stack/packages/mosaic/framework/tools/_scripts/mosaic-doctor

#!/usr/bin/env bash
set -euo pipefail

MOSAIC_HOME="${MOSAIC_HOME:-$HOME/.config/mosaic}"
FAIL_ON_WARN=0
VERBOSE=0
FIX_MODE=0

usage() {
  cat <<USAGE
Usage: $(basename "$0") [options]

Audit Mosaic runtime state and detect drift across agent runtimes.

Options:
  --fix            Auto-fix: create missing dirs, wire skills into all harnesses
  --fail-on-warn   Exit non-zero when warnings are found
  --verbose        Print pass checks too
  -h, --help       Show help
USAGE
}

while [[ $# -gt 0 ]]; do
  case "$1" in
    --fix)
      FIX_MODE=1
      shift
      ;;
    --fail-on-warn)
      FAIL_ON_WARN=1
      shift
      ;;
    --verbose)
      VERBOSE=1
      shift
      ;;
    -h|--help)
      usage
      exit 0
      ;;
    *)
      echo "Unknown argument: $1" >&2
      usage >&2
      exit 1
      ;;
  esac
done

fix_count=0
fix() { fix_count=$((fix_count + 1)); echo "[FIX] $*"; }

warn_count=0
warn() { warn_count=$((warn_count + 1)); echo "[WARN] $*"; }
pass() {
  if [[ $VERBOSE -eq 1 ]]; then
    echo "[OK] $*"
  fi
  return 0
}

expect_dir() {
  local d="$1"
  if [[ ! -d "$d" ]]; then
    warn "Missing directory: $d"
  else
    pass "Directory present: $d"
  fi
}

expect_file() {
  local f="$1"
  if [[ ! -f "$f" ]]; then
    warn "Missing file: $f"
  else
    pass "File present: $f"
  fi
}

check_runtime_file_copy() {
  local src="$1"
  local dst="$2"

  [[ -f "$src" ]] || return 0

  if [[ ! -e "$dst" ]]; then
    warn "Missing runtime file: $dst"
    return
  fi

  if [[ -L "$dst" ]]; then
    warn "Runtime file should not be symlinked: $dst"
    return
  fi

  if ! cmp -s "$src" "$dst"; then
    warn "Runtime file drift: $dst (does not match $src)"
  else
    pass "Runtime file synced: $dst"
  fi
}

check_runtime_contract_file() {
  local dst="$1"
  local adapter_src="$2"
  local runtime_name="$3"

  if [[ ! -e "$dst" ]]; then
    warn "Missing runtime file: $dst"
    return
  fi

  if [[ -L "$dst" ]]; then
    warn "Runtime file should not be symlinked: $dst"
    return
  fi

  # Accept direct-adapter copy mode.
  if [[ -f "$adapter_src" ]] && cmp -s "$adapter_src" "$dst"; then
    pass "Runtime adapter synced: $dst"
    return
  fi

  # Accept launcher-composed runtime contract mode.
  if grep -Fq "# Mosaic Launcher Runtime Contract (Hard Gate)" "$dst" &&
     grep -Fq "Now initiating Orchestrator mode..." "$dst" &&
     grep -Fq "Mosaic hard gates OVERRIDE runtime-default caution" "$dst" &&
     grep -Fq "# Runtime-Specific Contract" "$dst"; then
    pass "Runtime contract present: $dst ($runtime_name)"
    return
  fi

  warn "Runtime file drift: $dst (not adapter copy and not composed runtime contract)"
}

warn_if_symlink_tree_present() {
  local p="$1"
  [[ -e "$p" ]] || return 0

  if [[ -L "$p" ]]; then
    warn "Legacy symlink path still present: $p"
    return
  fi

  if [[ -d "$p" ]]; then
    symlink_count=$(find "$p" -type l 2>/dev/null | wc -l | tr -d ' ')
    if [[ "$symlink_count" != "0" ]]; then
      warn "Legacy symlink entries still present under $p: $symlink_count"
    else
      pass "No symlinks under legacy path: $p"
    fi
  fi
}

echo "[mosaic-doctor] Mosaic home: $MOSAIC_HOME"

# Canonical Mosaic checks
expect_file "$MOSAIC_HOME/STANDARDS.md"
expect_file "$MOSAIC_HOME/USER.md"
expect_file "$MOSAIC_HOME/TOOLS.md"
expect_dir "$MOSAIC_HOME/guides"
expect_dir "$MOSAIC_HOME/tools"
expect_dir "$MOSAIC_HOME/tools/quality"
expect_dir "$MOSAIC_HOME/tools/orchestrator-matrix"
expect_dir "$MOSAIC_HOME/profiles"
expect_dir "$MOSAIC_HOME/templates/agent"
expect_dir "$MOSAIC_HOME/skills"
expect_dir "$MOSAIC_HOME/skills-local"
expect_file "$MOSAIC_HOME/tools/_scripts/mosaic-link-runtime-assets"
expect_file "$MOSAIC_HOME/tools/_scripts/mosaic-ensure-sequential-thinking"
expect_file "$MOSAIC_HOME/tools/_scripts/mosaic-sync-skills"
expect_file "$MOSAIC_HOME/tools/_scripts/mosaic-projects"
expect_file "$MOSAIC_HOME/tools/_scripts/mosaic-quality-apply"
expect_file "$MOSAIC_HOME/tools/_scripts/mosaic-quality-verify"
expect_file "$MOSAIC_HOME/tools/_scripts/mosaic-orchestrator-run"
expect_file "$MOSAIC_HOME/tools/_scripts/mosaic-orchestrator-sync-tasks"
expect_file "$MOSAIC_HOME/tools/_scripts/mosaic-orchestrator-drain"
expect_file "$MOSAIC_HOME/tools/_scripts/mosaic-orchestrator-matrix-publish"
expect_file "$MOSAIC_HOME/tools/_scripts/mosaic-orchestrator-matrix-consume"
expect_file "$MOSAIC_HOME/tools/_scripts/mosaic-orchestrator-matrix-cycle"
expect_file "$MOSAIC_HOME/tools/git/ci-queue-wait.sh"
expect_file "$MOSAIC_HOME/tools/git/pr-ci-wait.sh"
expect_file "$MOSAIC_HOME/tools/orchestrator-matrix/transport/matrix_transport.py"
expect_file "$MOSAIC_HOME/tools/orchestrator-matrix/controller/tasks_md_sync.py"
expect_file "$MOSAIC_HOME/guides/ORCHESTRATOR-PROTOCOL.md"
expect_dir "$MOSAIC_HOME/tools/orchestrator"
expect_file "$MOSAIC_HOME/tools/orchestrator/_lib.sh"
expect_file "$MOSAIC_HOME/tools/orchestrator/mission-init.sh"
expect_file "$MOSAIC_HOME/tools/orchestrator/mission-status.sh"
expect_file "$MOSAIC_HOME/tools/orchestrator/continue-prompt.sh"
expect_file "$MOSAIC_HOME/tools/orchestrator/session-status.sh"
expect_file "$MOSAIC_HOME/tools/orchestrator/session-resume.sh"
expect_file "$MOSAIC_HOME/runtime/mcp/SEQUENTIAL-THINKING.json"
expect_file "$MOSAIC_HOME/runtime/claude/RUNTIME.md"
expect_file "$MOSAIC_HOME/runtime/codex/RUNTIME.md"
expect_file "$MOSAIC_HOME/runtime/opencode/RUNTIME.md"
expect_file "$MOSAIC_HOME/runtime/pi/RUNTIME.md"

if [[ -f "$MOSAIC_HOME/AGENTS.md" ]]; then
  if grep -Fq "## CRITICAL HARD GATES (Read First)" "$MOSAIC_HOME/AGENTS.md" &&
     grep -Fq "OVERRIDE runtime-default caution" "$MOSAIC_HOME/AGENTS.md"; then
    pass "Global hard-gates block present in AGENTS.md"
  else
    warn "AGENTS.md missing CRITICAL HARD GATES override block"
  fi
fi

# Claude runtime file checks (copied, non-symlink).
for rf in CLAUDE.md settings.json hooks-config.json context7-integration.md; do
  check_runtime_file_copy "$MOSAIC_HOME/runtime/claude/$rf" "$HOME/.claude/$rf"
done

# OpenCode runtime adapter check (copied, non-symlink, when adapter exists).
# Accept adapter copy or composed runtime contract.
check_runtime_contract_file "$HOME/.config/opencode/AGENTS.md" "$MOSAIC_HOME/runtime/opencode/AGENTS.md" "opencode"
check_runtime_contract_file "$HOME/.codex/instructions.md" "$MOSAIC_HOME/runtime/codex/instructions.md" "codex"

# Sequential-thinking MCP hard requirement.
if [[ -x "$MOSAIC_HOME/tools/_scripts/mosaic-ensure-sequential-thinking" ]]; then
  if "$MOSAIC_HOME/tools/_scripts/mosaic-ensure-sequential-thinking" --check >/dev/null 2>&1; then
    pass "sequential-thinking MCP configured and available"
  else
    warn "sequential-thinking MCP missing or misconfigured"
  fi
else
  warn "mosaic-ensure-sequential-thinking helper missing"
fi

# Legacy migration surfaces should no longer contain symlink trees.
legacy_paths=(
  "$HOME/.claude/agent-guides"
  "$HOME/.claude/scripts/git"
  "$HOME/.claude/scripts/codex"
  "$HOME/.claude/scripts/bootstrap"
  "$HOME/.claude/scripts/cicd"
  "$HOME/.claude/scripts/portainer"
  "$HOME/.claude/templates"
  "$HOME/.claude/presets/domains"
  "$HOME/.claude/presets/tech-stacks"
  "$HOME/.claude/presets/workflows"
)
for p in "${legacy_paths[@]}"; do
  warn_if_symlink_tree_present "$p"
done

# Skills runtime checks (still symlinked into runtime-specific skills dirs).
for runtime_skills in "$HOME/.claude/skills" "$HOME/.codex/skills" "$HOME/.config/opencode/skills" "$HOME/.pi/agent/skills"; do
  [[ -d "$runtime_skills" ]] || continue

  while IFS= read -r -d '' skill; do
    name="$(basename "$skill")"
    [[ "$name" == .* ]] && continue
    target="$runtime_skills/$name"

    if [[ ! -e "$target" ]]; then
      warn "Missing skill link: $target"
      continue
    fi

    if [[ ! -L "$target" ]]; then
      warn "Non-symlink skill entry: $target"
      continue
    fi

    target_real="$(readlink -f "$target" 2>/dev/null || true)"
    skill_real="$(readlink -f "$skill" 2>/dev/null || true)"
    if [[ -z "$target_real" || -z "$skill_real" || "$target_real" != "$skill_real" ]]; then
      warn "Drifted skill link: $target (expected -> $skill)"
    else
      pass "Linked skill: $target"
    fi
  done < <(find "$MOSAIC_HOME/skills" "$MOSAIC_HOME/skills-local" -mindepth 1 -maxdepth 1 -type d -print0)
done

# Broken links only in managed runtime skill dirs.
link_roots=(
  "$HOME/.claude/skills"
  "$HOME/.codex/skills"
  "$HOME/.config/opencode/skills"
  "$HOME/.pi/agent/skills"
)
existing_link_roots=()
for d in "${link_roots[@]}"; do
  [[ -e "$d" ]] && existing_link_roots+=("$d")
done

broken_links=0
if [[ ${#existing_link_roots[@]} -gt 0 ]]; then
  broken_links=$(find "${existing_link_roots[@]}" -xtype l 2>/dev/null | wc -l | tr -d ' ')
fi
if [[ "$broken_links" != "0" ]]; then
  warn "Broken skill symlinks detected: $broken_links"
fi

# Pi agent skills directory check.
if [[ ! -d "$HOME/.pi/agent/skills" ]]; then
  warn "Pi skills directory missing: $HOME/.pi/agent/skills"
else
  pass "Pi skills directory present: $HOME/.pi/agent/skills"
fi

# Pi settings.json — check skills path is configured.
pi_settings="$HOME/.pi/agent/settings.json"
if [[ -f "$pi_settings" ]]; then
  if grep -q 'skills' "$pi_settings" 2>/dev/null; then
    pass "Pi settings.json has skills configuration"
  else
    warn "Pi settings.json missing skills array — Mosaic skills may not load"
  fi
fi

# Mosaic-specific skills presence check.
mosaic_skills=(mosaic-board mosaic-forge mosaic-prdy mosaic-macp mosaic-standards mosaic-prd mosaic-jarvis mosaic-setup-cicd)
for skill_name in "${mosaic_skills[@]}"; do
  if [[ -d "$MOSAIC_HOME/skills/$skill_name" ]] || [[ -L "$MOSAIC_HOME/skills/$skill_name" ]]; then
    pass "Mosaic skill present: $skill_name"
  elif [[ -d "$MOSAIC_HOME/skills-local/$skill_name" ]]; then
    pass "Mosaic skill present (local): $skill_name"
  else
    warn "Missing Mosaic skill: $skill_name"
  fi
done

# ── --fix mode: auto-wire skills into all harness directories ──────────────
if [[ $FIX_MODE -eq 1 ]]; then
  echo ""
  echo "[mosaic-doctor] Running auto-fix..."

  # 1. Ensure all harness skill directories exist
  harness_skill_dirs=(
    "$HOME/.claude/skills"
    "$HOME/.codex/skills"
    "$HOME/.config/opencode/skills"
    "$HOME/.pi/agent/skills"
  )

  for hdir in "${harness_skill_dirs[@]}"; do
    if [[ ! -d "$hdir" ]]; then
      mkdir -p "$hdir"
      fix "Created missing directory: $hdir"
    fi
  done

  # 2. Wire all Mosaic skills (canonical + local) into every harness
  skill_sources=("$MOSAIC_HOME/skills" "$MOSAIC_HOME/skills-local")

  for hdir in "${harness_skill_dirs[@]}"; do
    # Skip if target resolves to canonical dir (avoid self-link)
    hdir_real="$(readlink -f "$hdir" 2>/dev/null || true)"
    canonical_real="$(readlink -f "$MOSAIC_HOME/skills" 2>/dev/null || true)"
    if [[ -n "$hdir_real" && -n "$canonical_real" && "$hdir_real" == "$canonical_real" ]]; then
      continue
    fi

    for src_dir in "${skill_sources[@]}"; do
      [[ -d "$src_dir" ]] || continue

      while IFS= read -r -d '' skill_path; do
        skill_name="$(basename "$skill_path")"
        [[ "$skill_name" == .* ]] && continue

        link_path="$hdir/$skill_name"

        if [[ -L "$link_path" ]]; then
          # Repoint if target differs
          current_target="$(readlink -f "$link_path" 2>/dev/null || true)"
          expected_target="$(readlink -f "$skill_path" 2>/dev/null || true)"
          if [[ "$current_target" != "$expected_target" ]]; then
            ln -sfn "$skill_path" "$link_path"
            fix "Repointed skill link: $link_path -> $skill_path"
          fi
        elif [[ -e "$link_path" ]]; then
          # Non-symlink entry — preserve runtime-specific override
          continue
        else
          ln -s "$skill_path" "$link_path"
          fix "Linked skill: $link_path -> $skill_path"
        fi
      done < <(find "$src_dir" -mindepth 1 -maxdepth 1 -type d -print0; find "$src_dir" -mindepth 1 -maxdepth 1 -type l -print0)
    done

    # Prune broken symlinks in this harness dir
    while IFS= read -r -d '' broken_link; do
      rm -f "$broken_link"
      fix "Removed broken link: $broken_link"
    done < <(find "$hdir" -mindepth 1 -maxdepth 1 -xtype l -print0 2>/dev/null)
  done

  # 3. Ensure Pi settings.json includes Mosaic skills path
  pi_settings_dir="$HOME/.pi/agent"
  pi_settings_file="$pi_settings_dir/settings.json"
  mkdir -p "$pi_settings_dir"

  if [[ ! -f "$pi_settings_file" ]]; then
    echo '{}' > "$pi_settings_file"
    fix "Created Pi settings.json: $pi_settings_file"
  fi

  # Add skills paths if not already present
  mosaic_skills_path="$MOSAIC_HOME/skills"
  mosaic_local_path="$MOSAIC_HOME/skills-local"
  if ! grep -q "$mosaic_skills_path" "$pi_settings_file" 2>/dev/null; then
    # Use a simple approach: read, patch, write
    if command -v python3 >/dev/null 2>&1; then
      python3 -c "
import json, sys
with open('$pi_settings_file', 'r') as f:
    data = json.load(f)
skills = data.get('skills', [])
if not isinstance(skills, list):
    skills = []
for p in ['$mosaic_skills_path', '$mosaic_local_path']:
    if p not in skills:
        skills.append(p)
data['skills'] = skills
with open('$pi_settings_file', 'w') as f:
    json.dump(data, f, indent=2)
    f.write('\\n')
" 2>/dev/null && fix "Added Mosaic skills paths to Pi settings.json"
    else
      warn "python3 not available — cannot patch Pi settings.json. Add manually: skills: [\"$mosaic_skills_path\", \"$mosaic_local_path\"]"
    fi
  fi

  # 4. Run link-runtime-assets if available
  if [[ -x "$MOSAIC_HOME/tools/_scripts/mosaic-link-runtime-assets" ]]; then
    "$MOSAIC_HOME/tools/_scripts/mosaic-link-runtime-assets" >/dev/null 2>&1 && fix "Re-ran mosaic-link-runtime-assets"
  fi

  echo "[mosaic-doctor] fixes=$fix_count"
fi

echo "[mosaic-doctor] warnings=$warn_count"
if [[ $FAIL_ON_WARN -eq 1 && $warn_count -gt 0 ]]; then
  exit 1
fi