gsd-remix 1.0.0

package/get-shit-done/bin/gsd-tools.cjs

@@ -0,0 +1,1263 @@
+#!/usr/bin/env node
+
+/**
+ * @deprecated The supported programmatic surface is `gsd-remix-sdk query` (SDK query registry)
+ * and the `@gsd-remix/sdk` package. This Node CLI remains the compatibility implementation
+ * for shell scripts and older workflows; prefer calling the SDK from agents and automation.
+ *
+ * GSD Tools — CLI utility for GSD workflow operations
+ *
+ * Replaces repetitive inline bash patterns across ~50 GSD command/workflow/agent files.
+ * Centralizes: config parsing, model resolution, phase lookup, git commits, summary verification.
+ *
+ * Usage: node gsd-tools.cjs <command> [args] [--raw] [--pick <field>]
+ *
+ * Atomic Commands:
+ *   state load                         Load project config + state
+ *   state json                         Output STATE.md frontmatter as JSON
+ *   state update <field> <value>       Update a STATE.md field
+ *   state get [section]                Get STATE.md content or section
+ *   state patch --field val ...        Batch update STATE.md fields
+ *   state begin-phase --phase N --name S --plans C  Update STATE.md for new phase start
+ *   state signal-waiting --type T --question Q --options "A|B" --phase P  Write WAITING.json signal
+ *   state signal-resume                Remove WAITING.json signal
+ *   resolve-model <agent-type>         Get model for agent based on profile
+ *   find-phase <phase>                 Find phase directory by number
+ *   commit <message> [--files f1 f2] [--no-verify]   Commit planning docs
+ *   commit-to-subrepo <msg> --files f1 f2  Route commits to sub-repos
+ *   verify-summary <path>              Verify a SUMMARY.md file
+ *   generate-slug <text>               Convert text to URL-safe slug
+ *   current-timestamp [format]         Get timestamp (full|date|filename)
+ *   list-todos [area]                  Count and enumerate pending todos
+ *   verify-path-exists <path>          Check file/directory existence
+ *   config-ensure-section              Initialize .planning/config.json
+ *   history-digest                     Aggregate all SUMMARY.md data
+ *   summary-extract <path> [--fields]  Extract structured data from SUMMARY.md
+ *   state-snapshot                     Structured parse of STATE.md
+ *   phase-plan-index <phase>           Index plans with waves and status
+ *   websearch <query>                  Search web via Brave API (if configured)
+ *     [--limit N] [--freshness day|week|month]
+ *
+ * Phase Operations:
+ *   phase next-decimal <phase>         Calculate next decimal phase number
+ *   phase add <description> [--id ID]   Append new phase to roadmap + create dir
+ *   phase insert <after> <description> Insert decimal phase after existing
+ *   phase remove <phase> [--force]     Remove phase, renumber all subsequent
+ *   phase complete <phase>             Mark phase done, update state + roadmap
+ *
+ * Roadmap Operations:
+ *   roadmap get-phase <phase>          Extract phase section from ROADMAP.md
+ *   roadmap analyze                    Full roadmap parse with disk status
+ *   roadmap update-plan-progress <N>   Update progress table row from disk (PLAN vs SUMMARY counts)
+ *   roadmap annotate-dependencies <N>  Add wave dependency notes + cross-cutting constraints to ROADMAP.md
+ *
+ * Requirements Operations:
+ *   requirements mark-complete <ids>   Mark requirement IDs as complete in REQUIREMENTS.md
+ *                                      Accepts: REQ-01,REQ-02 or REQ-01 REQ-02 or [REQ-01, REQ-02]
+ *
+ * Milestone Operations:
+ *   milestone complete <version>       Archive milestone, create MILESTONES.md
+ *     [--name <name>]
+ *     [--archive-phases]               Move phase dirs to milestones/vX.Y-phases/
+ *
+ * Validation:
+ *   validate consistency               Check phase numbering, disk/roadmap sync
+ *   validate health [--repair]         Check .planning/ integrity, optionally repair
+ *   validate agents                    Check GSD agent installation status
+ *
+ * Progress:
+ *   progress [json|table|bar]          Render progress in various formats
+ *
+ * Todos:
+ *   todo complete <filename>           Move todo from pending to completed
+ *
+ * UAT Audit:
+ *   audit-uat                           Scan all phases for unresolved UAT/verification items
+ *   uat render-checkpoint --file <path> Render the current UAT checkpoint block
+ *
+ * Open Artifact Audit:
+ *   audit-open [--json]                 Scan all .planning/ artifact types for unresolved items
+ *
+ * Intel:
+ *   intel query <term>             Query intel files for a term
+ *   intel status                   Show intel file freshness
+ *   intel update                   Trigger intel refresh (returns agent spawn hint)
+ *   intel diff                     Show changed intel entries since last snapshot
+ *   intel snapshot                 Save current intel state as diff baseline
+ *   intel patch-meta <file>        Update _meta.updated_at in an intel file
+ *   intel validate                 Validate intel file structure
+ *   intel extract-exports <file>   Extract exported symbols from a source file
+ *
+ * Scaffolding:
+ *   scaffold context --phase <N>       Create CONTEXT.md template
+ *   scaffold uat --phase <N>           Create UAT.md template
+ *   scaffold verification --phase <N>  Create VERIFICATION.md template
+ *   scaffold phase-dir --phase <N>     Create phase directory
+ *     --name <name>
+ *
+ * Frontmatter CRUD:
+ *   frontmatter get <file> [--field k] Extract frontmatter as JSON
+ *   frontmatter set <file> --field k   Update single frontmatter field
+ *     --value jsonVal
+ *   frontmatter merge <file>           Merge JSON into frontmatter
+ *     --data '{json}'
+ *   frontmatter validate <file>        Validate required fields
+ *     --schema plan|summary|verification
+ *
+ * Verification Suite:
+ *   verify plan-structure <file>       Check PLAN.md structure + tasks
+ *   verify phase-completeness <phase>  Check all plans have summaries
+ *   verify references <file>           Check @-refs + paths resolve
+ *   verify commits <h1> [h2] ...      Batch verify commit hashes
+ *   verify artifacts <plan-file>       Check must_haves.artifacts
+ *   verify key-links <plan-file>       Check must_haves.key_links
+ *   verify schema-drift <phase> [--skip]  Detect schema file changes without push
+ *
+ * Template Fill:
+ *   template fill summary --phase N    Create pre-filled SUMMARY.md
+ *     [--plan M] [--name "..."]
+ *     [--fields '{json}']
+ *   template fill plan --phase N       Create pre-filled PLAN.md
+ *     [--plan M] [--type execute|tdd]
+ *     [--wave N] [--fields '{json}']
+ *   template fill verification         Create pre-filled VERIFICATION.md
+ *     --phase N [--fields '{json}']
+ *
+ * State Progression:
+ *   state advance-plan                 Increment plan counter
+ *   state record-metric --phase N      Record execution metrics
+ *     --plan M --duration Xmin
+ *     [--tasks N] [--files N]
+ *   state update-progress              Recalculate progress bar
+ *   state add-decision --summary "..."  Add decision to STATE.md
+ *     [--phase N] [--rationale "..."]
+ *     [--summary-file path] [--rationale-file path]
+ *   state add-blocker --text "..."     Add blocker
+ *     [--text-file path]
+ *   state resolve-blocker --text "..." Remove blocker
+ *   state record-session               Update session continuity
+ *     --stopped-at "..."
+ *     [--resume-file path]
+ *
+ * Compound Commands (workflow-specific initialization):
+ *   init execute-phase <phase>         All context for execute-phase workflow
+ *   init plan-phase <phase>            All context for plan-phase workflow
+ *   init new-project                   All context for new-project workflow
+ *   init new-milestone                 All context for new-milestone workflow
+ *   init quick <description>           All context for quick workflow
+ *   init resume                        All context for resume-project workflow
+ *   init verify-work <phase>           All context for verify-work workflow
+ *   init phase-op <phase>              Generic phase operation context
+ *   init todos [area]                  All context for todo workflows
+ *   init milestone-op                  All context for milestone operations
+ *   init map-codebase                  All context for map-codebase workflow
+ *   init progress                      All context for progress workflow
+ *
+ * Documentation:
+ *   docs-init                            Project context for docs-update workflow
+ *
+ * Learnings:
+ *   learnings list                       List all global learnings (JSON)
+ *   learnings query --tag <tag>          Query learnings by tag
+ *   learnings copy                       Copy from current project's LEARNINGS.md
+ *   learnings prune --older-than <dur>   Remove entries older than duration (e.g. 90d)
+ *   learnings delete <id>                Delete a learning by ID
+ *
+ * GSD-2 Migration:
+ *   from-gsd2 [--path <dir>] [--force] [--dry-run]
+ *             Import a GSD-2 (.gsd/) project back to GSD v1 (.planning/) format
+ */
+
+const fs = require('fs');
+const path = require('path');
+const core = require('./lib/core.cjs');
+const { error, findProjectRoot, getActiveWorkstream } = core;
+const state = require('./lib/state.cjs');
+const phase = require('./lib/phase.cjs');
+const roadmap = require('./lib/roadmap.cjs');
+const verify = require('./lib/verify.cjs');
+const config = require('./lib/config.cjs');
+const template = require('./lib/template.cjs');
+const milestone = require('./lib/milestone.cjs');
+const commands = require('./lib/commands.cjs');
+const init = require('./lib/init.cjs');
+const frontmatter = require('./lib/frontmatter.cjs');
+const profilePipeline = require('./lib/profile-pipeline.cjs');
+const profileOutput = require('./lib/profile-output.cjs');
+const workstream = require('./lib/workstream.cjs');
+const docs = require('./lib/docs.cjs');
+const learnings = require('./lib/learnings.cjs');
+
+// ─── Arg parsing helpers ──────────────────────────────────────────────────────
+
+/**
+ * Extract named --flag <value> pairs from an args array.
+ * Returns an object mapping flag names to their values (null if absent).
+ * Flags listed in `booleanFlags` are treated as boolean (no value consumed).
+ *
+ * parseNamedArgs(args, 'phase', 'plan')        → { phase: '3', plan: '1' }
+ * parseNamedArgs(args, [], ['amend', 'force'])  → { amend: true, force: false }
+ */
+function parseNamedArgs(args, valueFlags = [], booleanFlags = []) {
+  const result = {};
+  for (const flag of valueFlags) {
+    const idx = args.indexOf(`--${flag}`);
+    result[flag] = idx !== -1 && args[idx + 1] !== undefined && !args[idx + 1].startsWith('--')
+      ? args[idx + 1]
+      : null;
+  }
+  for (const flag of booleanFlags) {
+    result[flag] = args.includes(`--${flag}`);
+  }
+  return result;
+}
+
+/**
+ * Collect all tokens after --flag until the next --flag or end of args.
+ * Handles multi-word values like --name Foo Bar Version 1.
+ * Returns null if the flag is absent.
+ */
+function parseMultiwordArg(args, flag) {
+  const idx = args.indexOf(`--${flag}`);
+  if (idx === -1) return null;
+  const tokens = [];
+  for (let i = idx + 1; i < args.length; i++) {
+    if (args[i].startsWith('--')) break;
+    tokens.push(args[i]);
+  }
+  return tokens.length > 0 ? tokens.join(' ') : null;
+}
+
+// ─── CLI Router ───────────────────────────────────────────────────────────────
+
+async function main() {
+  const args = process.argv.slice(2);
+
+  // Optional cwd override for sandboxed subagents running outside project root.
+  let cwd = process.cwd();
+  const cwdEqArg = args.find(arg => arg.startsWith('--cwd='));
+  const cwdIdx = args.indexOf('--cwd');
+  if (cwdEqArg) {
+    const value = cwdEqArg.slice('--cwd='.length).trim();
+    if (!value) error('Missing value for --cwd');
+    args.splice(args.indexOf(cwdEqArg), 1);
+    cwd = path.resolve(value);
+  } else if (cwdIdx !== -1) {
+    const value = args[cwdIdx + 1];
+    if (!value || value.startsWith('--')) error('Missing value for --cwd');
+    args.splice(cwdIdx, 2);
+    cwd = path.resolve(value);
+  }
+
+  if (!fs.existsSync(cwd) || !fs.statSync(cwd).isDirectory()) {
+    error(`Invalid --cwd: ${cwd}`);
+  }
+
+  // Resolve worktree root: in a linked worktree, .planning/ lives in the main worktree.
+  // However, in monorepo worktrees where the subdirectory itself owns .planning/,
+  // skip worktree resolution — the CWD is already the correct project root.
+  const { resolveWorktreeRoot } = require('./lib/core.cjs');
+  if (!fs.existsSync(path.join(cwd, '.planning'))) {
+    const worktreeRoot = resolveWorktreeRoot(cwd);
+    if (worktreeRoot !== cwd) {
+      cwd = worktreeRoot;
+    }
+  }
+
+  // Optional workstream override for parallel milestone work.
+  // Priority: --ws flag > GSD_WORKSTREAM env var > session-scoped pointer > shared legacy pointer > null
+  const wsEqArg = args.find(arg => arg.startsWith('--ws='));
+  const wsIdx = args.indexOf('--ws');
+  let ws = null;
+  if (wsEqArg) {
+    ws = wsEqArg.slice('--ws='.length).trim();
+    if (!ws) error('Missing value for --ws');
+    args.splice(args.indexOf(wsEqArg), 1);
+  } else if (wsIdx !== -1) {
+    ws = args[wsIdx + 1];
+    if (!ws || ws.startsWith('--')) error('Missing value for --ws');
+    args.splice(wsIdx, 2);
+  } else if (process.env.GSD_WORKSTREAM) {
+    ws = process.env.GSD_WORKSTREAM.trim();
+  } else {
+    ws = getActiveWorkstream(cwd);
+  }
+  // Validate workstream name to prevent path traversal attacks.
+  if (ws && !/^[a-zA-Z0-9_-]+$/.test(ws)) {
+    error('Invalid workstream name: must be alphanumeric, hyphens, and underscores only');
+  }
+  // Set env var so all modules (planningDir, planningPaths) auto-resolve workstream paths
+  if (ws) {
+    process.env.GSD_WORKSTREAM = ws;
+  }
+
+  const rawIndex = args.indexOf('--raw');
+  const raw = rawIndex !== -1;
+  if (rawIndex !== -1) args.splice(rawIndex, 1);
+
+  // --pick <name>: extract a single field from JSON output (replaces jq dependency).
+  // Supports dot-notation (e.g., --pick workflow.research) and bracket notation
+  // for arrays (e.g., --pick directories[-1]).
+  const pickIdx = args.indexOf('--pick');
+  let pickField = null;
+  if (pickIdx !== -1) {
+    pickField = args[pickIdx + 1];
+    if (!pickField || pickField.startsWith('--')) error('Missing value for --pick');
+    args.splice(pickIdx, 2);
+  }
+
+  // --default <value>: for config-get, return this value instead of erroring
+  // when the key is absent. Allows workflows to express optional config reads
+  // without defensive `2>/dev/null || true` boilerplate (#1893).
+  const defaultIdx = args.indexOf('--default');
+  let defaultValue = undefined;
+  if (defaultIdx !== -1) {
+    defaultValue = args[defaultIdx + 1];
+    if (defaultValue === undefined) defaultValue = '';
+    args.splice(defaultIdx, 2);
+  }
+
+  const command = args[0];
+
+  if (!command) {
+    error('Usage: gsd-tools <command> [args] [--raw] [--pick <field>] [--cwd <path>] [--ws <name>]\nCommands: state, resolve-model, find-phase, commit, verify-summary, verify, frontmatter, template, generate-slug, current-timestamp, list-todos, verify-path-exists, config-ensure-section, config-new-project, init, workstream, docs-init');
+  }
+
+  // Reject flags that are never valid for any gsd-tools command. AI agents
+  // sometimes hallucinate --help or --version on tool invocations; silently
+  // ignoring them can cause destructive operations to proceed unchecked.
+  const NEVER_VALID_FLAGS = new Set(['-h', '--help', '-?', '--h', '--version', '-v', '--usage']);
+  for (const arg of args) {
+    if (NEVER_VALID_FLAGS.has(arg)) {
+      error(`Unknown flag: ${arg}\ngsd-tools does not accept help or version flags. Run "gsd-tools" with no arguments for usage.`);
+    }
+  }
+
+  // Multi-repo guard: resolve project root for commands that read/write .planning/.
+  // Skip for pure-utility commands that don't touch .planning/ to avoid unnecessary
+  // filesystem traversal on every invocation.
+  const SKIP_ROOT_RESOLUTION = new Set([
+    'generate-slug', 'current-timestamp', 'verify-path-exists',
+    'verify-summary', 'template', 'frontmatter', 'detect-custom-files',
+  ]);
+  if (!SKIP_ROOT_RESOLUTION.has(command)) {
+    cwd = findProjectRoot(cwd);
+  }
+
+  // When --pick is active, intercept stdout to extract the requested field.
+  if (pickField) {
+    const origWriteSync = fs.writeSync;
+    const chunks = [];
+    fs.writeSync = function (fd, data, ...rest) {
+      if (fd === 1) { chunks.push(String(data)); return; }
+      return origWriteSync.call(fs, fd, data, ...rest);
+    };
+    const cleanup = () => {
+      fs.writeSync = origWriteSync;
+      const captured = chunks.join('');
+      let jsonStr = captured;
+      if (jsonStr.startsWith('@file:')) {
+        jsonStr = fs.readFileSync(jsonStr.slice(6), 'utf-8');
+      }
+      try {
+        const obj = JSON.parse(jsonStr);
+        const value = extractField(obj, pickField);
+        const result = value === null || value === undefined ? '' : String(value);
+        origWriteSync.call(fs, 1, result);
+      } catch {
+        origWriteSync.call(fs, 1, captured);
+      }
+    };
+    try {
+      await runCommand(command, args, cwd, raw, defaultValue);
+      cleanup();
+    } catch (e) {
+      fs.writeSync = origWriteSync;
+      throw e;
+    }
+    return;
+  }
+
+  // Intercept stdout to transparently resolve @file: references (#1891).
+  // core.cjs output() writes @file:<path> when JSON > 50KB. The --pick path
+  // already resolves this, but the normal path wrote @file: to stdout, forcing
+  // every workflow to have a bash-specific `if [[ "$INIT" == @file:* ]]` check
+  // that breaks on PowerShell and other non-bash shells.
+  const origWriteSync2 = fs.writeSync;
+  const outChunks = [];
+  fs.writeSync = function (fd, data, ...rest) {
+    if (fd === 1) { outChunks.push(String(data)); return; }
+    return origWriteSync2.call(fs, fd, data, ...rest);
+  };
+  try {
+    await runCommand(command, args, cwd, raw, defaultValue);
+  } finally {
+    fs.writeSync = origWriteSync2;
+  }
+  let captured = outChunks.join('');
+  if (captured.startsWith('@file:')) {
+    captured = fs.readFileSync(captured.slice(6), 'utf-8');
+  }
+  origWriteSync2.call(fs, 1, captured);
+}
+
+/**
+ * Extract a field from an object using dot-notation and bracket syntax.
+ * Supports: 'field', 'parent.child', 'arr[-1]', 'arr[0]'
+ */
+function extractField(obj, fieldPath) {
+  const parts = fieldPath.split('.');
+  let current = obj;
+  for (const part of parts) {
+    if (current === null || current === undefined) return undefined;
+    const bracketMatch = part.match(/^(.+?)\[(-?\d+)]$/);
+    if (bracketMatch) {
+      const key = bracketMatch[1];
+      const index = parseInt(bracketMatch[2], 10);
+      current = current[key];
+      if (!Array.isArray(current)) return undefined;
+      current = index < 0 ? current[current.length + index] : current[index];
+    } else {
+      current = current[part];
+    }
+  }
+  return current;
+}
+
+async function runCommand(command, args, cwd, raw, defaultValue) {
+  switch (command) {
+    case 'state': {
+      const subcommand = args[1];
+      if (subcommand === 'json') {
+        state.cmdStateJson(cwd, raw);
+      } else if (subcommand === 'update') {
+        state.cmdStateUpdate(cwd, args[2], args[3]);
+      } else if (subcommand === 'get') {
+        state.cmdStateGet(cwd, args[2], raw);
+      } else if (subcommand === 'patch') {
+        const patches = {};
+        for (let i = 2; i < args.length; i += 2) {
+          const key = args[i].replace(/^--/, '');
+          const value = args[i + 1];
+          if (key && value !== undefined) {
+            patches[key] = value;
+          }
+        }
+        state.cmdStatePatch(cwd, patches, raw);
+      } else if (subcommand === 'advance-plan') {
+        state.cmdStateAdvancePlan(cwd, raw);
+      } else if (subcommand === 'record-metric') {
+        const { phase: p, plan, duration, tasks, files } = parseNamedArgs(args, ['phase', 'plan', 'duration', 'tasks', 'files']);
+        state.cmdStateRecordMetric(cwd, { phase: p, plan, duration, tasks, files }, raw);
+      } else if (subcommand === 'update-progress') {
+        state.cmdStateUpdateProgress(cwd, raw);
+      } else if (subcommand === 'add-decision') {
+        const { phase: p, summary, 'summary-file': summary_file, rationale, 'rationale-file': rationale_file } = parseNamedArgs(args, ['phase', 'summary', 'summary-file', 'rationale', 'rationale-file']);
+        state.cmdStateAddDecision(cwd, { phase: p, summary, summary_file, rationale: rationale || '', rationale_file }, raw);
+      } else if (subcommand === 'add-blocker') {
+        const { text, 'text-file': text_file } = parseNamedArgs(args, ['text', 'text-file']);
+        state.cmdStateAddBlocker(cwd, { text, text_file }, raw);
+      } else if (subcommand === 'resolve-blocker') {
+        state.cmdStateResolveBlocker(cwd, parseNamedArgs(args, ['text']).text, raw);
+      } else if (subcommand === 'record-session') {
+        const { 'stopped-at': stopped_at, 'resume-file': resume_file } = parseNamedArgs(args, ['stopped-at', 'resume-file']);
+        state.cmdStateRecordSession(cwd, { stopped_at, resume_file: resume_file || 'None' }, raw);
+      } else if (subcommand === 'begin-phase') {
+        const { phase: p, name, plans } = parseNamedArgs(args, ['phase', 'name', 'plans']);
+        state.cmdStateBeginPhase(cwd, p, name, plans !== null ? parseInt(plans, 10) : null, raw);
+      } else if (subcommand === 'signal-waiting') {
+        const { type, question, options, phase: p } = parseNamedArgs(args, ['type', 'question', 'options', 'phase']);
+        state.cmdSignalWaiting(cwd, type, question, options, p, raw);
+      } else if (subcommand === 'signal-resume') {
+        state.cmdSignalResume(cwd, raw);
+      } else if (subcommand === 'planned-phase') {
+        const { phase: p, name, plans } = parseNamedArgs(args, ['phase', 'name', 'plans']);
+        state.cmdStatePlannedPhase(cwd, p, plans !== null ? parseInt(plans, 10) : null, raw);
+      } else if (subcommand === 'validate') {
+        state.cmdStateValidate(cwd, raw);
+      } else if (subcommand === 'sync') {
+        const { verify } = parseNamedArgs(args, [], ['verify']);
+        state.cmdStateSync(cwd, { verify }, raw);
+      } else if (subcommand === 'prune') {
+        const { 'keep-recent': keepRecent, 'dry-run': dryRun } = parseNamedArgs(args, ['keep-recent'], ['dry-run']);
+        state.cmdStatePrune(cwd, { keepRecent: keepRecent || '3', dryRun: !!dryRun }, raw);
+      } else {
+        state.cmdStateLoad(cwd, raw);
+      }
+      break;
+    }
+
+    case 'resolve-model': {
+      commands.cmdResolveModel(cwd, args[1], raw);
+      break;
+    }
+
+    case 'find-phase': {
+      phase.cmdFindPhase(cwd, args[1], raw);
+      break;
+    }
+
+    case 'commit': {
+      const amend = args.includes('--amend');
+      const noVerify = args.includes('--no-verify');
+      const filesIndex = args.indexOf('--files');
+      // Collect all positional args between command name and first flag,
+      // then join them — handles both quoted ("multi word msg") and
+      // unquoted (multi word msg) invocations from different shells
+      const endIndex = filesIndex !== -1 ? filesIndex : args.length;
+      const messageArgs = args.slice(1, endIndex).filter(a => !a.startsWith('--'));
+      const message = messageArgs.join(' ') || undefined;
+      const files = filesIndex !== -1 ? args.slice(filesIndex + 1).filter(a => !a.startsWith('--')) : [];
+      commands.cmdCommit(cwd, message, files, raw, amend, noVerify);
+      break;
+    }
+
+    case 'check-commit': {
+      commands.cmdCheckCommit(cwd, raw);
+      break;
+    }
+
+    case 'commit-to-subrepo': {
+      const message = args[1];
+      const filesIndex = args.indexOf('--files');
+      const files = filesIndex !== -1 ? args.slice(filesIndex + 1).filter(a => !a.startsWith('--')) : [];
+      commands.cmdCommitToSubrepo(cwd, message, files, raw);
+      break;
+    }
+
+    case 'verify-summary': {
+      const summaryPath = args[1];
+      const countIndex = args.indexOf('--check-count');
+      const checkCount = countIndex !== -1 ? parseInt(args[countIndex + 1], 10) : 2;
+      verify.cmdVerifySummary(cwd, summaryPath, checkCount, raw);
+      break;
+    }
+
+    case 'template': {
+      const subcommand = args[1];
+      if (subcommand === 'select') {
+        template.cmdTemplateSelect(cwd, args[2], raw);
+      } else if (subcommand === 'fill') {
+        const templateType = args[2];
+        const { phase, plan, name, type, wave, fields: fieldsRaw } = parseNamedArgs(args, ['phase', 'plan', 'name', 'type', 'wave', 'fields']);
+        let fields = {};
+        if (fieldsRaw) {
+          const { safeJsonParse } = require('./lib/security.cjs');
+          const result = safeJsonParse(fieldsRaw, { label: '--fields' });
+          if (!result.ok) error(result.error);
+          fields = result.value;
+        }
+        template.cmdTemplateFill(cwd, templateType, {
+          phase, plan, name, fields,
+          type: type || 'execute',
+          wave: wave || '1',
+        }, raw);
+      } else {
+        error('Unknown template subcommand. Available: select, fill');
+      }
+      break;
+    }
+
+    case 'frontmatter': {
+      const subcommand = args[1];
+      const file = args[2];
+      if (subcommand === 'get') {
+        frontmatter.cmdFrontmatterGet(cwd, file, parseNamedArgs(args, ['field']).field, raw);
+      } else if (subcommand === 'set') {
+        const { field, value } = parseNamedArgs(args, ['field', 'value']);
+        frontmatter.cmdFrontmatterSet(cwd, file, field, value !== null ? value : undefined, raw);
+      } else if (subcommand === 'merge') {
+        frontmatter.cmdFrontmatterMerge(cwd, file, parseNamedArgs(args, ['data']).data, raw);
+      } else if (subcommand === 'validate') {
+        frontmatter.cmdFrontmatterValidate(cwd, file, parseNamedArgs(args, ['schema']).schema, raw);
+      } else {
+        error('Unknown frontmatter subcommand. Available: get, set, merge, validate');
+      }
+      break;
+    }
+
+    case 'verify': {
+      const subcommand = args[1];
+      if (subcommand === 'plan-structure') {
+        verify.cmdVerifyPlanStructure(cwd, args[2], raw);
+      } else if (subcommand === 'phase-completeness') {
+        verify.cmdVerifyPhaseCompleteness(cwd, args[2], raw);
+      } else if (subcommand === 'references') {
+        verify.cmdVerifyReferences(cwd, args[2], raw);
+      } else if (subcommand === 'commits') {
+        verify.cmdVerifyCommits(cwd, args.slice(2), raw);
+      } else if (subcommand === 'artifacts') {
+        verify.cmdVerifyArtifacts(cwd, args[2], raw);
+      } else if (subcommand === 'key-links') {
+        verify.cmdVerifyKeyLinks(cwd, args[2], raw);
+      } else if (subcommand === 'schema-drift') {
+        const skipFlag = args.includes('--skip');
+        verify.cmdVerifySchemaDrift(cwd, args[2], skipFlag, raw);
+      } else {
+        error('Unknown verify subcommand. Available: plan-structure, phase-completeness, references, commits, artifacts, key-links, schema-drift');
+      }
+      break;
+    }
+
+    case 'generate-slug': {
+      commands.cmdGenerateSlug(args[1], raw);
+      break;
+    }
+
+    case 'current-timestamp': {
+      commands.cmdCurrentTimestamp(args[1] || 'full', raw);
+      break;
+    }
+
+    case 'list-todos': {
+      commands.cmdListTodos(cwd, args[1], raw);
+      break;
+    }
+
+    case 'verify-path-exists': {
+      commands.cmdVerifyPathExists(cwd, args[1], raw);
+      break;
+    }
+
+    case 'config-ensure-section': {
+      config.cmdConfigEnsureSection(cwd, raw);
+      break;
+    }
+
+    case 'config-set': {
+      config.cmdConfigSet(cwd, args[1], args[2], raw);
+      break;
+    }
+
+    case "config-set-model-profile": {
+      config.cmdConfigSetModelProfile(cwd, args[1], raw);
+      break;
+    }
+
+    case 'config-get': {
+      config.cmdConfigGet(cwd, args[1], raw, defaultValue);
+      break;
+    }
+
+    case 'config-new-project': {
+      config.cmdConfigNewProject(cwd, args[1], raw);
+      break;
+    }
+
+    case 'config-path': {
+      config.cmdConfigPath(cwd, raw);
+      break;
+    }
+
+    case 'agent-skills': {
+      init.cmdAgentSkills(cwd, args[1], raw);
+      break;
+    }
+
+    case 'skill-manifest': {
+      init.cmdSkillManifest(cwd, args, raw);
+      break;
+    }
+
+    case 'history-digest': {
+      commands.cmdHistoryDigest(cwd, raw);
+      break;
+    }
+
+    case 'phases': {
+      const subcommand = args[1];
+      if (subcommand === 'list') {
+        const typeIndex = args.indexOf('--type');
+        const phaseIndex = args.indexOf('--phase');
+        const options = {
+          type: typeIndex !== -1 ? args[typeIndex + 1] : null,
+          phase: phaseIndex !== -1 ? args[phaseIndex + 1] : null,
+          includeArchived: args.includes('--include-archived'),
+        };
+        phase.cmdPhasesList(cwd, options, raw);
+      } else if (subcommand === 'clear') {
+        milestone.cmdPhasesClear(cwd, raw, args.slice(2));
+      } else {
+        error('Unknown phases subcommand. Available: list, clear');
+      }
+      break;
+    }
+
+    case 'roadmap': {
+      const subcommand = args[1];
+      if (subcommand === 'get-phase') {
+        roadmap.cmdRoadmapGetPhase(cwd, args[2], raw);
+      } else if (subcommand === 'analyze') {
+        roadmap.cmdRoadmapAnalyze(cwd, raw);
+      } else if (subcommand === 'update-plan-progress') {
+        roadmap.cmdRoadmapUpdatePlanProgress(cwd, args[2], raw);
+      } else if (subcommand === 'annotate-dependencies') {
+        roadmap.cmdRoadmapAnnotateDependencies(cwd, args[2], raw);
+      } else {
+        error('Unknown roadmap subcommand. Available: get-phase, analyze, update-plan-progress, annotate-dependencies');
+      }
+      break;
+    }
+
+    case 'requirements': {
+      const subcommand = args[1];
+      if (subcommand === 'mark-complete') {
+        milestone.cmdRequirementsMarkComplete(cwd, args.slice(2), raw);
+      } else {
+        error('Unknown requirements subcommand. Available: mark-complete');
+      }
+      break;
+    }
+
+    case 'phase': {
+      const subcommand = args[1];
+      if (subcommand === 'next-decimal') {
+        phase.cmdPhaseNextDecimal(cwd, args[2], raw);
+      } else if (subcommand === 'add') {
+        const idIdx = args.indexOf('--id');
+        let customId = null;
+        const descArgs = [];
+        for (let i = 2; i < args.length; i++) {
+          if (args[i] === '--id' && i + 1 < args.length) {
+            customId = args[i + 1];
+            i++; // skip value
+          } else {
+            descArgs.push(args[i]);
+          }
+        }
+        phase.cmdPhaseAdd(cwd, descArgs.join(' '), raw, customId);
+      } else if (subcommand === 'add-batch') {
+        // Accepts JSON array of descriptions via --descriptions '[...]' or positional args
+        const descFlagIdx = args.indexOf('--descriptions');
+        let descriptions;
+        if (descFlagIdx !== -1 && args[descFlagIdx + 1]) {
+          try { descriptions = JSON.parse(args[descFlagIdx + 1]); } catch (e) { error('--descriptions must be a JSON array'); }
+        } else {
+          descriptions = args.slice(2).filter(a => a !== '--raw');
+        }
+        phase.cmdPhaseAddBatch(cwd, descriptions, raw);
+      } else if (subcommand === 'insert') {
+        phase.cmdPhaseInsert(cwd, args[2], args.slice(3).join(' '), raw);
+      } else if (subcommand === 'remove') {
+        const forceFlag = args.includes('--force');
+        phase.cmdPhaseRemove(cwd, args[2], { force: forceFlag }, raw);
+      } else if (subcommand === 'complete') {
+        phase.cmdPhaseComplete(cwd, args[2], raw);
+      } else {
+        error('Unknown phase subcommand. Available: next-decimal, add, add-batch, insert, remove, complete');
+      }
+      break;
+    }
+
+    case 'milestone': {
+      const subcommand = args[1];
+      if (subcommand === 'complete') {
+        const milestoneName = parseMultiwordArg(args, 'name');
+        const archivePhases = args.includes('--archive-phases');
+        milestone.cmdMilestoneComplete(cwd, args[2], { name: milestoneName, archivePhases }, raw);
+      } else {
+        error('Unknown milestone subcommand. Available: complete');
+      }
+      break;
+    }
+
+    case 'validate': {
+      const subcommand = args[1];
+      if (subcommand === 'consistency') {
+        verify.cmdValidateConsistency(cwd, raw);
+      } else if (subcommand === 'health') {
+        const repairFlag = args.includes('--repair');
+        const backfillFlag = args.includes('--backfill');
+        verify.cmdValidateHealth(cwd, { repair: repairFlag, backfill: backfillFlag }, raw);
+      } else if (subcommand === 'agents') {
+        verify.cmdValidateAgents(cwd, raw);
+      } else {
+        error('Unknown validate subcommand. Available: consistency, health, agents');
+      }
+      break;
+    }
+
+    case 'progress': {
+      const subcommand = args[1] || 'json';
+      commands.cmdProgressRender(cwd, subcommand, raw);
+      break;
+    }
+
+    case 'audit-uat': {
+      const uat = require('./lib/uat.cjs');
+      uat.cmdAuditUat(cwd, raw);
+      break;
+    }
+
+    case 'audit-open': {
+      const { auditOpenArtifacts, formatAuditReport } = require('./lib/audit.cjs');
+      const includeRaw = args.includes('--json');
+      const result = auditOpenArtifacts(cwd);
+      if (includeRaw) {
+        core.output(result, raw);
+      } else {
+        core.output(formatAuditReport(result), raw);
+      }
+      break;
+    }
+
+    case 'uat': {
+      const subcommand = args[1];
+      const uat = require('./lib/uat.cjs');
+      if (subcommand === 'render-checkpoint') {
+        const options = parseNamedArgs(args, ['file']);
+        uat.cmdRenderCheckpoint(cwd, options, raw);
+      } else {
+        error('Unknown uat subcommand. Available: render-checkpoint');
+      }
+      break;
+    }
+
+    case 'stats': {
+      const subcommand = args[1] || 'json';
+      commands.cmdStats(cwd, subcommand, raw);
+      break;
+    }
+
+    case 'todo': {
+      const subcommand = args[1];
+      if (subcommand === 'complete') {
+        commands.cmdTodoComplete(cwd, args[2], raw);
+      } else if (subcommand === 'match-phase') {
+        commands.cmdTodoMatchPhase(cwd, args[2], raw);
+      } else {
+        error('Unknown todo subcommand. Available: complete, match-phase');
+      }
+      break;
+    }
+
+    case 'scaffold': {
+      const scaffoldType = args[1];
+      const scaffoldOptions = {
+        phase: parseNamedArgs(args, ['phase']).phase,
+        name: parseMultiwordArg(args, 'name'),
+      };
+      commands.cmdScaffold(cwd, scaffoldType, scaffoldOptions, raw);
+      break;
+    }
+
+    case 'init': {
+      const workflow = args[1];
+      switch (workflow) {
+        case 'execute-phase': {
+          const { validate: epValidate, tdd: epTdd } = parseNamedArgs(args, [], ['validate', 'tdd']);
+          init.cmdInitExecutePhase(cwd, args[2], raw, { validate: epValidate, tdd: epTdd });
+          break;
+        }
+        case 'plan-phase': {
+          const { validate: ppValidate, tdd: ppTdd } = parseNamedArgs(args, [], ['validate', 'tdd']);
+          init.cmdInitPlanPhase(cwd, args[2], raw, { validate: ppValidate, tdd: ppTdd });
+          break;
+        }
+        case 'new-project':
+          init.cmdInitNewProject(cwd, raw);
+          break;
+        case 'new-milestone':
+          init.cmdInitNewMilestone(cwd, raw);
+          break;
+        case 'quick':
+          init.cmdInitQuick(cwd, args.slice(2).join(' '), raw);
+          break;
+        case 'resume':
+          init.cmdInitResume(cwd, raw);
+          break;
+        case 'verify-work':
+          init.cmdInitVerifyWork(cwd, args[2], raw);
+          break;
+        case 'phase-op':
+          init.cmdInitPhaseOp(cwd, args[2], raw);
+          break;
+        case 'todos':
+          init.cmdInitTodos(cwd, args[2], raw);
+          break;
+        case 'milestone-op':
+          init.cmdInitMilestoneOp(cwd, raw);
+          break;
+        case 'map-codebase':
+          init.cmdInitMapCodebase(cwd, raw);
+          break;
+        case 'progress':
+          init.cmdInitProgress(cwd, raw);
+          break;
+        case 'manager':
+          init.cmdInitManager(cwd, raw);
+          break;
+        case 'new-workspace':
+          init.cmdInitNewWorkspace(cwd, raw);
+          break;
+        case 'list-workspaces':
+          init.cmdInitListWorkspaces(cwd, raw);
+          break;
+        case 'remove-workspace':
+          init.cmdInitRemoveWorkspace(cwd, args[2], raw);
+          break;
+        default:
+          error(`Unknown init workflow: ${workflow}\nAvailable: execute-phase, plan-phase, new-project, new-milestone, quick, resume, verify-work, phase-op, todos, milestone-op, map-codebase, progress, manager, new-workspace, list-workspaces, remove-workspace`);
+      }
+      break;
+    }
+
+    case 'phase-plan-index': {
+      phase.cmdPhasePlanIndex(cwd, args[1], raw);
+      break;
+    }
+
+    case 'state-snapshot': {
+      state.cmdStateSnapshot(cwd, raw);
+      break;
+    }
+
+    case 'summary-extract': {
+      const summaryPath = args[1];
+      const fieldsIndex = args.indexOf('--fields');
+      const fields = fieldsIndex !== -1 ? args[fieldsIndex + 1].split(',') : null;
+      commands.cmdSummaryExtract(cwd, summaryPath, fields, raw);
+      break;
+    }
+
+    case 'websearch': {
+      const query = args[1];
+      const limitIdx = args.indexOf('--limit');
+      const freshnessIdx = args.indexOf('--freshness');
+      await commands.cmdWebsearch(query, {
+        limit: limitIdx !== -1 ? parseInt(args[limitIdx + 1], 10) : 10,
+        freshness: freshnessIdx !== -1 ? args[freshnessIdx + 1] : null,
+      }, raw);
+      break;
+    }
+
+    // ─── Profiling Pipeline ────────────────────────────────────────────────
+
+    case 'scan-sessions': {
+      const pathIdx = args.indexOf('--path');
+      const sessionsPath = pathIdx !== -1 ? args[pathIdx + 1] : null;
+      const verboseFlag = args.includes('--verbose');
+      const jsonFlag = args.includes('--json');
+      await profilePipeline.cmdScanSessions(sessionsPath, { verbose: verboseFlag, json: jsonFlag }, raw);
+      break;
+    }
+
+    case 'extract-messages': {
+      const sessionIdx = args.indexOf('--session');
+      const sessionId = sessionIdx !== -1 ? args[sessionIdx + 1] : null;
+      const limitIdx = args.indexOf('--limit');
+      const limit = limitIdx !== -1 ? parseInt(args[limitIdx + 1], 10) : null;
+      const pathIdx = args.indexOf('--path');
+      const sessionsPath = pathIdx !== -1 ? args[pathIdx + 1] : null;
+      const projectArg = args[1];
+      if (!projectArg || projectArg.startsWith('--')) {
+        error('Usage: gsd-tools extract-messages <project> [--session <id>] [--limit N] [--path <dir>]\nRun scan-sessions first to see available projects.');
+      }
+      await profilePipeline.cmdExtractMessages(projectArg, { sessionId, limit }, raw, sessionsPath);
+      break;
+    }
+
+    case 'profile-sample': {
+      const pathIdx = args.indexOf('--path');
+      const sessionsPath = pathIdx !== -1 ? args[pathIdx + 1] : null;
+      const limitIdx = args.indexOf('--limit');
+      const limit = limitIdx !== -1 ? parseInt(args[limitIdx + 1], 10) : 150;
+      const maxPerIdx = args.indexOf('--max-per-project');
+      const maxPerProject = maxPerIdx !== -1 ? parseInt(args[maxPerIdx + 1], 10) : null;
+      const maxCharsIdx = args.indexOf('--max-chars');
+      const maxChars = maxCharsIdx !== -1 ? parseInt(args[maxCharsIdx + 1], 10) : 500;
+      await profilePipeline.cmdProfileSample(sessionsPath, { limit, maxPerProject, maxChars }, raw);
+      break;
+    }
+
+    // ─── Profile Output ──────────────────────────────────────────────────
+
+    case 'write-profile': {
+      const inputIdx = args.indexOf('--input');
+      const inputPath = inputIdx !== -1 ? args[inputIdx + 1] : null;
+      if (!inputPath) error('--input <analysis-json-path> is required');
+      const outputIdx = args.indexOf('--output');
+      const outputPath = outputIdx !== -1 ? args[outputIdx + 1] : null;
+      profileOutput.cmdWriteProfile(cwd, { input: inputPath, output: outputPath }, raw);
+      break;
+    }
+
+    case 'profile-questionnaire': {
+      const answersIdx = args.indexOf('--answers');
+      const answers = answersIdx !== -1 ? args[answersIdx + 1] : null;
+      profileOutput.cmdProfileQuestionnaire({ answers }, raw);
+      break;
+    }
+
+    case 'generate-dev-preferences': {
+      const analysisIdx = args.indexOf('--analysis');
+      const analysisPath = analysisIdx !== -1 ? args[analysisIdx + 1] : null;
+      const outputIdx = args.indexOf('--output');
+      const outputPath = outputIdx !== -1 ? args[outputIdx + 1] : null;
+      const stackIdx = args.indexOf('--stack');
+      const stack = stackIdx !== -1 ? args[stackIdx + 1] : null;
+      profileOutput.cmdGenerateDevPreferences(cwd, { analysis: analysisPath, output: outputPath, stack }, raw);
+      break;
+    }
+
+    case 'generate-claude-profile': {
+      const analysisIdx = args.indexOf('--analysis');
+      const analysisPath = analysisIdx !== -1 ? args[analysisIdx + 1] : null;
+      const outputIdx = args.indexOf('--output');
+      const outputPath = outputIdx !== -1 ? args[outputIdx + 1] : null;
+      const globalFlag = args.includes('--global');
+      profileOutput.cmdGenerateClaudeProfile(cwd, { analysis: analysisPath, output: outputPath, global: globalFlag }, raw);
+      break;
+    }
+
+    case 'generate-claude-md': {
+      const outputIdx = args.indexOf('--output');
+      const outputPath = outputIdx !== -1 ? args[outputIdx + 1] : null;
+      const autoFlag = args.includes('--auto');
+      const forceFlag = args.includes('--force');
+      profileOutput.cmdGenerateClaudeMd(cwd, { output: outputPath, auto: autoFlag, force: forceFlag }, raw);
+      break;
+    }
+
+    case 'workstream': {
+      const subcommand = args[1];
+      if (subcommand === 'create') {
+        const migrateNameIdx = args.indexOf('--migrate-name');
+        const noMigrate = args.includes('--no-migrate');
+        workstream.cmdWorkstreamCreate(cwd, args[2], {
+          migrate: !noMigrate,
+          migrateName: migrateNameIdx !== -1 ? args[migrateNameIdx + 1] : null,
+        }, raw);
+      } else if (subcommand === 'list') {
+        workstream.cmdWorkstreamList(cwd, raw);
+      } else if (subcommand === 'status') {
+        workstream.cmdWorkstreamStatus(cwd, args[2], raw);
+      } else if (subcommand === 'complete') {
+        workstream.cmdWorkstreamComplete(cwd, args[2], {}, raw);
+      } else if (subcommand === 'set') {
+        workstream.cmdWorkstreamSet(cwd, args[2], raw);
+      } else if (subcommand === 'get') {
+        workstream.cmdWorkstreamGet(cwd, raw);
+      } else if (subcommand === 'progress') {
+        workstream.cmdWorkstreamProgress(cwd, raw);
+      } else {
+        error('Unknown workstream subcommand. Available: create, list, status, complete, set, get, progress');
+      }
+      break;
+    }
+
+    // ─── Intel ────────────────────────────────────────────────────────────
+
+    case 'intel': {
+      const intel = require('./lib/intel.cjs');
+      const subcommand = args[1];
+      if (subcommand === 'query') {
+        const term = args[2];
+        if (!term) error('Usage: gsd-tools intel query <term>');
+        const planningDir = path.join(cwd, '.planning');
+        core.output(intel.intelQuery(term, planningDir), raw);
+      } else if (subcommand === 'status') {
+        const planningDir = path.join(cwd, '.planning');
+        const status = intel.intelStatus(planningDir);
+        if (!raw && status.files) {
+          for (const file of Object.values(status.files)) {
+            if (file.updated_at) {
+              file.updated_at = core.timeAgo(new Date(file.updated_at));
+            }
+          }
+        }
+        core.output(status, raw);
+      } else if (subcommand === 'diff') {
+        const planningDir = path.join(cwd, '.planning');
+        core.output(intel.intelDiff(planningDir), raw);
+      } else if (subcommand === 'snapshot') {
+        const planningDir = path.join(cwd, '.planning');
+        core.output(intel.intelSnapshot(planningDir), raw);
+      } else if (subcommand === 'patch-meta') {
+        const filePath = args[2];
+        if (!filePath) error('Usage: gsd-tools intel patch-meta <file-path>');
+        core.output(intel.intelPatchMeta(path.resolve(cwd, filePath)), raw);
+      } else if (subcommand === 'validate') {
+        const planningDir = path.join(cwd, '.planning');
+        core.output(intel.intelValidate(planningDir), raw);
+      } else if (subcommand === 'extract-exports') {
+        const filePath = args[2];
+        if (!filePath) error('Usage: gsd-tools intel extract-exports <file-path>');
+        core.output(intel.intelExtractExports(path.resolve(cwd, filePath)), raw);
+      } else if (subcommand === 'update') {
+        const planningDir = path.join(cwd, '.planning');
+        core.output(intel.intelUpdate(planningDir), raw);
+      } else {
+        error('Unknown intel subcommand. Available: query, status, update, diff, snapshot, patch-meta, validate, extract-exports');
+      }
+      break;
+    }
+
+    // ─── Graphify ──────────────────────────────────────────────────────────
+
+    case 'graphify': {
+      const graphify = require('./lib/graphify.cjs');
+      const subcommand = args[1];
+      if (subcommand === 'query') {
+        const term = args[2];
+        if (!term) error('Usage: gsd-tools graphify query <term>');
+        const budgetIdx = args.indexOf('--budget');
+        const budget = budgetIdx !== -1 ? parseInt(args[budgetIdx + 1], 10) : null;
+        core.output(graphify.graphifyQuery(cwd, term, { budget }), raw);
+      } else if (subcommand === 'status') {
+        core.output(graphify.graphifyStatus(cwd), raw);
+      } else if (subcommand === 'diff') {
+        core.output(graphify.graphifyDiff(cwd), raw);
+      } else if (subcommand === 'build') {
+        if (args[2] === 'snapshot') {
+          core.output(graphify.writeSnapshot(cwd), raw);
+        } else {
+          core.output(graphify.graphifyBuild(cwd), raw);
+        }
+      } else {
+        error('Unknown graphify subcommand. Available: build, query, status, diff');
+      }
+      break;
+    }
+
+    // ─── Documentation ────────────────────────────────────────────────────
+
+    case 'docs-init': {
+      docs.cmdDocsInit(cwd, raw);
+      break;
+    }
+
+    // ─── Learnings ─────────────────────────────────────────────────────────
+
+    case 'learnings': {
+      const subcommand = args[1];
+      if (subcommand === 'list') {
+        learnings.cmdLearningsList(raw);
+      } else if (subcommand === 'query') {
+        const tagIdx = args.indexOf('--tag');
+        const tag = tagIdx !== -1 ? args[tagIdx + 1] : null;
+        if (!tag) error('Usage: gsd-tools learnings query --tag <tag>');
+        learnings.cmdLearningsQuery(tag, raw);
+      } else if (subcommand === 'copy') {
+        learnings.cmdLearningsCopy(cwd, raw);
+      } else if (subcommand === 'prune') {
+        const olderIdx = args.indexOf('--older-than');
+        const olderThan = olderIdx !== -1 ? args[olderIdx + 1] : null;
+        if (!olderThan) error('Usage: gsd-tools learnings prune --older-than <duration>');
+        learnings.cmdLearningsPrune(olderThan, raw);
+      } else if (subcommand === 'delete') {
+        const id = args[2];
+        if (!id) error('Usage: gsd-tools learnings delete <id>');
+        learnings.cmdLearningsDelete(id, raw);
+      } else {
+        error('Unknown learnings subcommand. Available: list, query, copy, prune, delete');
+      }
+      break;
+    }
+
+    // ─── detect-custom-files ───────────────────────────────────────────────
+    // Detect user-added files inside GSD-managed directories that are not
+    // tracked in gsd-file-manifest.json. Used by the update workflow to back
+    // up custom files before the installer wipes those directories.
+    //
+    // This replaces the fragile bash pattern:
+    //   MANIFEST_FILES=$(node -e "require('$RUNTIME_DIR/...')" 2>/dev/null)
+    //   ${filepath#$RUNTIME_DIR/}   # unreliable path stripping
+    // which silently returns CUSTOM_COUNT=0 when $RUNTIME_DIR is unset or
+    // when the stripped path does not match the manifest key format (#1997).
+
+    case 'detect-custom-files': {
+      const configDirIdx = args.indexOf('--config-dir');
+      const configDir = configDirIdx !== -1 ? args[configDirIdx + 1] : null;
+      if (!configDir) {
+        error('Usage: gsd-tools detect-custom-files --config-dir <path>');
+      }
+      const resolvedConfigDir = path.resolve(configDir);
+      if (!fs.existsSync(resolvedConfigDir)) {
+        error(`Config directory not found: ${resolvedConfigDir}`);
+      }
+
+      const manifestPath = path.join(resolvedConfigDir, 'gsd-file-manifest.json');
+      if (!fs.existsSync(manifestPath)) {
+        // No manifest — cannot determine what is custom. Return empty list
+        // (same behaviour as saveLocalPatches in install.js when no manifest).
+        const out = { custom_files: [], custom_count: 0, manifest_found: false };
+        process.stdout.write(JSON.stringify(out, null, 2));
+        break;
+      }
+
+      let manifest;
+      try {
+        manifest = JSON.parse(fs.readFileSync(manifestPath, 'utf8'));
+      } catch {
+        const out = { custom_files: [], custom_count: 0, manifest_found: false, error: 'manifest parse error' };
+        process.stdout.write(JSON.stringify(out, null, 2));
+        break;
+      }
+
+      const manifestKeys = new Set(Object.keys(manifest.files || {}));
+
+      // GSD-managed directories to scan for user-added files.
+      // These are the directories the installer wipes on update.
+      const GSD_MANAGED_DIRS = [
+        'get-shit-done',
+        'agents',
+        path.join('commands', 'gsd'),
+        'hooks',
+        // OpenCode/Kilo flat command dir
+        'command',
+        // Codex/Copilot skills dir
+        'skills',
+      ];
+
+      function walkDir(dir, baseDir) {
+        const results = [];
+        if (!fs.existsSync(dir)) return results;
+        for (const entry of fs.readdirSync(dir, { withFileTypes: true })) {
+          const fullPath = path.join(dir, entry.name);
+          if (entry.isDirectory()) {
+            results.push(...walkDir(fullPath, baseDir));
+          } else {
+            // Use forward slashes for cross-platform manifest key compatibility
+            const relPath = path.relative(baseDir, fullPath).replace(/\\/g, '/');
+            results.push(relPath);
+          }
+        }
+        return results;
+      }
+
+      const customFiles = [];
+      for (const managedDir of GSD_MANAGED_DIRS) {
+        const absDir = path.join(resolvedConfigDir, managedDir);
+        if (!fs.existsSync(absDir)) continue;
+        for (const relPath of walkDir(absDir, resolvedConfigDir)) {
+          if (!manifestKeys.has(relPath)) {
+            customFiles.push(relPath);
+          }
+        }
+      }
+
+      const out = {
+        custom_files: customFiles,
+        custom_count: customFiles.length,
+        manifest_found: true,
+        manifest_version: manifest.version || null,
+      };
+      process.stdout.write(JSON.stringify(out, null, 2));
+      break;
+    }
+
+    // ─── GSD-2 Reverse Migration ───────────────────────────────────────────
+
+    case 'from-gsd2': {
+      const gsd2Import = require('./lib/gsd2-import.cjs');
+      gsd2Import.cmdFromGsd2(args.slice(1), cwd, raw);
+      break;
+    }
+
+    default:
+      error(`Unknown command: ${command}`);
+  }
+}
+
+main();