fix(workflow): protect orchestrator files during worktree merge (#1756) (#1764)

When a worktree branch outlives a milestone transition, git merge
silently overwrites STATE.md and ROADMAP.md with stale content and
resurrects archived phase directories. Fix by backing up orchestrator
files before merge, restoring after, and detecting resurrected files.

Fixes #1761

Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>

get-shit-done/workflows/execute-phase.md

@@ -485,12 +485,51 @@ Execute each selected wave in sequence. Within a wave: parallel if `PARALLELIZAT
      if [ -n "$WT_BRANCH" ] && [ "$WT_BRANCH" != "HEAD" ]; then
        CURRENT_BRANCH=$(git rev-parse --abbrev-ref HEAD)
 
+       # --- Orchestrator file protection (#1756) ---
+       # Snapshot orchestrator-owned files BEFORE merge. If the worktree
+       # branch outlived a milestone transition, its versions of STATE.md
+       # and ROADMAP.md are stale. Main always wins for these files.
+       STATE_BACKUP=$(mktemp)
+       ROADMAP_BACKUP=$(mktemp)
+       git show HEAD:.planning/STATE.md > "$STATE_BACKUP" 2>/dev/null || true
+       git show HEAD:.planning/ROADMAP.md > "$ROADMAP_BACKUP" 2>/dev/null || true
+
+       # Snapshot list of files on main BEFORE merge to detect resurrections
+       PRE_MERGE_FILES=$(git ls-files .planning/)
+
        # Merge the worktree branch into the current branch
        git merge "$WT_BRANCH" --no-edit -m "chore: merge executor worktree ($WT_BRANCH)" 2>&1 || {
          echo "⚠ Merge conflict from worktree $WT_BRANCH — resolve manually"
+         rm -f "$STATE_BACKUP" "$ROADMAP_BACKUP"
          continue
        }
 
+       # Restore orchestrator-owned files (main always wins)
+       if [ -s "$STATE_BACKUP" ]; then
+         cp "$STATE_BACKUP" .planning/STATE.md
+       fi
+       if [ -s "$ROADMAP_BACKUP" ]; then
+         cp "$ROADMAP_BACKUP" .planning/ROADMAP.md
+       fi
+       rm -f "$STATE_BACKUP" "$ROADMAP_BACKUP"
+
+       # Detect files deleted on main but re-added by worktree merge
+       # (e.g., archived phase directories that were intentionally removed)
+       DELETED_FILES=$(git diff --diff-filter=A --name-only HEAD~1 -- .planning/ 2>/dev/null || true)
+       for RESURRECTED in $DELETED_FILES; do
+         # Check if this file was NOT in main's pre-merge tree
+         if ! echo "$PRE_MERGE_FILES" | grep -qxF "$RESURRECTED"; then
+           git rm -f "$RESURRECTED" 2>/dev/null || true
+         fi
+       done
+
+       # Amend merge commit with restored files if any changed
+       if ! git diff --quiet .planning/STATE.md .planning/ROADMAP.md 2>/dev/null || \
+          [ -n "$DELETED_FILES" ]; then
+         git add .planning/STATE.md .planning/ROADMAP.md 2>/dev/null || true
+         git commit --amend --no-edit 2>/dev/null || true
+       fi
+
        # Remove the worktree
        git worktree remove "$WT" --force 2>/dev/null || true