@ai-is-gonna/get-tasks-done 0.2.0

package/get-tasks-done/bin/gtd-tools.cjs

@@ -0,0 +1,1264 @@
+#!/usr/bin/env node
+
+/**
+ * @deprecated The supported programmatic surface is `gtd-sdk query` (SDK query registry)
+ * and the `@ai-is-gonna/gtd-sdk` package. This Node CLI remains the compatibility implementation
+ * for shell scripts and older workflows; prefer calling the SDK from agents and automation.
+ *
+ * GTD Tools — CLI utility for GTD workflow operations
+ *
+ * Replaces repetitive inline bash patterns across ~50 GTD command/workflow/agent files.
+ * Centralizes: config parsing, model resolution, phase lookup, git commits, summary verification.
+ *
+ * Usage: node gtd-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 GTD 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
+ *   verify codebase-drift                Detect structural drift since last codebase map (#2003)
+ *
+ * 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 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
+ *
+ * GTD-2 Migration:
+ *   from-gtd2 [--path <dir>] [--force] [--dry-run]
+ *             Import a GTD-2 (.gtd/) project back to GTD v1 (.planning/) format
+ */
+
+const fs = require('fs');
+const path = require('path');
+const childProcess = require('child_process');
+const core = require('./lib/core.cjs');
+const { error, findProjectRoot, ERROR_REASON } = core;
+const { getActiveWorkstream } = require('./lib/planning-workspace.cjs');
+const { resolveActiveWorkstream, applyResolvedWorkstreamEnv } = require('./lib/active-workstream-store.cjs');
+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');
+const gapChecker = require('./lib/gap-checker.cjs');
+const { routeStateCommand } = require('./lib/state-command-router.cjs');
+const { routeVerifyCommand } = require('./lib/verify-command-router.cjs');
+const { routeInitCommand } = require('./lib/init-command-router.cjs');
+const { routePhaseCommand } = require('./lib/phase-command-router.cjs');
+const { routePhasesCommand } = require('./lib/phases-command-router.cjs');
+const { routeValidateCommand } = require('./lib/validate-command-router.cjs');
+const { routeRoadmapCommand } = require('./lib/roadmap-command-router.cjs');
+
+function runSdkQueryShim(cwd, command, args) {
+  const sdkShim = path.resolve(__dirname, '..', '..', 'bin', 'gtd-sdk.js');
+  const hasLocalSdkShim = fs.existsSync(sdkShim);
+  const executable = hasLocalSdkShim ? process.execPath : 'gtd-sdk';
+  const shimArgs = hasLocalSdkShim
+    ? [sdkShim, 'query', command, ...args.slice(1)]
+    : ['query', command, ...args.slice(1)];
+  const result = childProcess.spawnSync(executable, shimArgs, {
+    cwd,
+    stdio: 'inherit',
+    env: {
+      ...process.env,
+      ...(core.getJsonErrorMode() ? { GTD_JSON_ERRORS: '1' } : {}),
+    },
+  });
+  process.exit(result.status ?? 1);
+}
+
+// ─── 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() {
+  let args = process.argv.slice(2);
+
+  // --json-errors / GTD_JSON_ERRORS=1: when active, error() emits structured
+  // JSON ({ ok: false, reason: <ERROR_REASON code>, message }) to stderr
+  // instead of "Error: <text>". Lets test suites assert on typed reason codes
+  // per CONTRIBUTING.md "Prohibited: Raw Text Matching" (#2974).
+  //
+  // Detect early — before any flag parsing that can fire error() — so even
+  // --cwd and workstream-resolution failures emit structured stderr (#3310).
+  // The argv splice must happen here too, otherwise the dispatcher below sees
+  // "--json-errors" as an unknown command. Default off — human operators keep
+  // their plain-text diagnostic.
+  const jsonErrorsIdx = args.indexOf('--json-errors');
+  if (jsonErrorsIdx !== -1) {
+    core.setJsonErrorMode(true);
+    args.splice(jsonErrorsIdx, 1);
+  } else if (process.env.GTD_JSON_ERRORS === '1') {
+    core.setJsonErrorMode(true);
+  }
+
+  // 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', ERROR_REASON.USAGE);
+    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', ERROR_REASON.USAGE);
+    args.splice(cwdIdx, 2);
+    cwd = path.resolve(value);
+  }
+
+  if (!fs.existsSync(cwd) || !fs.statSync(cwd).isDirectory()) {
+    error(`Invalid --cwd: ${cwd}`, ERROR_REASON.USAGE);
+  }
+
+  // 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 > GTD_WORKSTREAM env var > session/shared pointer > null.
+  let ws = null;
+  try {
+    const wsResolution = resolveActiveWorkstream(cwd, args, process.env, {
+      getStored: getActiveWorkstream,
+    });
+    ws = wsResolution.ws;
+    args = wsResolution.args;
+    // Set env var so all modules (planningDir, planningPaths) auto-resolve workstream paths.
+    applyResolvedWorkstreamEnv(wsResolution, process.env);
+  } catch (err) {
+    error(err.message || String(err));
+  }
+
+  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', ERROR_REASON.USAGE);
+    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);
+  }
+
+  let command = args[0];
+
+  // #3243: accept dotted canonical form (e.g. `state.update`) as well as the
+  // spaced form (`state update`). Workflow files and stale SDK binaries pass
+  // the dotted canonical form directly; any caller that bypasses the SDK
+  // client-side split hit "Unknown command" before this shim.
+  //
+  // Split on the FIRST dot only — `check.decision-coverage-plan` becomes
+  // command='check', args=['check','decision-coverage-plan',...rest].
+  // Parallel to dottedCommandToCjsArgv in sdk/src/query/query-fallback-bridge-adapter.ts;
+  // kept separate here to avoid SDK coupling (see TODO: extract to shared helper).
+  //
+  // Guard: head and rest must both be non-empty (rejects leading-dot args like
+  // ".hidden" and bare-dot ".").
+  const originalCommand = command; // preserved for "Unknown command" suggestion
+  if (typeof command === 'string' && command.includes('.')) {
+    const dotIdx = command.indexOf('.');
+    const head = command.slice(0, dotIdx);
+    const rest = command.slice(dotIdx + 1);
+    if (head && rest) {
+      command = head;
+      args = [head, rest, ...args.slice(1)];
+    }
+  }
+
+  // Top-level usage string — emitted by `gtd-tools` (no args) and by
+  // `gtd-tools --help` / any `--help` request below.
+  // CR feedback: the command list must enumerate every top-level command
+  // supported by the dispatcher so `--help` is actually useful for
+  // discovery; previously it was a partial subset that didn't include
+  // phase / roadmap / milestone / progress / etc.
+  const TOP_LEVEL_USAGE = 'Usage: gtd-tools <command> [args] [--raw] [--pick <field>] [--cwd <path>] [--ws <name>] [--json-errors]\n' +
+    'Commands: agent-skills, audit-open, audit-uat, check-commit, commit, commit-to-subrepo, ' +
+    'config-ensure-section, config-get, config-new-project, config-path, config-set, migrate-config, ' +
+    'current-timestamp, detect-custom-files, docs-init, extract-messages, find-phase, ' +
+    'export-phase-issues, from-gtd2, frontmatter, gap-analysis, generate-claude-md, generate-claude-profile, ' +
+    'generate-dev-preferences, generate-slug, graphify, history-digest, init, intel, ' +
+    'learnings, list-todos, milestone, orchestrate-tasks, phase, phase-plan-index, phases, profile-questionnaire, ' +
+    'profile-sample, progress, requirements, resolve-model, roadmap, scaffold, state, ' +
+    'template, validate, verify, verify-path-exists, verify-summary, work-task-issue, workstream, worktree\n\n' +
+    'Global flags:\n' +
+    '  --raw              Emit raw output without post-processing\n' +
+    '  --pick <field>     Extract a single field from JSON output (dot/bracket notation)\n' +
+    '  --cwd <path>       Override working directory for project-root resolution\n' +
+    '  --ws <name>        Override active workstream (or set GTD_WORKSTREAM)\n' +
+    '  --json-errors      Emit structured JSON error objects on stderr (or set GTD_JSON_ERRORS=1)\n\n' +
+    'For command-specific argument requirements, invoke the command without args ' +
+    '(e.g. `gtd-tools phase add`) — the resulting error lists what is required.';
+
+  if (!command) {
+    error(TOP_LEVEL_USAGE);
+  }
+
+  // #3019: a `--help` / `-h` flag in argv must render the top-level usage
+  // and exit 0 — not error out with "Unknown flag". The previous shape
+  // erred on agent-hallucinated flags, but it also blocked humans from
+  // discovering the command surface via subcommand help requests routed
+  // here from the SDK CLI's query dispatcher (after the cli.ts fix that
+  // stops harvesting --help as a global flag). Rendering top-level usage
+  // on --help is strictly better UX than the old short-circuit, which
+  // printed the SDK-level usage that doesn't mention any of these
+  // subcommands.
+  const HELP_FLAGS = new Set(['-h', '--help', '-?', '--h', '--usage']);
+  if (args.some((a) => HELP_FLAGS.has(a))) {
+    process.stdout.write(TOP_LEVEL_USAGE + '\n');
+    return;
+  }
+
+  // Reject version flags. AI agents sometimes hallucinate --version on tool
+  // invocations; silently ignoring it can cause destructive operations to
+  // proceed unchecked. (Help flags are handled above.)
+  const NEVER_VALID_FLAGS = new Set(['--version', '-v']);
+  for (const arg of args) {
+    if (NEVER_VALID_FLAGS.has(arg)) {
+      error(`Unknown flag: ${arg}\ngtd-tools does not accept version flags. Run "gtd-tools" with no arguments for usage.`, ERROR_REASON.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',
+    'worktree',
+  ]);
+  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, originalCommand);
+      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, originalCommand);
+  } 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, originalCommand) {
+  switch (command) {
+    case 'state': {
+      routeStateCommand({
+        state,
+        args,
+        cwd,
+        raw,
+        parseNamedArgs,
+        error,
+      });
+      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', ERROR_REASON.SDK_UNKNOWN_COMMAND);
+      }
+      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', ERROR_REASON.SDK_UNKNOWN_COMMAND);
+      }
+      break;
+    }
+
+    case 'verify': {
+      routeVerifyCommand({
+        verify,
+        args,
+        cwd,
+        raw,
+        error,
+      });
+      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 'migrate-config': {
+      // Explicit on-disk migration of legacy config keys to canonical shape (#3536).
+      // Wraps Configuration Module migrateOnDisk(); idempotent. async — must await.
+      await config.cmdMigrateConfig(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': {
+      routePhasesCommand({
+        phase,
+        milestone,
+        args,
+        cwd,
+        raw,
+        error,
+      });
+      break;
+    }
+
+    case 'roadmap': {
+      routeRoadmapCommand({
+        roadmap,
+        args,
+        cwd,
+        raw,
+        error,
+      });
+      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', ERROR_REASON.SDK_UNKNOWN_COMMAND);
+      }
+      break;
+    }
+
+    case 'gap-analysis': {
+      // Post-planning gap checker (#2493) — unified REQUIREMENTS.md +
+      // CONTEXT.md <decisions> coverage report against PLAN.md files.
+      gapChecker.cmdGapAnalysis(cwd, args.slice(1), raw);
+      break;
+    }
+
+    case 'phase': {
+      routePhaseCommand({
+        phase,
+        args,
+        cwd,
+        raw,
+        error,
+      });
+      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', ERROR_REASON.SDK_UNKNOWN_COMMAND);
+      }
+      break;
+    }
+
+    case 'validate': {
+      routeValidateCommand({
+        verify,
+        args,
+        cwd,
+        raw,
+        parseNamedArgs,
+        output: core.output,
+        error,
+      });
+      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 wantJson = args.includes('--json');
+      const result = auditOpenArtifacts(cwd);
+      if (wantJson) {
+        // core.output JSON-stringifies its first arg; pass the object directly.
+        core.output(result, raw);
+      } else {
+        // Human-readable report must bypass JSON encoding — use the rawValue
+        // form (third arg) which core.output emits verbatim.
+        core.output(null, true, formatAuditReport(result));
+      }
+      break;
+    }
+
+    case 'export-phase-issues': {
+      runSdkQueryShim(cwd, 'export-phase-issues', args);
+      break;
+    }
+
+    case 'work-task-issue': {
+      runSdkQueryShim(cwd, 'work-task-issue', args);
+      break;
+    }
+
+    case 'orchestrate-tasks': {
+      runSdkQueryShim(cwd, 'orchestrate-tasks', args);
+      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', ERROR_REASON.SDK_UNKNOWN_COMMAND);
+      }
+      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', ERROR_REASON.SDK_UNKNOWN_COMMAND);
+      }
+      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': {
+      routeInitCommand({
+        init,
+        args,
+        cwd,
+        raw,
+        parseNamedArgs,
+        error,
+      });
+      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: gtd-tools extract-messages <project> [--session <id>] [--limit N] [--path <dir>]\nRun scan-sessions first to see available projects.', ERROR_REASON.USAGE);
+      }
+      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', ERROR_REASON.USAGE);
+      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', ERROR_REASON.SDK_UNKNOWN_COMMAND);
+      }
+      break;
+    }
+
+    case 'worktree': {
+      const subcommand = args[1];
+      const worktreeSafety = require('./lib/worktree-safety.cjs');
+      if (subcommand === 'cleanup-wave') {
+        worktreeSafety.cmdWorktreeCleanupWave(cwd, args.slice(2));
+      } else {
+        error('Unknown worktree subcommand. Available: cleanup-wave', ERROR_REASON.SDK_UNKNOWN_COMMAND);
+      }
+      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: gtd-tools intel query <term>', ERROR_REASON.USAGE);
+        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: gtd-tools intel patch-meta <file-path>', ERROR_REASON.USAGE);
+        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: gtd-tools intel extract-exports <file-path>', ERROR_REASON.USAGE);
+        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', ERROR_REASON.SDK_UNKNOWN_COMMAND);
+      }
+      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: gtd-tools graphify query <term>', ERROR_REASON.USAGE);
+        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', ERROR_REASON.SDK_UNKNOWN_COMMAND);
+      }
+      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: gtd-tools learnings query --tag <tag>', ERROR_REASON.USAGE);
+        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: gtd-tools learnings prune --older-than <duration>', ERROR_REASON.USAGE);
+        learnings.cmdLearningsPrune(olderThan, raw);
+      } else if (subcommand === 'delete') {
+        const id = args[2];
+        if (!id) error('Usage: gtd-tools learnings delete <id>', ERROR_REASON.USAGE);
+        learnings.cmdLearningsDelete(id, raw);
+      } else {
+        error('Unknown learnings subcommand. Available: list, query, copy, prune, delete', ERROR_REASON.SDK_UNKNOWN_COMMAND);
+      }
+      break;
+    }
+
+    // ─── detect-custom-files ───────────────────────────────────────────────
+    // Detect user-added files inside GTD-managed directories that are not
+    // tracked in gtd-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: gtd-tools detect-custom-files --config-dir <path>', ERROR_REASON.USAGE);
+      }
+      const resolvedConfigDir = path.resolve(configDir);
+      if (!fs.existsSync(resolvedConfigDir)) {
+        error(`Config directory not found: ${resolvedConfigDir}`, ERROR_REASON.USAGE);
+      }
+
+      const manifestPath = path.join(resolvedConfigDir, 'gtd-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 || {}));
+
+      // GTD-managed directories to scan for user-added files.
+      // These are the directories the installer wipes on update.
+      const GTD_MANAGED_DIRS = [
+        'get-tasks-done',
+        'agents',
+        path.join('commands', 'gtd'),
+        'hooks',
+        '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 GTD_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;
+    }
+
+    // ─── GTD-2 Reverse Migration ───────────────────────────────────────────
+
+    case 'from-gtd2': {
+      const gtd2Import = require('./lib/gtd2-import.cjs');
+      gtd2Import.cmdFromGtd2(args.slice(1), cwd, raw);
+      break;
+    }
+
+    default: {
+      // #3243: if the caller passed a dotted form (e.g. "foo.bar"), the shim
+      // above split it so `command` here is the head ("foo"). Use
+      // originalCommand to reconstruct the original dotted form and suggest
+      // the spaced equivalent — surfacing a useful diagnostic instead of just
+      // "Unknown command: foo".
+      const wasDotted =
+        typeof originalCommand === 'string' &&
+        originalCommand !== command &&
+        originalCommand.includes('.');
+      let suggestion = '';
+      if (wasDotted) {
+        const dotIdx = originalCommand.indexOf('.');
+        const head = originalCommand.slice(0, dotIdx);
+        const rest = originalCommand.slice(dotIdx + 1);
+        suggestion = ` — did you mean: "${head} ${rest}"?`;
+      }
+      error(`Unknown command: ${command}${suggestion}`, ERROR_REASON.SDK_UNKNOWN_COMMAND);
+    }
+  }
+}
+
+main();