "$STATUS" != "closed" ]; then
  echo "❌ Error: Beads issue must be closed BEFORE merge"
  echo ""
  echo "Current status: $STATUS"
  echo "Expected: closed"
  echo ""
  echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━"
  echo "Why this matters:"
  echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━"
  echo ""
  echo "Issues should be closed at PR creation time, not merge time."
  echo "This ensures JSONL merges atomically with code (no post-merge mutations)."
  echo ""
  echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━"
  echo "Recovery options:"
  echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━"
  echo ""
  echo "Option 1: Close issue now (less ideal but works)"
  echo "  bd close $FEATURE_KEY --reason \"Closing before merge in PR #$PR_NUMBER\""
  echo "  bd sync && git push"
  echo "  # Then retry merge"
  echo ""
  echo "Option 2: Close and recreate PR (atomic pattern)"
  echo "  bd close $FEATURE_KEY --reason \"Work complete, ready for review\""
  echo "  bd sync && git push"
  echo "  gh pr close $PR_NUMBER"
  echo "  gh pr create  # Creates new PR with JSONL already closed"
  echo ""
  echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━"
  echo "Future prevention:"
  echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━"
  echo ""
  echo "When creating PRs, use create-pull-request skill which asks:"
  echo "  'Is work complete?' → YES closes issue BEFORE creating PR"
  echo ""
  exit 1
fi

echo "✅ Beads issue already closed (status: $STATUS)"
echo "   → JSONL will merge atomically with code"
echo ""

Why verify instead of close:

• Structural fix: Issues closed at PR creation (create-pull-request skill)
• Atomic merge: JSONL already on feature branch when PR created
• No post-merge mutations: Never need to modify JSONL on master
• Prevents hook conflicts: All Beads state changes on feature branch
• Clear workflow: Closed = "ready to ship", Open = "work in progress"

5. Present Merge Instructions to User (MANDATORY)

This confirmation is REQUIRED. Provide web UI link and clear instructions.

✅ PR #156 Ready to Merge

Feature: GUARD_SKILL_ACTIVATION
Branch: feature-GUARD_SKILL_ACTIVATION
Beads: bd-pso (closed ✅)

Status:
✅ CI: All checks passed
✅ Beads: Closed and committed to feature branch
✅ Conflicts: None
✅ Working tree: Clean

📝 Merge Instructions:

1. Open PR in GitHub web UI:
   https://github.com/​fengning-starsend/​prime-radiant-ai/​pull/​156

2. Click "Squash and merge" button

3. Verify squash commit message includes:
   - Feature title
   - PR number
   - All commits squashed

4. Check "Delete branch" checkbox ✅

5. Confirm merge

After you merge, say "cleanup" and I'll switch to master and pull latest.

Why human merges:

• GitHub web UI handles squash reliably
• User sees final commit message before merge
• No risk of gh pr merge local cleanup failures
• User controls exact timing of merge
• Web UI provides visual confirmation

6. Wait for Human to Merge

Do not proceed automatically. Wait for:

• User confirmation: "merged" / "done" / "cleanup"
• User explicitly asks to verify merge succeeded

7. Post-Merge Cleanup (After User Confirms)

# Verify PR actually merged
STATE=$(gh pr view $PR_NUMBER --json state -q .state)

if [ "$STATE" != "MERGED" ]; then
  echo "⚠️ PR not merged yet. Waiting for merge..."
  exit 1
fi

# Get merge commit hash
MERGE_COMMIT=$(gh pr view $PR_NUMBER --json mergeCommit -q '.mergeCommit.oid' | cut -c1-7)

# Switch to master
git checkout master

# Pull latest (includes merge)
git pull origin master

# Verify merge commit is on master (search recent 20 commits, not just HEAD)
git log --oneline -20 | grep -q "$MERGE_COMMIT"

# Delete local feature branch (remote already deleted via web UI)
git branch -d feature-$FEATURE_KEY 2>/​dev/​null || echo "Branch already deleted"

# Sync Beads (imports closure from git)
bd sync

7.5. Auto-Cache Docs to Serena (If Docs Exist)

After successful merge, cache docs for searchability:

DOC_DIR="docs/​$FEATURE_KEY"

if [ -d "$DOC_DIR" ]; then
  echo "💾 Caching docs to Serena..."

  # Get issue details
  ISSUE_JSON=$(bd show $FEATURE_KEY --json)
  ISSUE_TITLE=$(echo "$ISSUE_JSON" | jq -r '.title')
  ISSUE_TYPE=$(echo "$ISSUE_JSON" | jq -r '.type')

  # Combine all markdown files into cache
  CACHE_CONTENT="# $FEATURE_KEY: $ISSUE_TITLE

**Status:** closed (merged in PR #$PR_NUMBER)
**Type:** $ISSUE_TYPE
**Merged:** $(date +%Y-%m-%d)
**Source:** $DOC_DIR/

**[CACHE]** This is a searchable cache. Source of truth: git ($DOC_DIR/)

---

"

  # Append all markdown files
  find "$DOC_DIR" -name "*.md" -type f | while read file; do
    echo "## $(basename $file .md)" >> /​tmp/​cache_${FEATURE_KEY}.tmp
    echo "" >> /​tmp/​cache_${FEATURE_KEY}.tmp
    cat "$file" >> /​tmp/​cache_${FEATURE_KEY}.tmp
    echo "" >> /​tmp/​cache_${FEATURE_KEY}.tmp
    echo "---" >> /​tmp/​cache_${FEATURE_KEY}.tmp
    echo "" >> /​tmp/​cache_${FEATURE_KEY}.tmp
  done

  CACHE_CONTENT+=$(cat /​tmp/​cache_${FEATURE_KEY}.tmp)
  rm /​tmp/​cache_${FEATURE_KEY}.tmp

  # Write to Serena using MCP tool
  mcp__serena__write_memory(
    memory_file_name="${FEATURE_KEY}_merged",
    content="$CACHE_CONTENT"
  )

  echo "✅ Cached to Serena: ${FEATURE_KEY}_merged"
  echo "   Search with: /​search '@serena ${FEATURE_KEY}'"
else
  echo "ℹ️  No docs to cache (Beads only)"
fi

Why auto-cache:

• Merged work becomes searchable via Serena
• Clearly marked as [CACHE] (not source of truth)
• Enables fast cross-feature references
• No manual step required
• Only happens after successful merge

Verification:

• ✅ On master branch
• ✅ Latest merge pulled
• ✅ Local feature branch deleted
• ✅ Beads synced
• ✅ Docs cached to Serena (if exist)

8. Confirm Completion

✅ Merge Complete

Merged: GUARD_SKILL_ACTIVATION → master
Commit: a1b2c3d (squashed 50 commits)
Beads: bd-pso (closed, synced to master)

Workspace:
✅ On master branch
✅ Pulled latest changes
✅ Local branch deleted
✅ Beads state synced

Ready for next feature.

Integration Points

With Beads

• Verifies issue already closed (closed at PR creation time by create-pull-request skill)
• JSONL already in PR (merged atomically with code)
• Syncs after merge (imports from master)
• No post-merge mutations (prevents hook conflicts on master)

With create-pull-request

• Completes lifecycle: create-pull-request → fix-pr-feedback → merge-pr
• Same PR (no new PRs)
• Bidirectional linking (PR → Beads, Beads → PR)

With GitHub Web UI

• Human control (user decides when to merge)
• Visual confirmation (see commit message before merging)
• Reliable squash (GitHub handles it)
• Branch cleanup (delete via checkbox)

Safety Guardrails

Before preparing:

• ✅ Verify CI passing (block if failing)
• ✅ Verify no conflicts (block if conflicting)
• ⚠️ Check approvals (warn if missing, allow for solo dev)
• ✅ Verify working tree clean (block if dirty)

Auto-prep allowed:

• All checks passed
• No conflicts
• Working tree clean

Require user approval:

• Checks pending (ask if they want to wait)
• No approvals yet (warn but allow)
• CHANGES_REQUESTED (block, suggest fix-pr-feedback)

Never auto-prep:

• Failing CI checks
• Merge conflicts
• Dirty working tree
• User hasn't confirmed

Best Practices

1. Verify issue already closed - Should be closed at PR creation time
2. Clean working tree - No uncommitted changes before verification
3. Human merges - Trust web UI reliability
4. Wait for confirmation - Don't assume merge happened
5. Verify merge - Check PR state before cleanup
6. Sync Beads after - Import closure from master
7. Atomic merge pattern - JSONL merges with code (no post-merge mutations)

What This Skill Does

✅ Verify PR merge-readiness (CI, approvals, conflicts) ✅ Check working tree clean (block if dirty) ✅ Verify Beads issue already closed (error if not) ✅ Provide merge instructions with web UI link ✅ Wait for human to merge ✅ Clean up local workspace after merge ✅ Sync Beads state from master ✅ Auto-cache docs to Serena (if exist)

What This Skill DOESN'T Do

❌ Merge PR automatically (human does via web UI) ❌ Delete remote branch (human does via web UI checkbox) ❌ Skip user confirmation (always waits for "merged" confirmation) ❌ Close Beads issue (already closed at PR creation time by create-pull-request skill) ❌ Push to master (never, pre-push hook blocks) ❌ Modify JSONL on master (never - atomic merge pattern prevents this)

Anti-Patterns

❌ Closing Beads at merge time (should be closed at PR creation) ❌ Committing to master directly (pre-push hook blocks this) ❌ Auto-merging without human confirmation ❌ Skipping working tree check ❌ Not verifying merge succeeded before cleanup ❌ Modifying JSONL on master (causes hook conflicts)

Example Scenarios

Scenario 1: Clean Merge (Issue Already Closed)

User: "merge the PR"

AI:
1. Checks PR #156: CI passed ✅, No conflicts ✅
2. Checks working tree: Clean ✅
3. Verifies bd-pso status: closed ✅ (closed at PR creation)
4. Presents merge instructions with web UI link
5. Waits...

User: [Merges via web UI, deletes branch]

User: "merged"

AI:
6. Verifies PR state = MERGED
7. Switches to master, pulls
8. Deletes local branch
9. Syncs Beads
10. Caches docs to Serena
11. Confirms: "✅ Merge complete, workspace clean"

Scenario 2: Dirty Working Tree

User: "merge the PR"

AI:
1. Checks PR status: ✅ Ready
2. Checks working tree: ❌ Dirty (.beads/​beads.left.meta.json modified)
3. Asks: "Working tree has uncommitted changes. Options:
   a) Commit changes now
   b) Stash changes
   c) Abort merge prep"

User: "commit them"

AI:
4. Commits changes with Feature-Key trailer
5. Pushes to feature branch
6. Proceeds with Beads verification
7. Verifies issue closed ✅
8. Presents merge instructions

Scenario 3: Failing CI

User: "merge the PR"

AI:
1. Checks CI: ❌ 2 checks failing (lint, test)
2. Blocks merge prep
3. Suggests: "❌ Cannot prepare merge: CI checks failing

   Failing checks:
   - lint: Line too long
   - test: AssertionError in test_foo

   Suggestion: Use 'fix the PR' to address failures first."

Scenario 4: Issue Not Closed (Structural Problem)

User: "merge the PR"

AI:
1. Checks PR #200: CI passed ✅, No conflicts ✅
2. Checks working tree: Clean ✅
3. Checks Beads status: ❌ in_progress (NOT closed!)
4. Errors with recovery options:
   "❌ Error: Beads issue must be closed BEFORE merge

   Current status: in_progress
   Expected: closed

   Why this matters:
   Issues should be closed at PR creation time, not merge time.
   This ensures JSONL merges atomically with code.

   Recovery options:

   Option 1: Close issue now (less ideal but works)
     bd close bd-xyz --reason 'Closing before merge in PR #200'
     bd sync && git push
     # Then retry merge

   Option 2: Close and recreate PR (atomic pattern)
     bd close bd-xyz --reason 'Work complete, ready for review'
     bd sync && git push
     gh pr close 200
     gh pr create  # Creates new PR with JSONL already closed

   Future prevention:
   When creating PRs, use create-pull-request skill which asks:
     'Is work complete?' → YES closes issue BEFORE creating PR"

Scenario 5: User Merges Before Confirmation

User: "merge the PR"

AI:
1. Prepares merge (closes Beads, commits, pushes)
2. Presents merge instructions
3. Waits for confirmation...

User: [Merges immediately without saying anything]

User: "check if it merged"

AI:
4. Checks PR state: MERGED ✅
5. Proceeds with cleanup
6. Confirms completion

Troubleshooting

"Working tree dirty" error

Cause: Uncommitted changes in working tree Fix: Commit or stash changes, then retry

"PR not found" error

Cause: Not on a feature branch, or PR doesn't exist Fix: Switch to feature branch with open PR

"CI checks failing" error

Cause: Required checks not passing Fix: Use fix-pr-feedback skill to address failures

"Merge conflicts" error

Cause: Branch conflicts with master Fix: Rebase on master: git fetch origin master && git rebase origin/​master

"bd close failed" error

Cause: Beads issue doesn't exist or already closed Fix: Verify issue ID matches branch name

Future Enhancements

1. Auto-wait for CI - Poll until checks complete
2. Conflict auto-resolution - Attempt automatic rebase
3. Smart approval - Request review if needed
4. Post-merge validation - Verify deployment succeeded
5. Rollback support - Quick revert if issues found

---

Last Updated: 2025-11-13 Related Skills: create-pull-request, fix-pr-feedback, sync-feature-branch Helper Scripts: scripts/​bd-link-pr References:

• PR workflow: AGENTS.md
• Beads integration: .claude/​skills/​beads-workflow/​SKILL.md

Changelog:

• 2025-11-13: Initial creation with CI verification, approval checking, mandatory user confirmation
• 2025-11-13: BREAKING - Changed to human-merge workflow (Option A). AI prepares (closes Beads on feature branch), human merges via web UI, AI cleans up after confirmation. Fixes gh pr merge local cleanup failures.