@opengsd/get-shit-done-redux 1.0.0

package/get-shit-done/bin/lib/init.cjs

@@ -0,0 +1,2096 @@
+/**
+ * Init — Compound init commands for workflow bootstrapping
+ */
+
+const fs = require('fs');
+const path = require('path');
+const { execGit, platformWriteSync, platformReadSync } = require('./shell-command-projection.cjs');
+const { loadConfig, resolveModelInternal, findPhaseInternal, getRoadmapPhaseInternal, pathExistsInternal, gitWorktreeInfoInternal, generateSlugInternal, getMilestoneInfo, getMilestonePhaseFilter, stripShippedMilestones, extractCurrentMilestone, normalizePhaseName, toPosixPath, output, error, checkAgentsInstalled, phaseTokenMatches } = require('./core.cjs');
+const { planningPaths, planningDir, planningRoot, findContextMdIn } = require('./planning-workspace.cjs');
+const { maskIfSecret } = require('./secrets.cjs');
+const scanPhasePlans = require('./plan-scan.cjs');
+const { stateExtractField } = require('./state-document.cjs');
+const { formatGsdSlash, resolveRuntime } = require('./runtime-slash.cjs');
+const { determinePhaseStatus } = require('./commands.cjs');
+
+// Accept all bold/colon variants of the Requirements header (#2769):
+// **Requirements:** / **Requirements**: / **Requirements** : render the
+// same in markdown but differ textually.
+const REQUIREMENTS_HEADER_RE = /^\*\*Requirements:?\*\*[^\S\n]*:?[^\S\n]*([^\n]*)$/m;
+
+function listPhaseSummaryFiles(phaseDir) {
+  return scanPhasePlans(phaseDir).summaryFiles;
+}
+
+function listPhasePlanFiles(phaseDir) {
+  return scanPhasePlans(phaseDir).planFiles;
+}
+
+function getLatestCompletedMilestone(cwd) {
+  const milestonesPath = path.join(planningRoot(cwd), 'MILESTONES.md');
+  const content = platformReadSync(milestonesPath);
+  if (content === null) return null;
+
+  const match = content.match(/^##\s+(v[\d.]+)\s+(.+?)\s+\(Shipped:/m);
+  if (!match) return null;
+  return {
+    version: match[1],
+    name: match[2].trim(),
+  };
+}
+
+/**
+ * Inject `project_root` into an init result object.
+ * Workflows use this to prefix `.planning/` paths correctly when Claude's CWD
+ * differs from the project root (e.g., inside a sub-repo).
+ */
+function withProjectRoot(cwd, result) {
+  result.project_root = cwd;
+  // Inject agent installation status into all init outputs (#1371).
+  // Workflows that spawn named subagents use this to detect when agents
+  // are missing and would silently fall back to general-purpose.
+  const agentStatus = checkAgentsInstalled();
+  result.agents_installed = agentStatus.agents_installed;
+  result.missing_agents = agentStatus.missing_agents;
+  // Inject response_language into all init outputs (#1399).
+  // Workflows propagate this to subagent prompts so user-facing questions
+  // stay in the configured language across phase boundaries.
+  const config = loadConfig(cwd);
+  if (config.response_language) {
+    result.response_language = config.response_language;
+  }
+  // Inject project identity into all init outputs so handoff blocks
+  // can include project context for cross-session continuity.
+  if (config.project_code) {
+    result.project_code = config.project_code;
+  }
+  // Extract project title from PROJECT.md first H1 heading.
+  const projectMdPath = path.join(planningDir(cwd), 'PROJECT.md');
+  const content = platformReadSync(projectMdPath);
+  if (content) {
+    const h1Match = content.match(/^#\s+(.+)$/m);
+    if (h1Match) {
+      result.project_title = h1Match[1].trim();
+    }
+  }
+  return result;
+}
+
+/**
+ * Return git-worktree state for init payloads with robust nested-subdir
+ * detection across Windows short/long path forms and slash variants.
+ */
+function getInitGitState(cwd) {
+  const info = gitWorktreeInfoInternal(cwd);
+  const worktreeRoot = info.worktreeRoot;
+  const normalizeForCompare = (p) => {
+    if (typeof p !== 'string' || p.length === 0) return null;
+    let resolved;
+    try {
+      resolved = fs.realpathSync.native(p);
+    } catch {
+      resolved = path.resolve(p);
+    }
+    resolved = path.resolve(resolved);
+    if (process.platform === 'win32') {
+      return resolved.replace(/\//g, '\\').toLowerCase();
+    }
+    return resolved;
+  };
+
+  let inNestedSubdir = false;
+  if (info.inside) {
+    let resolvedByGitPrefix = false;
+    try {
+      const prefixResult = execGit(['rev-parse', '--show-prefix'], { cwd, timeout: 5000 });
+      if (prefixResult.exitCode === 0) {
+        const prefix = String(prefixResult.stdout || '').trim().replace(/\\/g, '/');
+        inNestedSubdir = prefix.length > 0 && prefix !== '.' && prefix !== './';
+        resolvedByGitPrefix = true;
+      }
+    } catch {}
+
+    if (!resolvedByGitPrefix) {
+      const rootNorm = normalizeForCompare(worktreeRoot);
+      const cwdNorm = normalizeForCompare(cwd);
+      if (rootNorm && cwdNorm) {
+        if (rootNorm === cwdNorm) {
+          inNestedSubdir = false;
+        } else {
+          const rel = path.relative(rootNorm, cwdNorm);
+          const relNorm = process.platform === 'win32' ? rel.replace(/\//g, '\\') : rel;
+          inNestedSubdir =
+            relNorm !== '' &&
+            relNorm !== '.' &&
+            !relNorm.startsWith('..') &&
+            !path.isAbsolute(relNorm);
+        }
+      } else {
+        inNestedSubdir = worktreeRoot !== null;
+      }
+    }
+  }
+
+  // Defensive final guard: if git reports the same root path as cwd (after
+  // slash/case normalization), we are at the worktree root, never nested.
+  if (inNestedSubdir && typeof worktreeRoot === 'string') {
+    const toComparableRaw = (p) => p.replace(/\\/g, '/').replace(/\/+$/g, '').toLowerCase();
+    if (toComparableRaw(worktreeRoot) === toComparableRaw(String(cwd))) {
+      inNestedSubdir = false;
+    }
+  }
+
+  return {
+    has_git: info.inside,
+    git_worktree_root: worktreeRoot,
+    in_nested_subdir: inNestedSubdir,
+  };
+}
+
+function cmdInitExecutePhase(cwd, phase, raw, options = {}) {
+  if (!phase) {
+    error('phase required for init execute-phase');
+  }
+
+  const config = loadConfig(cwd);
+  let phaseInfo = findPhaseInternal(cwd, phase);
+  const milestone = getMilestoneInfo(cwd);
+
+  const roadmapPhase = getRoadmapPhaseInternal(cwd, phase);
+
+  // If findPhaseInternal matched an archived phase from a prior milestone, but
+  // the phase exists in the current milestone's ROADMAP.md, ignore the archive
+  // match — we are initializing a new phase in the current milestone that
+  // happens to share a number with an archived one. Without this, phase_dir,
+  // phase_slug and related fields would point at artifacts from a previous
+  // milestone.
+  if (phaseInfo?.archived && roadmapPhase?.found) {
+    phaseInfo = null;
+  }
+
+  // Fallback to ROADMAP.md if no phase directory exists yet
+  if (!phaseInfo && roadmapPhase?.found) {
+    const phaseName = roadmapPhase.phase_name;
+    phaseInfo = {
+      found: true,
+      directory: null,
+      phase_number: roadmapPhase.phase_number,
+      phase_name: phaseName,
+      phase_slug: phaseName ? phaseName.toLowerCase().replace(/[^a-z0-9]+/g, '-').replace(/^-+|-+$/g, '') : null,
+      plans: [],
+      summaries: [],
+      incomplete_plans: [],
+      has_research: false,
+      has_context: false,
+      has_verification: false,
+      has_reviews: false,
+    };
+  }
+  const reqMatch = roadmapPhase?.section?.match(REQUIREMENTS_HEADER_RE);
+  const reqExtracted = reqMatch
+    ? reqMatch[1].replace(/[\[\]]/g, '').split(',').map(s => s.trim()).filter(Boolean).join(', ')
+    : null;
+  const phase_req_ids = (reqExtracted && reqExtracted !== 'TBD') ? reqExtracted : null;
+
+  const result = {
+    // Models
+    executor_model: resolveModelInternal(cwd, 'gsd-executor'),
+    verifier_model: resolveModelInternal(cwd, 'gsd-verifier'),
+
+    // Config flags
+    tdd_mode: options.tdd || config.tdd_mode || false,
+    commit_docs: config.commit_docs,
+    sub_repos: config.sub_repos,
+    parallelization: config.parallelization,
+    context_window: config.context_window,
+    branching_strategy: config.branching_strategy,
+    phase_branch_template: config.phase_branch_template,
+    milestone_branch_template: config.milestone_branch_template,
+    verifier_enabled: config.verifier,
+
+    // Phase info
+    phase_found: !!phaseInfo,
+    phase_dir: phaseInfo?.directory || null,
+    phase_number: phaseInfo?.phase_number || null,
+    phase_name: phaseInfo?.phase_name || null,
+    phase_slug: phaseInfo?.phase_slug || null,
+    phase_req_ids,
+
+    // Plan inventory
+    plans: phaseInfo?.plans || [],
+    summaries: phaseInfo?.summaries || [],
+    incomplete_plans: phaseInfo?.incomplete_plans || [],
+    plan_count: phaseInfo?.plans?.length || 0,
+    incomplete_count: phaseInfo?.incomplete_plans?.length || 0,
+
+    // Branch name (pre-computed)
+    branch_name: config.branching_strategy === 'phase' && phaseInfo
+      ? config.phase_branch_template
+          .replace('{project}', config.project_code || '')
+          .replace('{phase}', phaseInfo.phase_number)
+          .replace('{slug}', phaseInfo.phase_slug || 'phase')
+      : config.branching_strategy === 'milestone'
+        ? config.milestone_branch_template
+            .replace('{milestone}', milestone.version)
+            .replace('{slug}', generateSlugInternal(milestone.name) || 'milestone')
+        : null,
+
+    // Milestone info
+    milestone_version: milestone.version,
+    milestone_name: milestone.name,
+    milestone_slug: generateSlugInternal(milestone.name),
+
+    // File existence
+    state_exists: fs.existsSync(path.join(planningDir(cwd), 'STATE.md')),
+    roadmap_exists: fs.existsSync(path.join(planningDir(cwd), 'ROADMAP.md')),
+    config_exists: fs.existsSync(path.join(planningDir(cwd), 'config.json')),
+    // File paths
+    state_path: toPosixPath(path.relative(cwd, path.join(planningDir(cwd), 'STATE.md'))),
+    roadmap_path: toPosixPath(path.relative(cwd, path.join(planningDir(cwd), 'ROADMAP.md'))),
+    config_path: toPosixPath(path.relative(cwd, path.join(planningDir(cwd), 'config.json'))),
+  };
+
+  // Optional --validate: run state validation and include warnings (#1627)
+  if (options.validate) {
+    try {
+      const statePath = path.join(planningDir(cwd), 'STATE.md');
+      const stateContent = platformReadSync(statePath);
+      if (stateContent !== null) {
+        const status = stateExtractField(stateContent, 'Status') || '';
+        result.state_validation_ran = true;
+        // Simple inline validation — check for obvious drift
+        const warnings = [];
+        const phasesPath = planningPaths(cwd).phases;
+        if (phaseInfo && phaseInfo.directory && fs.existsSync(path.join(cwd, phaseInfo.directory))) {
+          const diskPlans = listPhasePlanFiles(path.join(cwd, phaseInfo.directory)).length;
+          const totalPlansRaw = stateExtractField(stateContent, 'Total Plans in Phase');
+          const totalPlansInPhase = totalPlansRaw ? parseInt(totalPlansRaw, 10) : null;
+          if (totalPlansInPhase !== null && diskPlans !== totalPlansInPhase) {
+            warnings.push(`Plan count mismatch: STATE.md says ${totalPlansInPhase}, disk has ${diskPlans}`);
+          }
+        }
+        result.state_warnings = warnings;
+      }
+    } catch { /* intentionally empty */ }
+  }
+
+  output(withProjectRoot(cwd, result), raw);
+}
+
+function cmdInitPlanPhase(cwd, phase, raw, options = {}) {
+  if (!phase) {
+    error('phase required for init plan-phase');
+  }
+
+  const config = loadConfig(cwd);
+  let phaseInfo = findPhaseInternal(cwd, phase);
+
+  const roadmapPhase = getRoadmapPhaseInternal(cwd, phase);
+
+  // If findPhaseInternal matched an archived phase from a prior milestone, but
+  // the phase exists in the current milestone's ROADMAP.md, ignore the archive
+  // match — we are planning a new phase in the current milestone that happens
+  // to share a number with an archived one. Without this, phase_dir,
+  // phase_slug, has_context and has_research would point at artifacts from a
+  // previous milestone.
+  if (phaseInfo?.archived && roadmapPhase?.found) {
+    phaseInfo = null;
+  }
+
+  // Fallback to ROADMAP.md if no phase directory exists yet
+  if (!phaseInfo && roadmapPhase?.found) {
+    const phaseName = roadmapPhase.phase_name;
+    phaseInfo = {
+      found: true,
+      directory: null,
+      phase_number: roadmapPhase.phase_number,
+      phase_name: phaseName,
+      phase_slug: phaseName ? phaseName.toLowerCase().replace(/[^a-z0-9]+/g, '-').replace(/^-+|-+$/g, '') : null,
+      plans: [],
+      summaries: [],
+      incomplete_plans: [],
+      has_research: false,
+      has_context: false,
+      has_verification: false,
+      has_reviews: false,
+    };
+  }
+  const reqMatch = roadmapPhase?.section?.match(REQUIREMENTS_HEADER_RE);
+  const reqExtracted = reqMatch
+    ? reqMatch[1].replace(/[\[\]]/g, '').split(',').map(s => s.trim()).filter(Boolean).join(', ')
+    : null;
+  const phase_req_ids = (reqExtracted && reqExtracted !== 'TBD') ? reqExtracted : null;
+
+  // #3287: compute the canonical directory name with project_code prefix so
+  // the first-touch mkdir in /gsd:plan-phase stays consistent with phase.add.
+  const phaseDirPlan = phaseInfo?.directory || null;
+  const phaseNumberPlan = phaseInfo?.phase_number || null;
+  const phaseNamePlan = phaseInfo?.phase_name || null;
+  const rawProjectCodePlan = config.project_code || '';
+  let expectedPhaseDirPlan = null;
+  if (!phaseDirPlan && phaseNumberPlan && phaseNamePlan) {
+    const paddedNum = normalizePhaseName(phaseNumberPlan);
+    const slug = generateSlugInternal(phaseNamePlan).substring(0, 60);
+    if (slug) {
+      const prefix = rawProjectCodePlan ? `${rawProjectCodePlan}-` : '';
+      const dirName = `${prefix}${paddedNum}-${slug}`;
+      expectedPhaseDirPlan = toPosixPath(path.relative(cwd, path.join(planningPaths(cwd).phases, dirName)));
+    }
+  }
+
+  const result = {
+    // Models
+    researcher_model: resolveModelInternal(cwd, 'gsd-phase-researcher'),
+    planner_model: resolveModelInternal(cwd, 'gsd-planner'),
+    checker_model: resolveModelInternal(cwd, 'gsd-plan-checker'),
+
+    // Workflow flags
+    tdd_mode: options.tdd || config.tdd_mode || false,
+    research_enabled: config.research,
+    plan_checker_enabled: config.plan_checker,
+    nyquist_validation_enabled: config.nyquist_validation,
+    commit_docs: config.commit_docs,
+    text_mode: config.text_mode,
+    // Auto-advance config — included so workflows don't need separate config-get
+    // calls for these values, which causes infinite config-read loops on some models
+    // (e.g. Kimi K2.5). See #2192.
+    auto_advance: !!(config.auto_advance),
+    auto_chain_active: !!(config._auto_chain_active),
+    mode: config.mode || 'interactive',
+
+    // Phase info
+    phase_found: !!phaseInfo,
+    phase_dir: phaseDirPlan,
+    expected_phase_dir: expectedPhaseDirPlan,
+    phase_number: phaseNumberPlan,
+    phase_name: phaseNamePlan,
+    phase_slug: phaseInfo?.phase_slug || null,
+    padded_phase: phaseNumberPlan ? normalizePhaseName(phaseNumberPlan) : null,
+    phase_req_ids,
+
+    // #3569: surface phase lifecycle status so /gsd:plan-phase can short-circuit
+    // on closed (Complete) phases instead of silently replanning over shipped
+    // code. Reuses determinePhaseStatus — the project-wide vocabulary
+    // (Pending | Planned | In Progress | Executed | Complete | Needs Review).
+    // No directory yet → Pending (phase has not been started).
+    phase_status: phaseDirPlan
+      ? determinePhaseStatus(
+          phaseInfo?.plans?.length || 0,
+          phaseInfo?.summaries?.length || 0,
+          path.join(cwd, phaseDirPlan),
+          'Pending',
+        )
+      : 'Pending',
+
+    // Existing artifacts
+    has_research: phaseInfo?.has_research || false,
+    has_context: phaseInfo?.has_context || false,
+    has_reviews: phaseInfo?.has_reviews || false,
+    has_plans: (phaseInfo?.plans?.length || 0) > 0,
+    plan_count: phaseInfo?.plans?.length || 0,
+
+    // Environment
+    planning_exists: fs.existsSync(planningDir(cwd)),
+    roadmap_exists: fs.existsSync(path.join(planningDir(cwd), 'ROADMAP.md')),
+
+    // File paths
+    state_path: toPosixPath(path.relative(cwd, path.join(planningDir(cwd), 'STATE.md'))),
+    roadmap_path: toPosixPath(path.relative(cwd, path.join(planningDir(cwd), 'ROADMAP.md'))),
+    requirements_path: toPosixPath(path.relative(cwd, path.join(planningDir(cwd), 'REQUIREMENTS.md'))),
+
+    // Pattern mapper output (null until PATTERNS.md exists in phase dir)
+    patterns_path: null,
+  };
+
+  if (phaseInfo?.directory) {
+    // Find *-CONTEXT.md in phase directory
+    const phaseDirFull = path.join(cwd, phaseInfo.directory);
+    try {
+      const files = fs.readdirSync(phaseDirFull);
+      const contextFile = findContextMdIn(phaseDirFull);
+      if (contextFile) {
+        result.context_path = toPosixPath(path.join(phaseInfo.directory, contextFile));
+      }
+      const researchFile = files.find(f => f.endsWith('-RESEARCH.md') || f === 'RESEARCH.md');
+      if (researchFile) {
+        result.research_path = toPosixPath(path.join(phaseInfo.directory, researchFile));
+      }
+      const verificationFile = files.find(f => f.endsWith('-VERIFICATION.md') || f === 'VERIFICATION.md');
+      if (verificationFile) {
+        result.verification_path = toPosixPath(path.join(phaseInfo.directory, verificationFile));
+      }
+      const uatFile = files.find(f => f.endsWith('-UAT.md') || f === 'UAT.md');
+      if (uatFile) {
+        result.uat_path = toPosixPath(path.join(phaseInfo.directory, uatFile));
+      }
+      const reviewsFile = files.find(f => f.endsWith('-REVIEWS.md') || f === 'REVIEWS.md');
+      if (reviewsFile) {
+        result.reviews_path = toPosixPath(path.join(phaseInfo.directory, reviewsFile));
+      }
+      const patternsFile = files.find(f => f.endsWith('-PATTERNS.md') || f === 'PATTERNS.md');
+      if (patternsFile) {
+        result.patterns_path = toPosixPath(path.join(phaseInfo.directory, patternsFile));
+      }
+    } catch { /* intentionally empty */ }
+  }
+
+  // Optional --validate: run state validation and include warnings (#1627)
+  if (options.validate) {
+    try {
+      const statePath = path.join(planningDir(cwd), 'STATE.md');
+      const stateContent = platformReadSync(statePath);
+      if (stateContent !== null) {
+        const warnings = [];
+        result.state_validation_ran = true;
+        const totalPlansRaw = stateExtractField(stateContent, 'Total Plans in Phase');
+        const totalPlansInPhase = totalPlansRaw ? parseInt(totalPlansRaw, 10) : null;
+        if (totalPlansInPhase !== null && phaseInfo && totalPlansInPhase !== (phaseInfo.plans?.length || 0)) {
+          warnings.push(`Plan count mismatch: STATE.md says ${totalPlansInPhase}, disk has ${phaseInfo.plans?.length || 0}`);
+        }
+        result.state_warnings = warnings;
+      }
+    } catch { /* intentionally empty */ }
+  }
+
+  output(withProjectRoot(cwd, result), raw);
+}
+
+function cmdInitNewProject(cwd, raw) {
+  const config = loadConfig(cwd);
+
+  // Detect Brave Search API key availability
+  const homedir = require('os').homedir();
+  const braveKeyFile = path.join(homedir, '.gsd', 'brave_api_key');
+  const hasBraveSearch = !!(process.env.BRAVE_API_KEY || fs.existsSync(braveKeyFile));
+
+  // Detect Firecrawl API key availability
+  const firecrawlKeyFile = path.join(homedir, '.gsd', 'firecrawl_api_key');
+  const hasFirecrawl = !!(process.env.FIRECRAWL_API_KEY || fs.existsSync(firecrawlKeyFile));
+
+  // Detect Exa API key availability
+  const exaKeyFile = path.join(homedir, '.gsd', 'exa_api_key');
+  const hasExaSearch = !!(process.env.EXA_API_KEY || fs.existsSync(exaKeyFile));
+
+  // Detect existing code (cross-platform — no Unix `find` dependency)
+  let hasCode = false;
+  let hasPackageFile = false;
+  try {
+    const codeExtensions = new Set([
+      '.ts', '.js', '.py', '.go', '.rs', '.swift', '.java',
+      '.kt', '.kts',           // Kotlin (Android, server-side)
+      '.c', '.cpp', '.h',      // C/C++
+      '.cs',                   // C#
+      '.rb',                   // Ruby
+      '.php',                  // PHP
+      '.dart',                 // Dart (Flutter)
+      '.m', '.mm',             // Objective-C / Objective-C++
+      '.scala',                // Scala
+      '.groovy',               // Groovy (Gradle build scripts)
+      '.lua',                  // Lua
+      '.r', '.R',              // R
+      '.zig',                  // Zig
+      '.ex', '.exs',           // Elixir
+      '.clj',                  // Clojure
+    ]);
+    const skipDirs = new Set(['node_modules', '.git', '.planning', '.claude', '.codex', '__pycache__', 'target', 'dist', 'build']);
+    function findCodeFiles(dir, depth) {
+      if (depth > 3) return false;
+      let entries;
+      try { entries = fs.readdirSync(dir, { withFileTypes: true }); } catch { return false; }
+      for (const entry of entries) {
+        if (entry.isFile() && codeExtensions.has(path.extname(entry.name))) return true;
+        if (entry.isDirectory() && !skipDirs.has(entry.name)) {
+          if (findCodeFiles(path.join(dir, entry.name), depth + 1)) return true;
+        }
+      }
+      return false;
+    }
+    hasCode = findCodeFiles(cwd, 0);
+  } catch { /* intentionally empty — best-effort detection */ }
+
+  hasPackageFile = pathExistsInternal(cwd, 'package.json') ||
+                   pathExistsInternal(cwd, 'requirements.txt') ||
+                   pathExistsInternal(cwd, 'Cargo.toml') ||
+                   pathExistsInternal(cwd, 'go.mod') ||
+                   pathExistsInternal(cwd, 'Package.swift') ||
+                   pathExistsInternal(cwd, 'build.gradle') ||
+                   pathExistsInternal(cwd, 'build.gradle.kts') ||
+                   pathExistsInternal(cwd, 'pom.xml') ||
+                   pathExistsInternal(cwd, 'Gemfile') ||
+                   pathExistsInternal(cwd, 'composer.json') ||
+                   pathExistsInternal(cwd, 'pubspec.yaml') ||
+                   pathExistsInternal(cwd, 'CMakeLists.txt') ||
+                   pathExistsInternal(cwd, 'Makefile') ||
+                   pathExistsInternal(cwd, 'build.zig') ||
+                   pathExistsInternal(cwd, 'mix.exs') ||
+                   pathExistsInternal(cwd, 'project.clj');
+
+  const result = {
+    // Models
+    researcher_model: resolveModelInternal(cwd, 'gsd-project-researcher'),
+    synthesizer_model: resolveModelInternal(cwd, 'gsd-research-synthesizer'),
+    roadmapper_model: resolveModelInternal(cwd, 'gsd-roadmapper'),
+
+    // Config
+    commit_docs: config.commit_docs,
+
+    // Existing state
+    project_exists: pathExistsInternal(cwd, '.planning/PROJECT.md'),
+    has_codebase_map: pathExistsInternal(cwd, '.planning/codebase'),
+    planning_exists: pathExistsInternal(cwd, '.planning'),
+
+    // Brownfield detection
+    has_existing_code: hasCode,
+    has_package_file: hasPackageFile,
+    is_brownfield: hasCode || hasPackageFile,
+    needs_codebase_map: (hasCode || hasPackageFile) && !pathExistsInternal(cwd, '.planning/codebase'),
+
+    // Git state (Bug #3491: detect parent worktree to avoid nested .git init)
+    ...getInitGitState(cwd),
+
+    // Enhanced search
+    brave_search_available: hasBraveSearch,
+    firecrawl_available: hasFirecrawl,
+    exa_search_available: hasExaSearch,
+
+    // File paths
+    project_path: '.planning/PROJECT.md',
+  };
+
+  output(withProjectRoot(cwd, result), raw);
+}
+
+function cmdInitNewMilestone(cwd, raw) {
+  const config = loadConfig(cwd);
+  const milestone = getMilestoneInfo(cwd);
+  const latestCompleted = getLatestCompletedMilestone(cwd);
+  const phasesDir = path.join(planningDir(cwd), 'phases');
+  let phaseDirCount = 0;
+
+  try {
+    if (fs.existsSync(phasesDir)) {
+      // Bug #2445: filter phase dirs to current milestone only so stale dirs
+      // from a prior milestone that were not archived don't inflate the count.
+      const isDirInMilestone = getMilestonePhaseFilter(cwd);
+      phaseDirCount = fs.readdirSync(phasesDir, { withFileTypes: true })
+        .filter(entry => entry.isDirectory() && isDirInMilestone(entry.name))
+        .length;
+    }
+  } catch {}
+
+  const result = {
+    // Models
+    researcher_model: resolveModelInternal(cwd, 'gsd-project-researcher'),
+    synthesizer_model: resolveModelInternal(cwd, 'gsd-research-synthesizer'),
+    roadmapper_model: resolveModelInternal(cwd, 'gsd-roadmapper'),
+
+    // Config
+    commit_docs: config.commit_docs,
+    research_enabled: config.research,
+
+    // Current milestone
+    current_milestone: milestone.version,
+    current_milestone_name: milestone.name,
+    latest_completed_milestone: latestCompleted?.version || null,
+    latest_completed_milestone_name: latestCompleted?.name || null,
+    phase_dir_count: phaseDirCount,
+    phase_archive_path: latestCompleted ? toPosixPath(path.relative(cwd, path.join(planningRoot(cwd), 'milestones', `${latestCompleted.version}-phases`))) : null,
+
+    // File existence
+    project_exists: pathExistsInternal(cwd, '.planning/PROJECT.md'),
+    roadmap_exists: fs.existsSync(path.join(planningDir(cwd), 'ROADMAP.md')),
+    state_exists: fs.existsSync(path.join(planningDir(cwd), 'STATE.md')),
+
+    // File paths
+    project_path: '.planning/PROJECT.md',
+    roadmap_path: toPosixPath(path.relative(cwd, path.join(planningDir(cwd), 'ROADMAP.md'))),
+    state_path: toPosixPath(path.relative(cwd, path.join(planningDir(cwd), 'STATE.md'))),
+  };
+
+  output(withProjectRoot(cwd, result), raw);
+}
+
+function cmdInitQuick(cwd, description, raw) {
+  const config = loadConfig(cwd);
+  const now = new Date();
+  const slug = description ? generateSlugInternal(description)?.substring(0, 40) : null;
+
+  // Generate collision-resistant quick task ID: YYMMDD-xxx
+  // xxx = 2-second precision blocks since midnight, encoded as 3-char Base36 (lowercase)
+  // Range: 000 (00:00:00) to xbz (23:59:58), guaranteed 3 chars for any time of day.
+  // Provides ~2s uniqueness window per user — practically collision-free across a team.
+  const yy = String(now.getFullYear()).slice(-2);
+  const mm = String(now.getMonth() + 1).padStart(2, '0');
+  const dd = String(now.getDate()).padStart(2, '0');
+  const dateStr = yy + mm + dd;
+  const secondsSinceMidnight = now.getHours() * 3600 + now.getMinutes() * 60 + now.getSeconds();
+  const timeBlocks = Math.floor(secondsSinceMidnight / 2);
+  const timeEncoded = timeBlocks.toString(36).padStart(3, '0');
+  const quickId = dateStr + '-' + timeEncoded;
+  const branchSlug = slug || 'quick';
+  const quickBranchName = config.quick_branch_template
+    ? config.quick_branch_template
+        .replace('{num}', quickId)
+        .replace('{quick}', quickId)
+        .replace('{slug}', branchSlug)
+    : null;
+
+  const result = {
+    // Models
+    planner_model: resolveModelInternal(cwd, 'gsd-planner'),
+    executor_model: resolveModelInternal(cwd, 'gsd-executor'),
+    checker_model: resolveModelInternal(cwd, 'gsd-plan-checker'),
+    verifier_model: resolveModelInternal(cwd, 'gsd-verifier'),
+
+    // Config
+    commit_docs: config.commit_docs,
+    branch_name: quickBranchName,
+
+    // Quick task info
+    quick_id: quickId,
+    slug: slug,
+    description: description || null,
+
+    // Timestamps
+    date: now.toISOString().split('T')[0],
+    timestamp: now.toISOString(),
+
+    // Paths
+    quick_dir: '.planning/quick',
+    task_dir: slug ? `.planning/quick/${quickId}-${slug}` : null,
+
+    // File existence
+    roadmap_exists: fs.existsSync(path.join(planningDir(cwd), 'ROADMAP.md')),
+    planning_exists: fs.existsSync(planningRoot(cwd)),
+
+  };
+
+  output(withProjectRoot(cwd, result), raw);
+}
+
+/**
+ * Init handler for ingest-docs workflow (#2801).
+ *
+ * Returns the minimal set of fields that ingest-docs.md needs to detect
+ * whether a project/planning dir exists and choose new vs merge mode.
+ * Mirrors the initIngestDocs SDK handler in sdk/src/query/init.ts.
+ */
+function cmdInitIngestDocs(cwd, raw) {
+  const config = loadConfig(cwd);
+  const result = {
+    project_exists: pathExistsInternal(cwd, '.planning/PROJECT.md'),
+    planning_exists: fs.existsSync(planningRoot(cwd)),
+    ...getInitGitState(cwd),
+    project_path: '.planning/PROJECT.md',
+    commit_docs: config.commit_docs,
+  };
+  output(withProjectRoot(cwd, result), raw);
+}
+
+function cmdInitResume(cwd, raw) {
+  const config = loadConfig(cwd);
+
+  // Check for interrupted agent
+  let interruptedAgentId = null;
+  const agentIdRaw = platformReadSync(path.join(planningRoot(cwd), 'current-agent-id.txt'));
+  if (agentIdRaw !== null) interruptedAgentId = agentIdRaw.trim();
+
+  const result = {
+    // File existence
+    state_exists: fs.existsSync(path.join(planningDir(cwd), 'STATE.md')),
+    roadmap_exists: fs.existsSync(path.join(planningDir(cwd), 'ROADMAP.md')),
+    project_exists: pathExistsInternal(cwd, '.planning/PROJECT.md'),
+    planning_exists: fs.existsSync(planningRoot(cwd)),
+
+    // File paths
+    state_path: toPosixPath(path.relative(cwd, path.join(planningDir(cwd), 'STATE.md'))),
+    roadmap_path: toPosixPath(path.relative(cwd, path.join(planningDir(cwd), 'ROADMAP.md'))),
+    project_path: '.planning/PROJECT.md',
+
+    // Agent state
+    has_interrupted_agent: !!interruptedAgentId,
+    interrupted_agent_id: interruptedAgentId,
+
+    // Config
+    commit_docs: config.commit_docs,
+  };
+
+  output(withProjectRoot(cwd, result), raw);
+}
+
+function cmdInitVerifyWork(cwd, phase, raw) {
+  if (!phase) {
+    error('phase required for init verify-work');
+  }
+
+  const config = loadConfig(cwd);
+  let phaseInfo = findPhaseInternal(cwd, phase);
+
+  // If findPhaseInternal matched an archived phase from a prior milestone, but
+  // the phase exists in the current milestone's ROADMAP.md, ignore the archive
+  // match — same pattern as cmdInitPhaseOp.
+  if (phaseInfo?.archived) {
+    const roadmapPhase = getRoadmapPhaseInternal(cwd, phase);
+    if (roadmapPhase?.found) {
+      phaseInfo = null;
+    }
+  }
+
+  // Fallback to ROADMAP.md if no phase directory exists yet
+  if (!phaseInfo) {
+    const roadmapPhase = getRoadmapPhaseInternal(cwd, phase);
+    if (roadmapPhase?.found) {
+      const phaseName = roadmapPhase.phase_name;
+      phaseInfo = {
+        found: true,
+        directory: null,
+        phase_number: roadmapPhase.phase_number,
+        phase_name: phaseName,
+        phase_slug: phaseName ? phaseName.toLowerCase().replace(/[^a-z0-9]+/g, '-').replace(/^-+|-+$/g, '') : null,
+        plans: [],
+        summaries: [],
+        incomplete_plans: [],
+        has_research: false,
+        has_context: false,
+        has_verification: false,
+      };
+    }
+  }
+
+  const result = {
+    // Models
+    planner_model: resolveModelInternal(cwd, 'gsd-planner'),
+    checker_model: resolveModelInternal(cwd, 'gsd-plan-checker'),
+
+    // Config
+    commit_docs: config.commit_docs,
+
+    // Phase info
+    phase_found: !!phaseInfo,
+    phase_dir: phaseInfo?.directory || null,
+    phase_number: phaseInfo?.phase_number || null,
+    phase_name: phaseInfo?.phase_name || null,
+
+    // Existing artifacts
+    has_verification: phaseInfo?.has_verification || false,
+  };
+
+  output(withProjectRoot(cwd, result), raw);
+}
+
+function cmdInitPhaseOp(cwd, phase, raw) {
+  const config = loadConfig(cwd);
+  let phaseInfo = findPhaseInternal(cwd, phase);
+
+  // If the only disk match comes from an archived milestone, prefer the
+  // current milestone's ROADMAP entry so discuss-phase and similar flows
+  // don't attach to shipped work that reused the same phase number.
+  if (phaseInfo?.archived) {
+    const roadmapPhase = getRoadmapPhaseInternal(cwd, phase);
+    if (roadmapPhase?.found) {
+      const phaseName = roadmapPhase.phase_name;
+      phaseInfo = {
+        found: true,
+        directory: null,
+        phase_number: roadmapPhase.phase_number,
+        phase_name: phaseName,
+        phase_slug: phaseName ? phaseName.toLowerCase().replace(/[^a-z0-9]+/g, '-').replace(/^-+|-+$/g, '') : null,
+        plans: [],
+        summaries: [],
+        incomplete_plans: [],
+        has_research: false,
+        has_context: false,
+        has_verification: false,
+      };
+    }
+  }
+
+  // Fallback to ROADMAP.md if no directory exists (e.g., Plans: TBD)
+  if (!phaseInfo) {
+    const roadmapPhase = getRoadmapPhaseInternal(cwd, phase);
+    if (roadmapPhase?.found) {
+      const phaseName = roadmapPhase.phase_name;
+      phaseInfo = {
+        found: true,
+        directory: null,
+        phase_number: roadmapPhase.phase_number,
+        phase_name: phaseName,
+        phase_slug: phaseName ? phaseName.toLowerCase().replace(/[^a-z0-9]+/g, '-').replace(/^-+|-+$/g, '') : null,
+        plans: [],
+        summaries: [],
+        incomplete_plans: [],
+        has_research: false,
+        has_context: false,
+        has_verification: false,
+      };
+    }
+  }
+
+  // #3287: compute the canonical directory name with project_code prefix so
+  // the first-touch mkdir in /gsd:discuss-phase stays consistent with phase.add.
+  const phaseDir = phaseInfo?.directory || null;
+  const phaseNumber = phaseInfo?.phase_number || null;
+  const phaseName = phaseInfo?.phase_name || null;
+  const rawProjectCode = config.project_code || '';
+  let expectedPhaseDir = null;
+  if (!phaseDir && phaseNumber && phaseName) {
+    const paddedNum = normalizePhaseName(phaseNumber);
+    const slug = generateSlugInternal(phaseName).substring(0, 60);
+    if (slug) {
+      const prefix = rawProjectCode ? `${rawProjectCode}-` : '';
+      const dirName = `${prefix}${paddedNum}-${slug}`;
+      expectedPhaseDir = toPosixPath(path.relative(cwd, path.join(planningPaths(cwd).phases, dirName)));
+    }
+  }
+
+  const result = {
+    // Config
+    commit_docs: config.commit_docs,
+    // #2997: secret config keys may be either booleans (availability flags) or
+    // string API keys (when user did `gsd-tools config-set brave_search XXX`).
+    // Pass booleans through; mask string values so the init bundle never echoes
+    // plaintext credentials. SDK init.ts mirrors this masking.
+    brave_search: typeof config.brave_search === 'string' ? maskIfSecret('brave_search', config.brave_search) : config.brave_search,
+    firecrawl: typeof config.firecrawl === 'string' ? maskIfSecret('firecrawl', config.firecrawl) : config.firecrawl,
+    exa_search: typeof config.exa_search === 'string' ? maskIfSecret('exa_search', config.exa_search) : config.exa_search,
+
+    // Phase info
+    phase_found: !!phaseInfo,
+    phase_dir: phaseDir,
+    expected_phase_dir: expectedPhaseDir,
+    phase_number: phaseNumber,
+    phase_name: phaseName,
+    phase_slug: phaseInfo?.phase_slug || null,
+    padded_phase: phaseNumber ? normalizePhaseName(phaseNumber) : null,
+
+    // Existing artifacts
+    has_research: phaseInfo?.has_research || false,
+    has_context: phaseInfo?.has_context || false,
+    has_plans: (phaseInfo?.plans?.length || 0) > 0,
+    has_verification: phaseInfo?.has_verification || false,
+    has_reviews: phaseInfo?.has_reviews || false,
+    plan_count: phaseInfo?.plans?.length || 0,
+
+    // File existence
+    roadmap_exists: fs.existsSync(path.join(planningDir(cwd), 'ROADMAP.md')),
+    planning_exists: fs.existsSync(planningDir(cwd)),
+
+    // File paths
+    state_path: toPosixPath(path.relative(cwd, path.join(planningDir(cwd), 'STATE.md'))),
+    roadmap_path: toPosixPath(path.relative(cwd, path.join(planningDir(cwd), 'ROADMAP.md'))),
+    requirements_path: toPosixPath(path.relative(cwd, path.join(planningDir(cwd), 'REQUIREMENTS.md'))),
+  };
+
+  if (phaseInfo?.directory) {
+    const phaseDirFull = path.join(cwd, phaseInfo.directory);
+    try {
+      const files = fs.readdirSync(phaseDirFull);
+      const contextFile = findContextMdIn(phaseDirFull);
+      if (contextFile) {
+        result.context_path = toPosixPath(path.join(phaseInfo.directory, contextFile));
+      }
+      const researchFile = files.find(f => f.endsWith('-RESEARCH.md') || f === 'RESEARCH.md');
+      if (researchFile) {
+        result.research_path = toPosixPath(path.join(phaseInfo.directory, researchFile));
+      }
+      const verificationFile = files.find(f => f.endsWith('-VERIFICATION.md') || f === 'VERIFICATION.md');
+      if (verificationFile) {
+        result.verification_path = toPosixPath(path.join(phaseInfo.directory, verificationFile));
+      }
+      const uatFile = files.find(f => f.endsWith('-UAT.md') || f === 'UAT.md');
+      if (uatFile) {
+        result.uat_path = toPosixPath(path.join(phaseInfo.directory, uatFile));
+      }
+      const reviewsFile = files.find(f => f.endsWith('-REVIEWS.md') || f === 'REVIEWS.md');
+      if (reviewsFile) {
+        result.reviews_path = toPosixPath(path.join(phaseInfo.directory, reviewsFile));
+      }
+    } catch { /* intentionally empty */ }
+  }
+
+  output(withProjectRoot(cwd, result), raw);
+}
+
+function cmdInitTodos(cwd, area, raw) {
+  const config = loadConfig(cwd);
+  const now = new Date();
+
+  // List todos (reuse existing logic)
+  const pendingDir = path.join(planningDir(cwd), 'todos', 'pending');
+  let count = 0;
+  const todos = [];
+
+  try {
+    const files = fs.readdirSync(pendingDir).filter(f => f.endsWith('.md'));
+    for (const file of files) {
+      const content = platformReadSync(path.join(pendingDir, file));
+      if (content === null) continue;
+      try {
+        const createdMatch = content.match(/^created:\s*(.+)$/m);
+        const titleMatch = content.match(/^title:\s*(.+)$/m);
+        const areaMatch = content.match(/^area:\s*(.+)$/m);
+        const todoArea = areaMatch ? areaMatch[1].trim() : 'general';
+
+        if (area && todoArea !== area) continue;
+
+        count++;
+        todos.push({
+          file,
+          created: createdMatch ? createdMatch[1].trim() : 'unknown',
+          title: titleMatch ? titleMatch[1].trim() : 'Untitled',
+          area: todoArea,
+          path: toPosixPath(path.relative(cwd, path.join(planningDir(cwd), 'todos', 'pending', file))),
+        });
+      } catch { /* intentionally empty */ }
+    }
+  } catch { /* intentionally empty */ }
+
+  const result = {
+    // Config
+    commit_docs: config.commit_docs,
+
+    // Timestamps
+    date: now.toISOString().split('T')[0],
+    timestamp: now.toISOString(),
+
+    // Todo inventory
+    todo_count: count,
+    todos,
+    area_filter: area || null,
+
+    // Paths
+    pending_dir: toPosixPath(path.relative(cwd, path.join(planningDir(cwd), 'todos', 'pending'))),
+    completed_dir: toPosixPath(path.relative(cwd, path.join(planningDir(cwd), 'todos', 'completed'))),
+
+    // File existence
+    planning_exists: fs.existsSync(planningDir(cwd)),
+    todos_dir_exists: fs.existsSync(path.join(planningDir(cwd), 'todos')),
+    pending_dir_exists: fs.existsSync(path.join(planningDir(cwd), 'todos', 'pending')),
+  };
+
+  output(withProjectRoot(cwd, result), raw);
+}
+
+function cmdInitMilestoneOp(cwd, raw) {
+  const config = loadConfig(cwd);
+  const milestone = getMilestoneInfo(cwd);
+
+  // Count phases
+  let phaseCount = 0;
+  let completedPhases = 0;
+  const phasesDir = path.join(planningDir(cwd), 'phases');
+
+  // Bug #2633 — ROADMAP.md (current milestone section) is the authority for
+  // phase counts, NOT the on-disk `.planning/phases/` directory. After
+  // `phases clear` between milestones, on-disk dirs will be a subset of the
+  // roadmap until each phase is materialized; reading from disk causes
+  // `all_phases_complete: true` to fire prematurely.
+  let roadmapPhaseNumbers = [];
+  try {
+    const roadmapPath = path.join(planningDir(cwd), 'ROADMAP.md');
+    const roadmapRaw = fs.readFileSync(roadmapPath, 'utf-8');
+    const currentSection = extractCurrentMilestone(roadmapRaw, cwd);
+    const phasePattern = /#{2,4}\s*Phase\s+(\d+[A-Z]?(?:\.\d+)*)\s*:/gi;
+    let m;
+    while ((m = phasePattern.exec(currentSection)) !== null) {
+      roadmapPhaseNumbers.push(m[1]);
+    }
+  } catch { /* intentionally empty */ }
+
+  // Canonicalize a phase token by stripping leading zeros from the integer
+  // head while preserving any [A-Z]? suffix and dotted segments. So "03" →
+  // "3", "03A" → "3A", "03.1" → "3.1", "3A" → "3A". Disk dirs that pad
+  // ("03-alpha") then match roadmap tokens ("Phase 3") without ever
+  // collapsing distinct tokens like "3" / "3A" / "3.1" into the same bucket.
+  const canonicalizePhase = (tok) => {
+    const m = tok.match(/^(\d+)([A-Z]?(?:\.\d+)*)$/);
+    return m ? String(parseInt(m[1], 10)) + m[2] : tok;
+  };
+  const diskPhaseDirs = new Map();
+  try {
+    const entries = fs.readdirSync(phasesDir, { withFileTypes: true });
+    for (const e of entries) {
+      if (!e.isDirectory()) continue;
+      const m = e.name.match(/^(\d+[A-Z]?(?:\.\d+)*)/);
+      if (!m) continue;
+      diskPhaseDirs.set(canonicalizePhase(m[1]), e.name);
+    }
+  } catch { /* intentionally empty */ }
+
+  if (roadmapPhaseNumbers.length > 0) {
+    phaseCount = roadmapPhaseNumbers.length;
+    for (const num of roadmapPhaseNumbers) {
+      const dirName = diskPhaseDirs.get(canonicalizePhase(num));
+      if (!dirName) continue;
+      try {
+        const hasSummary = listPhaseSummaryFiles(path.join(phasesDir, dirName)).length > 0;
+        if (hasSummary) completedPhases++;
+      } catch { /* intentionally empty */ }
+    }
+  } else {
+    // Fallback: no parseable ROADMAP — preserve legacy on-disk behavior.
+    try {
+      const entries = fs.readdirSync(phasesDir, { withFileTypes: true });
+      const dirs = entries.filter(e => e.isDirectory()).map(e => e.name);
+      phaseCount = dirs.length;
+      for (const dir of dirs) {
+        try {
+          const hasSummary = listPhaseSummaryFiles(path.join(phasesDir, dir)).length > 0;
+          if (hasSummary) completedPhases++;
+        } catch { /* intentionally empty */ }
+      }
+    } catch { /* intentionally empty */ }
+  }
+
+  // Check archive
+  const archiveDir = path.join(planningRoot(cwd), 'archive');
+  let archivedMilestones = [];
+  try {
+    archivedMilestones = fs.readdirSync(archiveDir, { withFileTypes: true })
+      .filter(e => e.isDirectory())
+      .map(e => e.name);
+  } catch { /* intentionally empty */ }
+
+  const result = {
+    // Config
+    commit_docs: config.commit_docs,
+
+    // Current milestone
+    milestone_version: milestone.version,
+    milestone_name: milestone.name,
+    milestone_slug: generateSlugInternal(milestone.name),
+
+    // Phase counts
+    phase_count: phaseCount,
+    completed_phases: completedPhases,
+    all_phases_complete: phaseCount > 0 && phaseCount === completedPhases,
+
+    // Archive
+    archived_milestones: archivedMilestones,
+    archive_count: archivedMilestones.length,
+
+    // File existence
+    project_exists: pathExistsInternal(cwd, '.planning/PROJECT.md'),
+    roadmap_exists: fs.existsSync(path.join(planningDir(cwd), 'ROADMAP.md')),
+    state_exists: fs.existsSync(path.join(planningDir(cwd), 'STATE.md')),
+    archive_exists: fs.existsSync(path.join(planningRoot(cwd), 'archive')),
+    phases_dir_exists: fs.existsSync(path.join(planningDir(cwd), 'phases')),
+  };
+
+  output(withProjectRoot(cwd, result), raw);
+}
+
+function cmdInitMapCodebase(cwd, raw) {
+  const config = loadConfig(cwd);
+  const now = new Date();
+
+  // Check for existing codebase maps
+  const codebaseDir = path.join(planningRoot(cwd), 'codebase');
+  let existingMaps = [];
+  try {
+    existingMaps = fs.readdirSync(codebaseDir).filter(f => f.endsWith('.md'));
+  } catch { /* intentionally empty */ }
+
+  const result = {
+    // Models
+    mapper_model: resolveModelInternal(cwd, 'gsd-codebase-mapper'),
+
+    // Config
+    commit_docs: config.commit_docs,
+    search_gitignored: config.search_gitignored,
+    parallelization: config.parallelization,
+    subagent_timeout: config.subagent_timeout,
+
+    // Timestamps
+    date: now.toISOString().split('T')[0],
+    timestamp: now.toISOString(),
+
+    // Paths
+    codebase_dir: '.planning/codebase',
+
+    // Existing maps
+    existing_maps: existingMaps,
+    has_maps: existingMaps.length > 0,
+
+    // File existence
+    planning_exists: pathExistsInternal(cwd, '.planning'),
+    codebase_dir_exists: pathExistsInternal(cwd, '.planning/codebase'),
+  };
+
+  output(withProjectRoot(cwd, result), raw);
+}
+
+function cmdInitManager(cwd, raw) {
+  const config = loadConfig(cwd);
+  const milestone = getMilestoneInfo(cwd);
+  // Resolve the runtime once so every emitted slash-command reference uses
+  // the routable shape for this install (#3584). Hyphen form for skills-based
+  // runtimes, $gsd-<cmd> shell-var for codex.
+  const _slashRuntime = resolveRuntime(cwd);
+
+  // Use planningPaths for forward-compatibility with workstream scoping (#1268)
+  const paths = planningPaths(cwd);
+
+  // Validate prerequisites
+  if (!fs.existsSync(paths.roadmap)) {
+    error(`No ROADMAP.md found. Run ${formatGsdSlash('new-milestone', _slashRuntime)} first.`);
+  }
+  if (!fs.existsSync(paths.state)) {
+    error(`No STATE.md found. Run ${formatGsdSlash('new-milestone', _slashRuntime)} first.`);
+  }
+  const rawContent = fs.readFileSync(paths.roadmap, 'utf-8');
+  const content = extractCurrentMilestone(rawContent, cwd);
+  const phasesDir = paths.phases;
+  const isDirInMilestone = getMilestonePhaseFilter(cwd);
+
+  // Pre-compute directory listing once (avoids O(N) readdirSync per phase)
+  const _phaseDirEntries = (() => {
+    try {
+      return fs.readdirSync(phasesDir, { withFileTypes: true })
+        .filter(e => e.isDirectory())
+        .map(e => e.name);
+    } catch { return []; }
+  })();
+
+  // Pre-extract all checkbox states in a single pass (avoids O(N) regex per phase)
+  const _checkboxStates = new Map();
+  const _cbPattern = /-\s*\[(x| )\]\s*.*Phase\s+(\d+[A-Z]?(?:\.\d+)*)[:\s]/gi;
+  let _cbMatch;
+  while ((_cbMatch = _cbPattern.exec(content)) !== null) {
+    _checkboxStates.set(_cbMatch[2], _cbMatch[1].toLowerCase() === 'x');
+  }
+
+  const phasePattern = /#{2,4}\s*Phase\s+(\d+[A-Z]?(?:\.\d+)*)\s*:\s*([^\n]+)/gi;
+  const phases = [];
+  let match;
+
+  while ((match = phasePattern.exec(content)) !== null) {
+    const phaseNum = match[1];
+    const phaseName = match[2].replace(/\(INSERTED\)/i, '').trim();
+
+    const sectionStart = match.index;
+    const restOfContent = content.slice(sectionStart);
+    // #3691: `\d` → `\d[\d.]*` so decimal phase headings (e.g. `### Phase 02.3:`) are
+    // recognised as section boundaries.
+    const nextHeader = restOfContent.match(/\n#{2,4}\s+Phase\s+\d[\d.]*/i);
+    const sectionEnd = nextHeader ? sectionStart + nextHeader.index : content.length;
+    const section = content.slice(sectionStart, sectionEnd);
+
+    const goalMatch = section.match(/\*\*Goal(?::\*\*|\*\*:)\s*([^\n]+)/i);
+    const goal = goalMatch ? goalMatch[1].trim() : null;
+
+    const dependsMatch = section.match(/\*\*Depends on(?::\*\*|\*\*:)\s*([^\n]+)/i);
+    const depends_on = dependsMatch ? dependsMatch[1].trim() : null;
+
+    const normalized = normalizePhaseName(phaseNum);
+    let diskStatus = 'no_directory';
+    let planCount = 0;
+    let summaryCount = 0;
+    let hasContext = false;
+    let hasResearch = false;
+    let lastActivity = null;
+    let isActive = false;
+
+    try {
+      const dirs = _phaseDirEntries.filter(isDirInMilestone);
+      const dirMatch = dirs.find(d => phaseTokenMatches(d, normalized));
+
+      if (dirMatch) {
+        const fullDir = path.join(phasesDir, dirMatch);
+        const phaseFiles = fs.readdirSync(fullDir);
+        planCount = listPhasePlanFiles(fullDir).length;
+        summaryCount = listPhaseSummaryFiles(fullDir).length;
+        hasContext = findContextMdIn(fullDir) !== null;
+        hasResearch = phaseFiles.some(f => f.endsWith('-RESEARCH.md') || f === 'RESEARCH.md');
+
+        if (summaryCount >= planCount && planCount > 0) diskStatus = 'complete';
+        else if (summaryCount > 0) diskStatus = 'partial';
+        else if (planCount > 0) diskStatus = 'planned';
+        else if (hasResearch) diskStatus = 'researched';
+        else if (hasContext) diskStatus = 'discussed';
+        else diskStatus = 'empty';
+
+        // Activity detection: check most recent file mtime
+        const now = Date.now();
+        let newestMtime = 0;
+        for (const f of phaseFiles) {
+          try {
+            const stat = fs.statSync(path.join(fullDir, f));
+            if (stat.mtimeMs > newestMtime) newestMtime = stat.mtimeMs;
+          } catch { /* intentionally empty */ }
+        }
+        if (newestMtime > 0) {
+          lastActivity = new Date(newestMtime).toISOString();
+          isActive = (now - newestMtime) < 300000; // 5 minutes
+        }
+      }
+    } catch { /* intentionally empty */ }
+
+    // Check ROADMAP checkbox status (pre-extracted above the loop)
+    const roadmapComplete = _checkboxStates.get(phaseNum) || false;
+    if (roadmapComplete && diskStatus !== 'complete') {
+      diskStatus = 'complete';
+    }
+
+    phases.push({
+      number: phaseNum,
+      name: phaseName,
+      goal,
+      depends_on,
+      disk_status: diskStatus,
+      has_context: hasContext,
+      has_research: hasResearch,
+      plan_count: planCount,
+      summary_count: summaryCount,
+      roadmap_complete: roadmapComplete,
+      last_activity: lastActivity,
+      is_active: isActive,
+    });
+  }
+
+  // Compute display names: truncate to keep table aligned
+  const MAX_NAME_WIDTH = 20;
+  for (const phase of phases) {
+    if (phase.name.length > MAX_NAME_WIDTH) {
+      phase.display_name = phase.name.slice(0, MAX_NAME_WIDTH - 1) + '…';
+    } else {
+      phase.display_name = phase.name;
+    }
+  }
+
+  // Dependency satisfaction: check if all depends_on phases are complete
+  const completedNums = new Set(phases.filter(p => p.disk_status === 'complete').map(p => p.number));
+
+  // Also include phases from previously shipped milestones — they are all
+  // complete by definition (a milestone only ships when all phases are done).
+  // rawContent is the full ROADMAP.md (including <details>-wrapped shipped
+  // milestone sections that extractCurrentMilestone strips out).
+  const _allCompletedPattern = /-\s*\[x\]\s*.*Phase\s+(\d+[A-Z]?(?:\.\d+)*)[:\s]/gi;
+  let _allMatch;
+  while ((_allMatch = _allCompletedPattern.exec(rawContent)) !== null) {
+    completedNums.add(_allMatch[1]);
+  }
+
+  for (const phase of phases) {
+    if (!phase.depends_on || /^none$/i.test(phase.depends_on.trim())) {
+      phase.deps_satisfied = true;
+    } else {
+      // Parse "Phase 1, Phase 3" or "1, 3" formats
+      const depNums = phase.depends_on.match(/\d+(?:\.\d+)*/g) || [];
+      phase.deps_satisfied = depNums.every(n => completedNums.has(n));
+      phase.dep_phases = depNums;
+    }
+  }
+
+  // Compact dependency display for dashboard
+  for (const phase of phases) {
+    phase.deps_display = (phase.dep_phases && phase.dep_phases.length > 0)
+      ? phase.dep_phases.join(',')
+      : '—';
+  }
+
+  for (const phase of phases) {
+    phase.is_next_to_discuss =
+      (phase.disk_status === 'empty' || phase.disk_status === 'no_directory') &&
+      phase.deps_satisfied;
+  }
+
+  // Check for WAITING.json signal
+  let waitingSignal = null;
+  try {
+    const waitingPath = path.join(cwd, '.planning', 'WAITING.json');
+    const waitingRaw = platformReadSync(waitingPath);
+    if (waitingRaw !== null) {
+      waitingSignal = JSON.parse(waitingRaw);
+    }
+  } catch { /* intentionally empty */ }
+
+  // Compute recommended actions (execute > plan > discuss)
+  // Skip BACKLOG phases (999.x numbering) — they are parked ideas, not active work
+  const recommendedActions = [];
+  for (const phase of phases) {
+    if (phase.disk_status === 'complete') continue;
+    if (/^999(?:\.|$)/.test(phase.number)) continue;
+
+    if (phase.disk_status === 'planned' && phase.deps_satisfied) {
+      recommendedActions.push({
+        phase: phase.number,
+        phase_name: phase.name,
+        action: 'execute',
+        reason: `${phase.plan_count} plans ready, dependencies met`,
+        command: `${formatGsdSlash('execute-phase', _slashRuntime)} ${phase.number}`,
+      });
+    } else if (phase.disk_status === 'discussed' || phase.disk_status === 'researched') {
+      recommendedActions.push({
+        phase: phase.number,
+        phase_name: phase.name,
+        action: 'plan',
+        reason: 'Context gathered, ready for planning',
+        command: `${formatGsdSlash('plan-phase', _slashRuntime)} ${phase.number}`,
+      });
+    } else if ((phase.disk_status === 'empty' || phase.disk_status === 'no_directory') && phase.is_next_to_discuss) {
+      recommendedActions.push({
+        phase: phase.number,
+        phase_name: phase.name,
+        action: 'discuss',
+        reason: 'Unblocked, ready to gather context',
+        command: `${formatGsdSlash('discuss-phase', _slashRuntime)} ${phase.number}`,
+      });
+    }
+  }
+
+  // Filter recommendations: no parallel execute/plan unless phases are independent
+  // Two phases are "independent" if neither depends on the other (directly or transitively)
+  const phaseMap = new Map(phases.map(p => [p.number, p]));
+
+  function reaches(from, to, visited = new Set()) {
+    if (visited.has(from)) return false;
+    visited.add(from);
+    const p = phaseMap.get(from);
+    if (!p || !p.dep_phases || p.dep_phases.length === 0) return false;
+    if (p.dep_phases.includes(to)) return true;
+    return p.dep_phases.some(dep => reaches(dep, to, visited));
+  }
+
+  function hasDepRelationship(numA, numB) {
+    return reaches(numA, numB) || reaches(numB, numA);
+  }
+
+  // Detect phases with active work (file modified in last 5 min)
+  const activeExecuting = phases.filter(p =>
+    p.disk_status === 'partial' ||
+    (p.disk_status === 'planned' && p.is_active)
+  );
+  const activePlanning = phases.filter(p =>
+    p.is_active && (p.disk_status === 'discussed' || p.disk_status === 'researched')
+  );
+
+  const filteredActions = recommendedActions.filter(action => {
+    if (action.action === 'execute' && activeExecuting.length > 0) {
+      // Only allow if independent of ALL actively-executing phases
+      return activeExecuting.every(active => !hasDepRelationship(action.phase, active.number));
+    }
+    if (action.action === 'plan' && activePlanning.length > 0) {
+      // Only allow if independent of ALL actively-planning phases
+      return activePlanning.every(active => !hasDepRelationship(action.phase, active.number));
+    }
+    return true;
+  });
+
+  // Exclude backlog phases (999.x) from completion accounting (#2129)
+  const nonBacklogPhases = phases.filter(p => !/^999(?:\.|$)/.test(p.number));
+  const completedCount = nonBacklogPhases.filter(p => p.disk_status === 'complete').length;
+
+  // Read manager flags from config (passthrough flags for each step)
+  // Validate: flags must be CLI-safe (only --flags, alphanumeric, hyphens, spaces)
+  const sanitizeFlags = (raw) => {
+    const val = typeof raw === 'string' ? raw : '';
+    if (!val) return '';
+    // Allow only --flag patterns with alphanumeric/hyphen values separated by spaces
+    const tokens = val.split(/\s+/).filter(Boolean);
+    const safe = tokens.every(t => /^--[a-zA-Z0-9][-a-zA-Z0-9]*$/.test(t) || /^[a-zA-Z0-9][-a-zA-Z0-9_.]*$/.test(t));
+    if (!safe) {
+      process.stderr.write(`gsd-tools: warning: manager.flags contains invalid tokens, ignoring: ${val}\n`);
+      return '';
+    }
+    return val;
+  };
+  const managerFlags = {
+    discuss: sanitizeFlags(config.manager && config.manager.flags && config.manager.flags.discuss),
+    plan: sanitizeFlags(config.manager && config.manager.flags && config.manager.flags.plan),
+    execute: sanitizeFlags(config.manager && config.manager.flags && config.manager.flags.execute),
+  };
+
+  const result = {
+    milestone_version: milestone.version,
+    milestone_name: milestone.name,
+    phases,
+    phase_count: phases.length,
+    completed_count: completedCount,
+    in_progress_count: phases.filter(p => ['partial', 'planned', 'discussed', 'researched'].includes(p.disk_status)).length,
+    recommended_actions: filteredActions,
+    waiting_signal: waitingSignal,
+    all_complete: completedCount === nonBacklogPhases.length && nonBacklogPhases.length > 0,
+    project_exists: pathExistsInternal(cwd, '.planning/PROJECT.md'),
+    roadmap_exists: true,
+    state_exists: true,
+    manager_flags: managerFlags,
+  };
+
+  output(withProjectRoot(cwd, result), raw);
+}
+
+function cmdInitProgress(cwd, raw) {
+  try {
+    const { pruneOrphanedWorktrees } = require('./core.cjs');
+    pruneOrphanedWorktrees(cwd);
+  } catch (_) {}
+  const config = loadConfig(cwd);
+  const milestone = getMilestoneInfo(cwd);
+
+  // Analyze phases — filter to current milestone and include ROADMAP-only phases
+  const phasesDir = path.join(planningDir(cwd), 'phases');
+  const phases = [];
+  let currentPhase = null;
+  let nextPhase = null;
+
+  // Build set of phases defined in ROADMAP for the current milestone
+  const roadmapPhaseNums = new Set();
+  const roadmapPhaseNames = new Map();
+  const roadmapCheckboxStates = new Map();
+  try {
+    const roadmapContent = extractCurrentMilestone(
+      fs.readFileSync(path.join(planningDir(cwd), 'ROADMAP.md'), 'utf-8'), cwd
+    );
+    const headingPattern = /#{2,4}\s*Phase\s+(\d+[A-Z]?(?:\.\d+)*)\s*:\s*([^\n]+)/gi;
+    let hm;
+    while ((hm = headingPattern.exec(roadmapContent)) !== null) {
+      roadmapPhaseNums.add(hm[1]);
+      roadmapPhaseNames.set(hm[1], hm[2].replace(/\(INSERTED\)/i, '').trim());
+    }
+    // #2646: parse `- [x] Phase N` checkbox states so ROADMAP-only phases
+    // inherit completion from the ROADMAP when no phase directory exists.
+    const cbPattern = /-\s*\[(x| )\]\s*.*Phase\s+(\d+[A-Z]?(?:\.\d+)*)[:\s]/gi;
+    let cbm;
+    while ((cbm = cbPattern.exec(roadmapContent)) !== null) {
+      roadmapCheckboxStates.set(cbm[2], cbm[1].toLowerCase() === 'x');
+    }
+  } catch { /* intentionally empty */ }
+
+  const isDirInMilestone = getMilestonePhaseFilter(cwd);
+  const seenPhaseNums = new Set();
+
+  try {
+    const entries = fs.readdirSync(phasesDir, { withFileTypes: true });
+    const dirs = entries.filter(e => e.isDirectory()).map(e => e.name)
+      .filter(isDirInMilestone)
+      .sort((a, b) => {
+        const pa = a.match(/^(\d+[A-Z]?(?:\.\d+)*)/i);
+        const pb = b.match(/^(\d+[A-Z]?(?:\.\d+)*)/i);
+        if (!pa || !pb) return a.localeCompare(b);
+        return parseInt(pa[1], 10) - parseInt(pb[1], 10);
+      });
+
+    for (const dir of dirs) {
+      const match = dir.match(/^(\d+[A-Z]?(?:\.\d+)*)-?(.*)/i);
+      const phaseNumber = match ? match[1] : dir;
+      const phaseName = match && match[2] ? match[2] : null;
+      seenPhaseNums.add(phaseNumber.replace(/^0+/, '') || '0');
+
+      const phasePath = path.join(phasesDir, dir);
+      const phaseFiles = fs.readdirSync(phasePath);
+
+      const plans = listPhasePlanFiles(phasePath);
+      const summaries = listPhaseSummaryFiles(phasePath);
+      const hasResearch = phaseFiles.some(f => f.endsWith('-RESEARCH.md') || f === 'RESEARCH.md');
+
+      const status = summaries.length >= plans.length && plans.length > 0 ? 'complete' :
+                     plans.length > 0 ? 'in_progress' :
+                     hasResearch ? 'researched' : 'pending';
+
+      const phaseInfo = {
+        number: phaseNumber,
+        name: phaseName,
+        directory: toPosixPath(path.relative(cwd, path.join(planningDir(cwd), 'phases', dir))),
+        status,
+        plan_count: plans.length,
+        summary_count: summaries.length,
+        has_research: hasResearch,
+      };
+
+      phases.push(phaseInfo);
+
+      // Find current (first incomplete with plans) and next (first pending)
+      if (!currentPhase && (status === 'in_progress' || status === 'researched')) {
+        currentPhase = phaseInfo;
+      }
+      if (!nextPhase && status === 'pending') {
+        nextPhase = phaseInfo;
+      }
+    }
+  } catch { /* intentionally empty */ }
+
+  // Add phases defined in ROADMAP but not yet scaffolded to disk. When the
+  // ROADMAP has a `- [x] Phase N` checkbox, honor it as 'complete' so
+  // completed_count and status reflect the ROADMAP source of truth (#2646).
+  for (const [num, name] of roadmapPhaseNames) {
+    const stripped = num.replace(/^0+/, '') || '0';
+    if (!seenPhaseNums.has(stripped)) {
+      const checkboxComplete =
+        roadmapCheckboxStates.get(num) === true ||
+        roadmapCheckboxStates.get(stripped) === true;
+      const status = checkboxComplete ? 'complete' : 'not_started';
+      const phaseInfo = {
+        number: num,
+        name: name.toLowerCase().replace(/[^a-z0-9]+/g, '-').replace(/^-+|-+$/g, ''),
+        directory: null,
+        status,
+        plan_count: 0,
+        summary_count: 0,
+        has_research: false,
+      };
+      phases.push(phaseInfo);
+      if (!nextPhase && !currentPhase && status !== 'complete') {
+        nextPhase = phaseInfo;
+      }
+    }
+  }
+
+  // Re-sort phases by number after adding ROADMAP-only phases
+  phases.sort((a, b) => parseInt(a.number, 10) - parseInt(b.number, 10));
+
+  // Check for paused work
+  let pausedAt = null;
+  const state = platformReadSync(path.join(planningDir(cwd), 'STATE.md'));
+  if (state !== null) {
+    const pauseMatch = state.match(/\*\*Paused At:\*\*\s*(.+)/);
+    if (pauseMatch) pausedAt = pauseMatch[1].trim();
+  }
+
+  const result = {
+    // Models
+    executor_model: resolveModelInternal(cwd, 'gsd-executor'),
+    planner_model: resolveModelInternal(cwd, 'gsd-planner'),
+
+    // Config
+    commit_docs: config.commit_docs,
+
+    // Milestone
+    milestone_version: milestone.version,
+    milestone_name: milestone.name,
+
+    // Phase overview
+    phases,
+    phase_count: phases.length,
+    completed_count: phases.filter(p => p.status === 'complete').length,
+    in_progress_count: phases.filter(p => p.status === 'in_progress').length,
+
+    // Current state
+    current_phase: currentPhase,
+    next_phase: nextPhase,
+    paused_at: pausedAt,
+    has_work_in_progress: !!currentPhase,
+
+    // File existence
+    project_exists: pathExistsInternal(cwd, '.planning/PROJECT.md'),
+    roadmap_exists: fs.existsSync(path.join(planningDir(cwd), 'ROADMAP.md')),
+    state_exists: fs.existsSync(path.join(planningDir(cwd), 'STATE.md')),
+    // File paths
+    state_path: toPosixPath(path.relative(cwd, path.join(planningDir(cwd), 'STATE.md'))),
+    roadmap_path: toPosixPath(path.relative(cwd, path.join(planningDir(cwd), 'ROADMAP.md'))),
+    project_path: '.planning/PROJECT.md',
+    config_path: toPosixPath(path.relative(cwd, path.join(planningDir(cwd), 'config.json'))),
+  };
+
+  output(withProjectRoot(cwd, result), raw);
+}
+
+/**
+ * Detect child git repos in a directory (one level deep).
+ * Returns array of { name, path, has_uncommitted } objects.
+ */
+function detectChildRepos(dir) {
+  const repos = [];
+  let entries;
+  try { entries = fs.readdirSync(dir, { withFileTypes: true }); } catch { return repos; }
+  for (const entry of entries) {
+    if (!entry.isDirectory()) continue;
+    if (entry.name.startsWith('.')) continue;
+    const fullPath = path.join(dir, entry.name);
+    const gitDir = path.join(fullPath, '.git');
+    if (fs.existsSync(gitDir)) {
+      const statusResult = execGit(['status', '--porcelain'], { cwd: fullPath, timeout: 5000 });
+      const hasUncommitted = statusResult.exitCode === 0 && statusResult.stdout.length > 0;
+      repos.push({ name: entry.name, path: fullPath, has_uncommitted: hasUncommitted });
+    }
+  }
+  return repos;
+}
+
+function cmdInitNewWorkspace(cwd, raw) {
+  const homedir = process.env.HOME || require('os').homedir();
+  const defaultBase = path.join(homedir, 'gsd-workspaces');
+
+  // Detect child git repos for interactive selection
+  const childRepos = detectChildRepos(cwd);
+
+  // Check if git worktree is available
+  const gitVersion = execGit(['--version'], { timeout: 5000 });
+  const worktreeAvailable = gitVersion.exitCode === 0;
+
+  const result = {
+    default_workspace_base: defaultBase,
+    child_repos: childRepos,
+    child_repo_count: childRepos.length,
+    worktree_available: worktreeAvailable,
+    is_git_repo: pathExistsInternal(cwd, '.git'),
+    cwd_repo_name: path.basename(cwd),
+  };
+
+  output(withProjectRoot(cwd, result), raw);
+}
+
+function cmdInitListWorkspaces(cwd, raw) {
+  const homedir = process.env.HOME || require('os').homedir();
+  const defaultBase = path.join(homedir, 'gsd-workspaces');
+
+  const workspaces = [];
+  if (fs.existsSync(defaultBase)) {
+    let entries;
+    try { entries = fs.readdirSync(defaultBase, { withFileTypes: true }); } catch { entries = []; }
+    for (const entry of entries) {
+      if (!entry.isDirectory()) continue;
+      const wsPath = path.join(defaultBase, entry.name);
+      const manifestPath = path.join(wsPath, 'WORKSPACE.md');
+      if (!fs.existsSync(manifestPath)) continue;
+
+      let repoCount = 0;
+      let hasProject = false;
+      let strategy = 'unknown';
+      const manifest = platformReadSync(manifestPath);
+      if (manifest !== null) {
+        const strategyMatch = manifest.match(/^Strategy:\s*(.+)$/m);
+        if (strategyMatch) strategy = strategyMatch[1].trim();
+        // Count table rows (lines starting with |, excluding header and separator)
+        const tableRows = manifest.split('\n').filter(l => l.match(/^\|\s*\w/) && !l.includes('Repo') && !l.includes('---'));
+        repoCount = tableRows.length;
+      }
+      hasProject = fs.existsSync(path.join(wsPath, '.planning', 'PROJECT.md'));
+
+      workspaces.push({
+        name: entry.name,
+        path: wsPath,
+        repo_count: repoCount,
+        strategy,
+        has_project: hasProject,
+      });
+    }
+  }
+
+  const result = {
+    workspace_base: defaultBase,
+    workspaces,
+    workspace_count: workspaces.length,
+  };
+
+  output(result, raw);
+}
+
+function cmdInitRemoveWorkspace(cwd, name, raw) {
+  const homedir = process.env.HOME || require('os').homedir();
+  const defaultBase = path.join(homedir, 'gsd-workspaces');
+
+  if (!name) {
+    error('workspace name required for init remove-workspace');
+  }
+
+  const wsPath = path.join(defaultBase, name);
+  const manifestPath = path.join(wsPath, 'WORKSPACE.md');
+
+  if (!fs.existsSync(wsPath)) {
+    error(`Workspace not found: ${wsPath}`);
+  }
+
+  // Parse manifest for repo info
+  const repos = [];
+  let strategy = 'unknown';
+  const manifestContent = platformReadSync(manifestPath);
+  if (manifestContent !== null) {
+    try {
+      const manifest = manifestContent;
+      const strategyMatch = manifest.match(/^Strategy:\s*(.+)$/m);
+      if (strategyMatch) strategy = strategyMatch[1].trim();
+
+      // Parse table rows for repo names and source paths
+      const lines = manifest.split('\n');
+      for (const line of lines) {
+        const match = line.match(/^\|\s*(\S+)\s*\|\s*(\S+)\s*\|\s*(\S+)\s*\|\s*(\S+)\s*\|$/);
+        if (match && match[1] !== 'Repo' && !match[1].includes('---')) {
+          repos.push({ name: match[1], source: match[2], branch: match[3], strategy: match[4] });
+        }
+      }
+    } catch { /* best-effort */ }
+  }
+
+  // Check for uncommitted changes in workspace repos
+  const dirtyRepos = [];
+  for (const repo of repos) {
+    const repoPath = path.join(wsPath, repo.name);
+    if (!fs.existsSync(repoPath)) continue;
+    const statusResult = execGit(['status', '--porcelain'], { cwd: repoPath, timeout: 5000 });
+    if (statusResult.exitCode === 0 && statusResult.stdout.length > 0) {
+      dirtyRepos.push(repo.name);
+    }
+  }
+
+  const result = {
+    workspace_name: name,
+    workspace_path: wsPath,
+    has_manifest: fs.existsSync(manifestPath),
+    strategy,
+    repos,
+    repo_count: repos.length,
+    dirty_repos: dirtyRepos,
+    has_dirty_repos: dirtyRepos.length > 0,
+  };
+
+  output(result, raw);
+}
+
+/**
+ * Build a formatted agent skills block for injection into Task() prompts.
+ *
+ * Reads `config.agent_skills[agentType]` and validates each skill path exists
+ * within the project root. Returns a formatted `<agent_skills>` block or empty
+ * string if no skills are configured.
+ *
+ * @param {object} config - Loaded project config
+ * @param {string} agentType - The agent type (e.g., 'gsd-executor', 'gsd-planner')
+ * @param {string} projectRoot - Absolute path to project root (for path validation)
+ * @returns {string} Formatted skills block or empty string
+ */
+function buildAgentSkillsBlock(config, agentType, projectRoot) {
+  const { validatePath } = require('./security.cjs');
+  const os = require('os');
+  const { getGlobalSkillDir, getGlobalSkillDisplayPath } = require('./runtime-homes.cjs');
+  const runtime = (config && config.runtime) || 'claude';
+  const globalSkillsBase = require('./runtime-homes.cjs').getGlobalSkillsBase(runtime);
+
+  if (!config || !config.agent_skills || !agentType) return '';
+
+  let skillPaths = config.agent_skills[agentType];
+  if (!skillPaths) return '';
+
+  // Normalize single string to array
+  if (typeof skillPaths === 'string') skillPaths = [skillPaths];
+  if (!Array.isArray(skillPaths) || skillPaths.length === 0) return '';
+
+  const validPaths = [];
+  for (const skillPath of skillPaths) {
+    if (typeof skillPath !== 'string') continue;
+
+    // Support global: prefix for skills installed at the runtime's global skills directory (#1992, #3126)
+    if (skillPath.startsWith('global:')) {
+      const skillName = skillPath.slice(7);
+      // Explicit empty-name guard before regex for clearer error message
+      if (!skillName) {
+        process.stderr.write(`[agent-skills] WARNING: "global:" prefix with empty skill name — skipping\n`);
+        continue;
+      }
+      // Sanitize: skill name must be alphanumeric, hyphens, or underscores only
+      if (!/^[a-zA-Z0-9_-]+$/.test(skillName)) {
+        process.stderr.write(`[agent-skills] WARNING: Invalid global skill name "${skillName}" — skipping\n`);
+        continue;
+      }
+      // Cline is rules-based and has no global skills directory
+      if (globalSkillsBase === null) {
+        process.stderr.write(`[agent-skills] WARNING: Runtime "${runtime}" does not use a skills directory — "global:${skillName}" is not supported on this runtime\n`);
+        continue;
+      }
+      const globalSkillDir = getGlobalSkillDir(runtime, skillName);
+      const globalSkillMd = path.join(globalSkillDir, 'SKILL.md');
+      const displayPath = getGlobalSkillDisplayPath(runtime, skillName);
+      if (!fs.existsSync(globalSkillMd)) {
+        process.stderr.write(`[agent-skills] WARNING: Global skill not found at "${displayPath}/SKILL.md" — skipping\n`);
+        continue;
+      }
+      // Symlink escape guard: validatePath resolves symlinks and enforces
+      // containment within globalSkillsBase. Prevents a skill directory
+      // symlinked to an arbitrary location from being injected (#1992).
+      const pathCheck = validatePath(globalSkillMd, globalSkillsBase, { allowAbsolute: true });
+      if (!pathCheck.safe) {
+        process.stderr.write(`[agent-skills] WARNING: Global skill "${skillName}" failed path check (symlink escape?) — skipping\n`);
+        continue;
+      }
+      validPaths.push({ ref: `${globalSkillDir}/SKILL.md`, display: displayPath });
+      continue;
+    }
+
+    // Validate path safety — must resolve within project root
+    const pathCheck = validatePath(skillPath, projectRoot);
+    if (!pathCheck.safe) {
+      process.stderr.write(`[agent-skills] WARNING: Skipping unsafe path "${skillPath}": ${pathCheck.error}\n`);
+      continue;
+    }
+
+    // Check that the skill directory and SKILL.md exist
+    const skillMdPath = path.join(projectRoot, skillPath, 'SKILL.md');
+    if (!fs.existsSync(skillMdPath)) {
+      process.stderr.write(`[agent-skills] WARNING: Skill not found at "${skillPath}/SKILL.md" — skipping\n`);
+      continue;
+    }
+
+    validPaths.push({ ref: `${skillPath}/SKILL.md`, display: skillPath });
+  }
+
+  if (validPaths.length === 0) return '';
+
+  const lines = validPaths.map(p => `- @${p.ref}`).join('\n');
+  return `<agent_skills>\nRead these user-configured skills:\n${lines}\n</agent_skills>`;
+}
+
+/**
+ * Command: output the agent skills block for a given agent type.
+ * Used by workflows: SKILLS=$(node "$TOOLS" agent-skills gsd-executor 2>/dev/null)
+ */
+function cmdAgentSkills(cwd, agentType, raw) {
+  if (!agentType) {
+    // No agent type — output empty string silently
+    output('', raw, '');
+    return;
+  }
+
+  const config = loadConfig(cwd);
+  const block = buildAgentSkillsBlock(config, agentType, cwd);
+  // Output raw text (not JSON) so workflows can embed it directly
+  if (block) {
+    process.stdout.write(block);
+  }
+  process.exit(0);
+}
+
+/**
+ * Generate a skill manifest from a skills directory.
+ *
+ * Scans the canonical skill discovery roots and returns a normalized
+ * inventory object with discovered skills, root metadata, and installation
+ * summary flags. A legacy `skillsDir` override is still accepted for focused
+ * scans, but the default mode is multi-root discovery.
+ *
+ * @param {string} cwd - Project root directory
+ * @param {string|null} [skillsDir] - Optional absolute path to a specific skills directory
+ * @returns {{
+ *   skills: Array<{name: string, description: string, triggers: string[], path: string, file_path: string, root: string, scope: string, installed: boolean, deprecated: boolean}>,
+ *   roots: Array<{root: string, path: string, scope: string, present: boolean, skill_count?: number, command_count?: number, deprecated?: boolean}>,
+ *   installation: { gsd_skills_installed: boolean, legacy_claude_commands_installed: boolean },
+ *   counts: { skills: number, roots: number }
+ * }}
+ */
+function buildSkillManifest(cwd, skillsDir = null) {
+  const { extractFrontmatter } = require('./frontmatter.cjs');
+  const { getGlobalSkillsBase } = require('./runtime-homes.cjs');
+  const os = require('os');
+
+  const canonicalRoots = skillsDir ? [{
+    root: path.resolve(skillsDir),
+    path: path.resolve(skillsDir),
+    scope: 'custom',
+    present: fs.existsSync(skillsDir),
+    kind: 'skills',
+  }] : [
+    {
+      root: '.claude/skills',
+      path: path.join(cwd, '.claude', 'skills'),
+      scope: 'project',
+      kind: 'skills',
+    },
+    {
+      root: '.agents/skills',
+      path: path.join(cwd, '.agents', 'skills'),
+      scope: 'project',
+      kind: 'skills',
+    },
+    {
+      root: '.cursor/skills',
+      path: path.join(cwd, '.cursor', 'skills'),
+      scope: 'project',
+      kind: 'skills',
+    },
+    {
+      root: '.github/skills',
+      path: path.join(cwd, '.github', 'skills'),
+      scope: 'project',
+      kind: 'skills',
+    },
+    {
+      root: '.codex/skills',
+      path: path.join(cwd, '.codex', 'skills'),
+      scope: 'project',
+      kind: 'skills',
+    },
+    {
+      root: '~/.claude/skills',
+      path: getGlobalSkillsBase('claude'),
+      scope: 'global',
+      kind: 'skills',
+    },
+    {
+      root: '~/.codex/skills',
+      path: getGlobalSkillsBase('codex'),
+      scope: 'global',
+      kind: 'skills',
+    },
+    {
+      root: '.claude/get-shit-done/skills',
+      path: path.join(os.homedir(), '.claude', 'get-shit-done', 'skills'),
+      scope: 'import-only',
+      kind: 'skills',
+      deprecated: true,
+    },
+    {
+      root: '.claude/commands/gsd',
+      path: path.join(os.homedir(), '.claude', 'commands', 'gsd'),
+      scope: 'legacy-commands',
+      kind: 'commands',
+      deprecated: true,
+    },
+  ];
+
+  const skills = [];
+  const roots = [];
+  let legacyClaudeCommandsInstalled = false;
+  for (const rootInfo of canonicalRoots) {
+    const rootPath = rootInfo.path;
+    const rootSummary = {
+      root: rootInfo.root,
+      path: rootPath,
+      scope: rootInfo.scope,
+      present: fs.existsSync(rootPath),
+      deprecated: !!rootInfo.deprecated,
+    };
+
+    if (!rootSummary.present) {
+      roots.push(rootSummary);
+      continue;
+    }
+
+    if (rootInfo.kind === 'commands') {
+      let entries = [];
+      try {
+        entries = fs.readdirSync(rootPath, { withFileTypes: true });
+      } catch {
+        roots.push(rootSummary);
+        continue;
+      }
+
+      const commandFiles = entries.filter(entry => entry.isFile() && entry.name.endsWith('.md'));
+      rootSummary.command_count = commandFiles.length;
+      if (rootSummary.command_count > 0) legacyClaudeCommandsInstalled = true;
+      roots.push(rootSummary);
+      continue;
+    }
+
+    let entries;
+    try {
+      entries = fs.readdirSync(rootPath, { withFileTypes: true });
+    } catch {
+      roots.push(rootSummary);
+      continue;
+    }
+
+    let skillCount = 0;
+    for (const entry of entries) {
+      if (!entry.isDirectory()) continue;
+
+      const skillMdPath = path.join(rootPath, entry.name, 'SKILL.md');
+      const content = platformReadSync(skillMdPath);
+      if (content === null) continue;
+
+      const frontmatter = extractFrontmatter(content);
+      const name = frontmatter.name || entry.name;
+      const description = frontmatter.description || '';
+
+      // Extract trigger lines from body text (after frontmatter)
+      const triggers = [];
+      const bodyMatch = content.match(/^---[\s\S]*?---\s*\n([\s\S]*)$/);
+      if (bodyMatch) {
+        const body = bodyMatch[1];
+        const triggerLines = body.match(/^TRIGGER\s+when:\s*(.+)$/gmi);
+        if (triggerLines) {
+          for (const line of triggerLines) {
+            const m = line.match(/^TRIGGER\s+when:\s*(.+)$/i);
+            if (m) triggers.push(m[1].trim());
+          }
+        }
+      }
+
+      skills.push({
+        name,
+        description,
+        triggers,
+        path: entry.name,
+        file_path: `${entry.name}/SKILL.md`,
+        root: rootInfo.root,
+        scope: rootInfo.scope,
+        installed: rootInfo.scope !== 'import-only',
+        deprecated: !!rootInfo.deprecated,
+      });
+      skillCount++;
+    }
+
+    rootSummary.skill_count = skillCount;
+    roots.push(rootSummary);
+  }
+
+  skills.sort((a, b) => {
+    const rootCmp = a.root.localeCompare(b.root);
+    return rootCmp !== 0 ? rootCmp : a.name.localeCompare(b.name);
+  });
+
+  const gsdSkillsInstalled = skills.some(skill => skill.name.startsWith('gsd-'));
+
+  return {
+    skills,
+    roots,
+    installation: {
+      gsd_skills_installed: gsdSkillsInstalled,
+      legacy_claude_commands_installed: legacyClaudeCommandsInstalled,
+    },
+    counts: {
+      skills: skills.length,
+      roots: roots.length,
+    },
+  };
+}
+
+/**
+ * Command: generate skill manifest JSON.
+ *
+ * Options:
+ *   --skills-dir <path>  Optional absolute path to a single skills directory
+ *   --write              Also write to .planning/skill-manifest.json
+ */
+function cmdSkillManifest(cwd, args, raw) {
+  const skillsDirIdx = args.indexOf('--skills-dir');
+  const skillsDir = skillsDirIdx >= 0 && args[skillsDirIdx + 1]
+    ? args[skillsDirIdx + 1]
+    : null;
+
+  const manifest = buildSkillManifest(cwd, skillsDir);
+
+  // Optionally write to .planning/skill-manifest.json
+  if (args.includes('--write')) {
+    const planningDir = path.join(cwd, '.planning');
+    if (fs.existsSync(planningDir)) {
+      const manifestPath = path.join(planningDir, 'skill-manifest.json');
+      platformWriteSync(manifestPath, JSON.stringify(manifest, null, 2));
+    }
+  }
+
+  output(manifest, raw);
+}
+
+module.exports = {
+  cmdInitExecutePhase,
+  cmdInitPlanPhase,
+  cmdInitNewProject,
+  cmdInitNewMilestone,
+  cmdInitQuick,
+  cmdInitIngestDocs,
+  cmdInitResume,
+  cmdInitVerifyWork,
+  cmdInitPhaseOp,
+  cmdInitTodos,
+  cmdInitMilestoneOp,
+  cmdInitMapCodebase,
+  cmdInitProgress,
+  cmdInitManager,
+  cmdInitNewWorkspace,
+  cmdInitListWorkspaces,
+  cmdInitRemoveWorkspace,
+  detectChildRepos,
+  buildAgentSkillsBlock,
+  cmdAgentSkills,
+  buildSkillManifest,
+  cmdSkillManifest,
+};