Doctor

Session-start health checks for swain projects. Validates and repairs health across all swain skills — governance, tools, directories, settings, scripts, caches, and runtime state. Auto-migrates stale .beads/ directories to .tickets/ and removes them. Idempotent — run it every session; it only writes when repairs are needed.

Run checks in the order listed below. Collect all findings into a summary table at the end.

Preflight integration

A lightweight shell script (skills/swain-doctor/scripts/swain-preflight.sh) performs quick checks before invoking the full doctor. If preflight exits 0, swain-doctor is skipped for the session. If it exits 1, swain-doctor runs normally.

The preflight checks are a subset of this skill's checks — governance files, .agents directory, .tickets health, script permissions. It runs as pure bash with zero agent tokens. See AGENTS.md § Session startup for the invocation flow.

When invoked directly by the user (not via the auto-invoke flow), swain-doctor always runs regardless of preflight status.

Session-start governance check

Detect the agent platform and locate the context file:

| Platform | Context file | Detection | |----------|-------------|-----------| | Claude Code | CLAUDE.md (project root) | Default — use if no other platform detected | | Cursor | .cursor/rules/swain-governance.mdc | .cursor/ directory exists |
Check whether governance rules are already present:
```
grep -l "swain governance" CLAUDE.md AGENTS.md .cursor/rules/swain-governance.mdc 2>/dev/null
```
If any file matches, governance is already installed. Proceed to Legacy skill cleanup.
If no match, run Legacy skill cleanup, then proceed to Governance injection.

Legacy skill cleanup

Clean up renamed and retired skill directories using fingerprint checks. Read references/legacy-cleanup.md for the full procedure. Data source: skills/swain-doctor/references/legacy-skills.json.

Platform dotfolder cleanup

Remove dotfolder stubs (.windsurf/, .cursor/, etc.) for agent platforms that are not installed. Read references/platform-cleanup.md for the detection and cleanup procedure. Requires jq.

Governance injection

Inject governance rules into the platform context file when missing. Read references/governance-injection.md for Claude Code and Cursor injection procedures. Source: skills/swain-doctor/references/AGENTS.content.md.

Tickets directory validation

Validates .tickets/ health — YAML frontmatter, stale locks. Skip if .tickets/ does not exist. Read references/tickets-validation.md for the full procedure.

Stale .beads/ migration and cleanup

Auto-migrates .beads/ → .tickets/ if present. Skip if .beads/ does not exist. Read references/beads-migration.md for the migration procedure.

Governance content reference

The canonical governance rules live in skills/swain-doctor/references/AGENTS.content.md. Both swain-doctor and swain-init read from this single source of truth. If the upstream rules change in a future swain release, update that file and bump the skill version. Consumers who want the updated rules can delete the  block from their context file and re-run this skill.

Tool availability

Check required (git, jq) and optional (tk, uv, gh, tmux, fswatch) tools. Never install automatically. Read references/tool-availability.md for the check commands, degradation notes, and reporting format.

Runtime checks

Memory directory, settings validation, script permissions, .agents directory, and status cache bootstrap. Read references/runtime-checks.md for the full procedures and bash commands.

tk health (extended .tickets checks)

Verify vendored tk is executable at skills/swain-do/bin/tk and check for stale lock files. Skip if .tickets/ does not exist. See references/tickets-validation.md for details.

Lifecycle directory migration

Detect old phase directories from before ADR-003's three-track normalization. Old directory names: Draft/, Planned/, Review/, Approved/, Testing/, Implemented/, Adopted/, Deprecated/, Archived/, Sunset/, Validated/.

Detection

OLD_PHASES="Draft Planned Review Approved Testing Implemented Adopted Deprecated Archived Sunset Validated"
for dir in docs/*/; do
  for phase in $OLD_PHASES; do
    if [[ -d "${dir}${phase}" ]]; then
      # Check for non-empty (ignore hidden files)
      if find "${dir}${phase}" -maxdepth 1 -not -name '.*' -print -quit 2>/dev/null | grep -q .; then
        echo "  Old directory: ${dir}${phase}"
      fi
    fi
  done
done

Remediation

List each old directory and its artifact count.
Explain: "ADR-003 normalized artifact lifecycle phases into three tracks. Old phase directories need migration."
Check for the migration script: skills/swain-design/scripts/migrate-lifecycle-dirs.py
- If available: offer to run uv run python3 skills/swain-design/scripts/migrate-lifecycle-dirs.py --dry-run first, then the real migration.
- If unavailable: provide manual git mv instructions using the phase mapping from ADR-003.
After migration, clean up empty old directories.

Status values

ok — no old directories found
repaired — migration script ran successfully
warning — old directories found, user chose not to migrate now

Superpowers detection

Check whether superpowers skills are installed:

SUPERPOWERS_SKILLS="brainstorming writing-plans test-driven-development verification-before-completion subagent-driven-development executing-plans"
found=0
missing=0
missing_names=""
for skill in $SUPERPOWERS_SKILLS; do
  if ls .agents/skills/$skill/SKILL.md .claude/skills/$skill/SKILL.md 2>/dev/null | head -1 | grep -q .; then
    found=$((found + 1))
  else
    missing=$((missing + 1))
    missing_names="$missing_names $skill"
  fi
done

Status values

ok — all superpowers skills detected
warning — some or all superpowers skills missing. Report which are missing and note: "Superpowers provides brainstorming, TDD, plan writing, and verification skills that chain with swain-design and swain-do. Install with: npx @anthropic/claude-code-skills add obra/superpowers"
partial — some skills present, some missing. List the missing ones — a partial install may indicate a failed update.

Superpowers is strongly recommended but not required. This is always a warning, never a blocker.

Stale worktree detection

Enumerate all linked worktrees and classify their health. Skip if the repo has no linked worktrees (i.e., git worktree list --porcelain returns only the main worktree entry) — this check produces no output in a clean repo.

Detection

git worktree list --porcelain

Parse each linked worktree (exclude the main worktree — the first entry in the output):

git worktree list --porcelain | awk '
  /^worktree / { path=$2 }
  /^branch /   { branch=$2 }
  /^$/         { if (path != "") print path, branch; path=""; branch="" }
' | tail -n +2

For each linked worktree:

Orphaned — directory does not exist on disk ([ ! -d "$path" ]):
- WARN: "Orphaned worktree: <path> (directory missing). Clean up with: git worktree prune"
Stale (merged) — directory exists and branch is fully merged into main:
```
git merge-base --is-ancestor "$branch" origin/main
```
- WARN: "Stale worktree: <path> (branch <branch> already merged into main). Safe to remove: git worktree remove <path> && git branch -d <branch>"
Active (unmerged) — directory exists and branch has commits not in main:
- INFO: "Active worktree: <path> (branch <branch>, N commits ahead of main). Do not remove — work in progress."

Do not remove any worktree automatically. All output is advisory.

Status values

ok — no linked worktrees, or all are active
warning — one or more stale or orphaned worktrees found (provide cleanup commands per item)

Summary report

After all checks complete, output a concise summary table:

swain-doctor summary:
  Governance ......... ok
  Legacy cleanup ..... ok (nothing to clean)
  Platform dotfolders  ok (nothing to clean)
  .tickets/ .......... ok
  Stale .beads/ ...... ok (not present)
  Tools .............. ok (1 optional missing: fswatch)
  Memory directory ... ok
  Settings ........... ok
  Script permissions . ok
  .agents directory .. ok
  Status cache ....... seeded
  tk health .......... ok
  Worktrees .......... ok
  Superpowers ........ ok (6/6 skills detected)

3 checks performed repairs. 0 issues remain.

Use these status values:

ok — nothing to do
repaired — issue found and fixed automatically
warning — issue found, user action recommended (give specifics)
skipped — check could not run (e.g., jq missing for JSON validation)

If any checks have warnings, list them below the table with remediation steps.