gsd-opencode 1.22.1 → 1.33.0

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

@@ -5,18 +5,77 @@
 const fs = require('fs');
 const path = require('path');
 const { execSync } = require('child_process');
-const { loadConfig, resolveModelInternal, findPhaseInternal, getRoadmapPhaseInternal, pathExistsInternal, generateSlugInternal, getMilestoneInfo, normalizePhaseName, toPosixPath, output, error } = require('./core.cjs');
+const { loadConfig, resolveModelInternal, findPhaseInternal, getRoadmapPhaseInternal, pathExistsInternal, generateSlugInternal, getMilestoneInfo, getMilestonePhaseFilter, stripShippedMilestones, extractCurrentMilestone, normalizePhaseName, planningPaths, planningDir, planningRoot, toPosixPath, output, error, checkAgentsInstalled, phaseTokenMatches } = require('./core.cjs');
 
-function cmdInitExecutePhase(cwd, phase, raw) {
+function getLatestCompletedMilestone(cwd) {
+  const milestonesPath = path.join(planningRoot(cwd), 'MILESTONES.md');
+  if (!fs.existsSync(milestonesPath)) return null;
+
+  try {
+    const content = fs.readFileSync(milestonesPath, 'utf-8');
+    const match = content.match(/^##\s+(v[\d.]+)\s+(.+?)\s+\(Shipped:/m);
+    if (!match) return null;
+    return {
+      version: match[1],
+      name: match[2].trim(),
+    };
+  } catch {
+    return null;
+  }
+}
+
+/**
+ * Inject `project_root` into an init result object.
+ * Workflows use this to prefix `.planning/` paths correctly when OpenCode'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;
+  }
+  return result;
+}
+
+function cmdInitExecutePhase(cwd, phase, raw, options = {}) {
   if (!phase) {
     error('phase required for init execute-phase');
   }
 
   const config = loadConfig(cwd);
-  const phaseInfo = findPhaseInternal(cwd, phase);
+  let phaseInfo = findPhaseInternal(cwd, phase);
   const milestone = getMilestoneInfo(cwd);
 
   const roadmapPhase = getRoadmapPhaseInternal(cwd, phase);
+
+  // 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(/^-+|-+$/g, '') : null,
+      plans: [],
+      summaries: [],
+      incomplete_plans: [],
+      has_research: false,
+      has_context: false,
+      has_verification: false,
+      has_reviews: false,
+    };
+  }
   const reqMatch = roadmapPhase?.section?.match(/^\*\*Requirements\*\*:[^\S\n]*([^\n]*)$/m);
   const reqExtracted = reqMatch
     ? reqMatch[1].replace(/[\[\]]/g, '').split(',').map(s => s.trim()).filter(Boolean).join(', ')
@@ -30,7 +89,9 @@ function cmdInitExecutePhase(cwd, phase, raw) {
 
     // Config flags
     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,
@@ -54,6 +115,7 @@ function cmdInitExecutePhase(cwd, phase, raw) {
     // 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'
@@ -68,27 +130,74 @@ function cmdInitExecutePhase(cwd, phase, raw) {
     milestone_slug: generateSlugInternal(milestone.name),
 
     // File existence
-    state_exists: pathExistsInternal(cwd, '.planning/STATE.md'),
-    roadmap_exists: pathExistsInternal(cwd, '.planning/ROADMAP.md'),
-    config_exists: pathExistsInternal(cwd, '.planning/config.json'),
+    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: '.planning/STATE.md',
-    roadmap_path: '.planning/ROADMAP.md',
-    config_path: '.planning/config.json',
+    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'))),
   };
 
-  output(result, raw);
+  // Optional --validate: run state validation and include warnings (#1627)
+  if (options.validate) {
+    try {
+      const { cmdStateValidate } = require('./state.cjs');
+      // Capture validate output by temporarily redirecting
+      const statePath = path.join(planningDir(cwd), 'STATE.md');
+      if (fs.existsSync(statePath)) {
+        const stateContent = fs.readFileSync(statePath, 'utf-8');
+        const { stateExtractField } = require('./state.cjs');
+        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 files = fs.readdirSync(path.join(cwd, phaseInfo.directory));
+          const diskPlans = files.filter(f => f.match(/-PLAN\.md$/i)).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) {
+function cmdInitPlanPhase(cwd, phase, raw, options = {}) {
   if (!phase) {
     error('phase required for init plan-phase');
   }
 
   const config = loadConfig(cwd);
-  const phaseInfo = findPhaseInternal(cwd, phase);
+  let phaseInfo = findPhaseInternal(cwd, phase);
 
   const roadmapPhase = getRoadmapPhaseInternal(cwd, phase);
+
+  // 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(/^-+|-+$/g, '') : null,
+      plans: [],
+      summaries: [],
+      incomplete_plans: [],
+      has_research: false,
+      has_context: false,
+      has_verification: false,
+      has_reviews: false,
+    };
+  }
   const reqMatch = roadmapPhase?.section?.match(/^\*\*Requirements\*\*:[^\S\n]*([^\n]*)$/m);
   const reqExtracted = reqMatch
     ? reqMatch[1].replace(/[\[\]]/g, '').split(',').map(s => s.trim()).filter(Boolean).join(', ')
@@ -106,6 +215,7 @@ function cmdInitPlanPhase(cwd, phase, raw) {
     plan_checker_enabled: config.plan_checker,
     nyquist_validation_enabled: config.nyquist_validation,
     commit_docs: config.commit_docs,
+    text_mode: config.text_mode,
 
     // Phase info
     phase_found: !!phaseInfo,
@@ -113,23 +223,24 @@ function cmdInitPlanPhase(cwd, phase, raw) {
     phase_number: phaseInfo?.phase_number || null,
     phase_name: phaseInfo?.phase_name || null,
     phase_slug: phaseInfo?.phase_slug || null,
-    padded_phase: phaseInfo?.phase_number?.padStart(2, '0') || null,
+    padded_phase: phaseInfo?.phase_number ? normalizePhaseName(phaseInfo.phase_number) : null,
     phase_req_ids,
 
     // 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: pathExistsInternal(cwd, '.planning'),
-    roadmap_exists: pathExistsInternal(cwd, '.planning/ROADMAP.md'),
+    planning_exists: fs.existsSync(planningDir(cwd)),
+    roadmap_exists: fs.existsSync(path.join(planningDir(cwd), 'ROADMAP.md')),
 
     // File paths
-    state_path: '.planning/STATE.md',
-    roadmap_path: '.planning/ROADMAP.md',
-    requirements_path: '.planning/REQUIREMENTS.md',
+    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) {
@@ -153,10 +264,33 @@ function cmdInitPlanPhase(cwd, phase, raw) {
       if (uatFile) {
         result.uat_path = toPosixPath(path.join(phaseInfo.directory, uatFile));
       }
-    } catch {}
+      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(result, raw);
+  // Optional --validate: run state validation and include warnings (#1627)
+  if (options.validate) {
+    try {
+      const statePath = path.join(planningDir(cwd), 'STATE.md');
+      if (fs.existsSync(statePath)) {
+        const { stateExtractField } = require('./state.cjs');
+        const stateContent = fs.readFileSync(statePath, 'utf-8');
+        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) {
@@ -167,23 +301,67 @@ function cmdInitNewProject(cwd, raw) {
   const braveKeyFile = path.join(homedir, '.gsd', 'brave_api_key');
   const hasBraveSearch = !!(process.env.BRAVE_API_KEY || fs.existsSync(braveKeyFile));
 
-  // Detect existing code
+  // 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 files = execSync('find . -maxdepth 3 \\( -name "*.ts" -o -name "*.js" -o -name "*.py" -o -name "*.go" -o -name "*.rs" -o -name "*.swift" -o -name "*.java" \\) 2>/dev/null | grep -v node_modules | grep -v .git | head -5', {
-      cwd,
-      encoding: 'utf-8',
-      stdio: ['pipe', 'pipe', 'pipe'],
-    });
-    hasCode = files.trim().length > 0;
-  } catch {}
+    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', '.OpenCode', '.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, '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
@@ -210,17 +388,30 @@ function cmdInitNewProject(cwd, raw) {
 
     // Enhanced search
     brave_search_available: hasBraveSearch,
+    firecrawl_available: hasFirecrawl,
+    exa_search_available: hasExaSearch,
 
     // File paths
     project_path: '.planning/PROJECT.md',
   };
 
-  output(result, raw);
+  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)) {
+      phaseDirCount = fs.readdirSync(phasesDir, { withFileTypes: true })
+        .filter(entry => entry.isDirectory())
+        .length;
+    }
+  } catch {}
 
   const result = {
     // Models
@@ -235,19 +426,23 @@ function cmdInitNewMilestone(cwd, raw) {
     // 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: pathExistsInternal(cwd, '.planning/ROADMAP.md'),
-    state_exists: pathExistsInternal(cwd, '.planning/STATE.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: '.planning/ROADMAP.md',
-    state_path: '.planning/STATE.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(result, raw);
+  output(withProjectRoot(cwd, result), raw);
 }
 
 function cmdInitQuick(cwd, description, raw) {
@@ -255,18 +450,25 @@ function cmdInitQuick(cwd, description, raw) {
   const now = new Date();
   const slug = description ? generateSlugInternal(description)?.substring(0, 40) : null;
 
-  // Find next quick task number
-  const quickDir = path.join(cwd, '.planning', 'quick');
-  let nextNum = 1;
-  try {
-    const existing = fs.readdirSync(quickDir)
-      .filter(f => /^\d+-/.test(f))
-      .map(f => parseInt(f.split('-')[0], 10))
-      .filter(n => !isNaN(n));
-    if (existing.length > 0) {
-      nextNum = Math.max(...existing) + 1;
-    }
-  } catch {}
+  // 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
@@ -277,9 +479,10 @@ function cmdInitQuick(cwd, description, raw) {
 
     // Config
     commit_docs: config.commit_docs,
+    branch_name: quickBranchName,
 
     // Quick task info
-    next_num: nextNum,
+    quick_id: quickId,
     slug: slug,
     description: description || null,
 
@@ -289,15 +492,15 @@ function cmdInitQuick(cwd, description, raw) {
 
     // Paths
     quick_dir: '.planning/quick',
-    task_dir: slug ? `.planning/quick/${nextNum}-${slug}` : null,
+    task_dir: slug ? `.planning/quick/${quickId}-${slug}` : null,
 
     // File existence
-    roadmap_exists: pathExistsInternal(cwd, '.planning/ROADMAP.md'),
-    planning_exists: pathExistsInternal(cwd, '.planning'),
+    roadmap_exists: fs.existsSync(path.join(planningDir(cwd), 'ROADMAP.md')),
+    planning_exists: fs.existsSync(planningRoot(cwd)),
 
   };
 
-  output(result, raw);
+  output(withProjectRoot(cwd, result), raw);
 }
 
 function cmdInitResume(cwd, raw) {
@@ -306,19 +509,19 @@ function cmdInitResume(cwd, raw) {
   // Check for interrupted agent
   let interruptedAgentId = null;
   try {
-    interruptedAgentId = fs.readFileSync(path.join(cwd, '.planning', 'current-agent-id.txt'), 'utf-8').trim();
-  } catch {}
+    interruptedAgentId = fs.readFileSync(path.join(planningRoot(cwd), 'current-agent-id.txt'), 'utf-8').trim();
+  } catch { /* intentionally empty */ }
 
   const result = {
     // File existence
-    state_exists: pathExistsInternal(cwd, '.planning/STATE.md'),
-    roadmap_exists: pathExistsInternal(cwd, '.planning/ROADMAP.md'),
+    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: pathExistsInternal(cwd, '.planning'),
+    planning_exists: fs.existsSync(planningRoot(cwd)),
 
     // File paths
-    state_path: '.planning/STATE.md',
-    roadmap_path: '.planning/ROADMAP.md',
+    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
@@ -329,7 +532,7 @@ function cmdInitResume(cwd, raw) {
     commit_docs: config.commit_docs,
   };
 
-  output(result, raw);
+  output(withProjectRoot(cwd, result), raw);
 }
 
 function cmdInitVerifyWork(cwd, phase, raw) {
@@ -338,7 +541,28 @@ function cmdInitVerifyWork(cwd, phase, raw) {
   }
 
   const config = loadConfig(cwd);
-  const phaseInfo = findPhaseInternal(cwd, phase);
+  let phaseInfo = findPhaseInternal(cwd, phase);
+
+  // 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
@@ -358,13 +582,36 @@ function cmdInitVerifyWork(cwd, phase, raw) {
     has_verification: phaseInfo?.has_verification || false,
   };
 
-  output(result, raw);
+  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);
@@ -390,6 +637,8 @@ function cmdInitPhaseOp(cwd, phase, raw) {
     // Config
     commit_docs: config.commit_docs,
     brave_search: config.brave_search,
+    firecrawl: config.firecrawl,
+    exa_search: config.exa_search,
 
     // Phase info
     phase_found: !!phaseInfo,
@@ -397,23 +646,24 @@ function cmdInitPhaseOp(cwd, phase, raw) {
     phase_number: phaseInfo?.phase_number || null,
     phase_name: phaseInfo?.phase_name || null,
     phase_slug: phaseInfo?.phase_slug || null,
-    padded_phase: phaseInfo?.phase_number?.padStart(2, '0') || null,
+    padded_phase: phaseInfo?.phase_number ? normalizePhaseName(phaseInfo.phase_number) : 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: pathExistsInternal(cwd, '.planning/ROADMAP.md'),
-    planning_exists: pathExistsInternal(cwd, '.planning'),
+    roadmap_exists: fs.existsSync(path.join(planningDir(cwd), 'ROADMAP.md')),
+    planning_exists: fs.existsSync(planningDir(cwd)),
 
     // File paths
-    state_path: '.planning/STATE.md',
-    roadmap_path: '.planning/ROADMAP.md',
-    requirements_path: '.planning/REQUIREMENTS.md',
+    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) {
@@ -436,10 +686,14 @@ function cmdInitPhaseOp(cwd, phase, raw) {
       if (uatFile) {
         result.uat_path = toPosixPath(path.join(phaseInfo.directory, uatFile));
       }
-    } catch {}
+      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(result, raw);
+  output(withProjectRoot(cwd, result), raw);
 }
 
 function cmdInitTodos(cwd, area, raw) {
@@ -447,7 +701,7 @@ function cmdInitTodos(cwd, area, raw) {
   const now = new Date();
 
   // List todos (reuse existing logic)
-  const pendingDir = path.join(cwd, '.planning', 'todos', 'pending');
+  const pendingDir = path.join(planningDir(cwd), 'todos', 'pending');
   let count = 0;
   const todos = [];
 
@@ -469,11 +723,11 @@ function cmdInitTodos(cwd, area, raw) {
           created: createdMatch ? createdMatch[1].trim() : 'unknown',
           title: titleMatch ? titleMatch[1].trim() : 'Untitled',
           area: todoArea,
-          path: '.planning/todos/pending/' + file,
+          path: toPosixPath(path.relative(cwd, path.join(planningDir(cwd), 'todos', 'pending', file))),
         });
-      } catch {}
+      } catch { /* intentionally empty */ }
     }
-  } catch {}
+  } catch { /* intentionally empty */ }
 
   const result = {
     // Config
@@ -489,16 +743,16 @@ function cmdInitTodos(cwd, area, raw) {
     area_filter: area || null,
 
     // Paths
-    pending_dir: '.planning/todos/pending',
-    completed_dir: '.planning/todos/completed',
+    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: pathExistsInternal(cwd, '.planning'),
-    todos_dir_exists: pathExistsInternal(cwd, '.planning/todos'),
-    pending_dir_exists: pathExistsInternal(cwd, '.planning/todos/pending'),
+    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(result, raw);
+  output(withProjectRoot(cwd, result), raw);
 }
 
 function cmdInitMilestoneOp(cwd, raw) {
@@ -508,7 +762,7 @@ function cmdInitMilestoneOp(cwd, raw) {
   // Count phases
   let phaseCount = 0;
   let completedPhases = 0;
-  const phasesDir = path.join(cwd, '.planning', 'phases');
+  const phasesDir = path.join(planningDir(cwd), 'phases');
   try {
     const entries = fs.readdirSync(phasesDir, { withFileTypes: true });
     const dirs = entries.filter(e => e.isDirectory()).map(e => e.name);
@@ -520,18 +774,18 @@ function cmdInitMilestoneOp(cwd, raw) {
         const phaseFiles = fs.readdirSync(path.join(phasesDir, dir));
         const hasSummary = phaseFiles.some(f => f.endsWith('-SUMMARY.md') || f === 'SUMMARY.md');
         if (hasSummary) completedPhases++;
-      } catch {}
+      } catch { /* intentionally empty */ }
     }
-  } catch {}
+  } catch { /* intentionally empty */ }
 
   // Check archive
-  const archiveDir = path.join(cwd, '.planning', '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 {}
+  } catch { /* intentionally empty */ }
 
   const result = {
     // Config
@@ -553,24 +807,24 @@ function cmdInitMilestoneOp(cwd, raw) {
 
     // File existence
     project_exists: pathExistsInternal(cwd, '.planning/PROJECT.md'),
-    roadmap_exists: pathExistsInternal(cwd, '.planning/ROADMAP.md'),
-    state_exists: pathExistsInternal(cwd, '.planning/STATE.md'),
-    archive_exists: pathExistsInternal(cwd, '.planning/archive'),
-    phases_dir_exists: pathExistsInternal(cwd, '.planning/phases'),
+    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(result, raw);
+  output(withProjectRoot(cwd, result), raw);
 }
 
 function cmdInitMapCodebase(cwd, raw) {
   const config = loadConfig(cwd);
 
   // Check for existing codebase maps
-  const codebaseDir = path.join(cwd, '.planning', 'codebase');
+  const codebaseDir = path.join(planningRoot(cwd), 'codebase');
   let existingMaps = [];
   try {
     existingMaps = fs.readdirSync(codebaseDir).filter(f => f.endsWith('.md'));
-  } catch {}
+  } catch { /* intentionally empty */ }
 
   const result = {
     // Models
@@ -580,6 +834,7 @@ function cmdInitMapCodebase(cwd, raw) {
     commit_docs: config.commit_docs,
     search_gitignored: config.search_gitignored,
     parallelization: config.parallelization,
+    subagent_timeout: config.subagent_timeout,
 
     // Paths
     codebase_dir: '.planning/codebase',
@@ -593,27 +848,324 @@ function cmdInitMapCodebase(cwd, raw) {
     codebase_dir_exists: pathExistsInternal(cwd, '.planning/codebase'),
   };
 
-  output(result, raw);
+  output(withProjectRoot(cwd, result), raw);
+}
+
+function cmdInitManager(cwd, raw) {
+  const config = loadConfig(cwd);
+  const milestone = getMilestoneInfo(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 /gsd-new-milestone first.');
+  }
+  if (!fs.existsSync(paths.state)) {
+    error('No STATE.md found. Run /gsd-new-milestone first.');
+  }
+  const rawContent = fs.readFileSync(paths.roadmap, 'utf-8');
+  const content = extractCurrentMilestone(rawContent, cwd);
+  const phasesDir = paths.phases;
+  const isDirInMilestone = getMilestonePhaseFilter(cwd);
+
+  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);
+    const nextHeader = restOfContent.match(/\n#{2,4}\s+Phase\s+\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 entries = fs.readdirSync(phasesDir, { withFileTypes: true });
+      const dirs = entries.filter(e => e.isDirectory()).map(e => e.name).filter(isDirInMilestone);
+      const dirMatch = dirs.find(d => phaseTokenMatches(d, normalized));
+
+      if (dirMatch) {
+        const fullDir = path.join(phasesDir, dirMatch);
+        const phaseFiles = fs.readdirSync(fullDir);
+        planCount = phaseFiles.filter(f => f.endsWith('-PLAN.md') || f === 'PLAN.md').length;
+        summaryCount = phaseFiles.filter(f => f.endsWith('-SUMMARY.md') || f === 'SUMMARY.md').length;
+        hasContext = phaseFiles.some(f => f.endsWith('-CONTEXT.md') || f === 'CONTEXT.md');
+        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
+    const checkboxPattern = new RegExp(`-\\s*\\[(x| )\\]\\s*.*Phase\\s+${phaseNum.replace(/[.*+?^${}()|[\]\\]/g, '\\$&')}[:\\s]`, 'i');
+    const checkboxMatch = content.match(checkboxPattern);
+    const roadmapComplete = checkboxMatch ? checkboxMatch[1] === 'x' : 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));
+  for (const phase of phases) {
+    if (!phase.depends_on || /^none$/i.test(phase.depends_on.trim())) {
+      phase.deps_satisfied = true;
+    } else {
+      // Parse "Phase 1, Phase 3" or "1, 3" formats
+      const depNums = phase.depends_on.match(/\d+(?:\.\d+)*/g) || [];
+      phase.deps_satisfied = depNums.every(n => completedNums.has(n));
+      phase.dep_phases = depNums;
+    }
+  }
+
+  // Compact dependency display for dashboard
+  for (const phase of phases) {
+    phase.deps_display = (phase.dep_phases && phase.dep_phases.length > 0)
+      ? phase.dep_phases.join(',')
+      : '—';
+  }
+
+  // Sliding window: discuss is sequential — only the first undiscussed phase is available
+  let foundNextToDiscuss = false;
+  for (const phase of phases) {
+    if (!foundNextToDiscuss && (phase.disk_status === 'empty' || phase.disk_status === 'no_directory')) {
+      phase.is_next_to_discuss = true;
+      foundNextToDiscuss = true;
+    } else {
+      phase.is_next_to_discuss = false;
+    }
+  }
+
+  // Check for WAITING.json signal
+  let waitingSignal = null;
+  try {
+    const waitingPath = path.join(cwd, '.planning', 'WAITING.json');
+    if (fs.existsSync(waitingPath)) {
+      waitingSignal = JSON.parse(fs.readFileSync(waitingPath, 'utf-8'));
+    }
+  } catch { /* intentionally empty */ }
+
+  // Compute recommended actions (execute > plan > discuss)
+  // Skip BACKLOG phases (999.x numbering) — they are parked ideas, not active work
+  const recommendedActions = [];
+  for (const phase of phases) {
+    if (phase.disk_status === 'complete') continue;
+    if (/^999(?:\.|$)/.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: `/gsd-execute-phase ${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: `/gsd-plan-phase ${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: `/gsd-discuss-phase ${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;
+  });
+
+  const completedCount = phases.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 === phases.length && phases.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) {
   const config = loadConfig(cwd);
   const milestone = getMilestoneInfo(cwd);
 
-  // Analyze phases
-  const phasesDir = path.join(cwd, '.planning', 'phases');
+  // 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();
+  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());
+    }
+  } 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).sort();
+    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+(?:\.\d+)*)-?(.*)/);
+      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);
@@ -629,7 +1181,7 @@ function cmdInitProgress(cwd, raw) {
       const phaseInfo = {
         number: phaseNumber,
         name: phaseName,
-        directory: '.planning/phases/' + dir,
+        directory: toPosixPath(path.relative(cwd, path.join(planningDir(cwd), 'phases', dir))),
         status,
         plan_count: plans.length,
         summary_count: summaries.length,
@@ -646,15 +1198,38 @@ function cmdInitProgress(cwd, raw) {
         nextPhase = phaseInfo;
       }
     }
-  } catch {}
+  } catch { /* intentionally empty */ }
+
+  // Add phases defined in ROADMAP but not yet scaffolded to disk
+  for (const [num, name] of roadmapPhaseNames) {
+    const stripped = num.replace(/^0+/, '') || '0';
+    if (!seenPhaseNums.has(stripped)) {
+      const phaseInfo = {
+        number: num,
+        name: name.toLowerCase().replace(/[^a-z0-9]+/g, '-').replace(/^-+|-+$/g, ''),
+        directory: null,
+        status: 'not_started',
+        plan_count: 0,
+        summary_count: 0,
+        has_research: false,
+      };
+      phases.push(phaseInfo);
+      if (!nextPhase && !currentPhase) {
+        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;
   try {
-    const state = fs.readFileSync(path.join(cwd, '.planning', 'STATE.md'), 'utf-8');
+    const state = fs.readFileSync(path.join(planningDir(cwd), 'STATE.md'), 'utf-8');
     const pauseMatch = state.match(/\*\*Paused At:\*\*\s*(.+)/);
     if (pauseMatch) pausedAt = pauseMatch[1].trim();
-  } catch {}
+  } catch { /* intentionally empty */ }
 
   const result = {
     // Models
@@ -682,18 +1257,248 @@ function cmdInitProgress(cwd, raw) {
 
     // File existence
     project_exists: pathExistsInternal(cwd, '.planning/PROJECT.md'),
-    roadmap_exists: pathExistsInternal(cwd, '.planning/ROADMAP.md'),
-    state_exists: pathExistsInternal(cwd, '.planning/STATE.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: '.planning/STATE.md',
-    roadmap_path: '.planning/ROADMAP.md',
+    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: '.planning/config.json',
+    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)) {
+      let hasUncommitted = false;
+      try {
+        const status = execSync('git status --porcelain', { cwd: fullPath, encoding: 'utf8', timeout: 5000 });
+        hasUncommitted = status.trim().length > 0;
+      } catch { /* best-effort */ }
+      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
+  let worktreeAvailable = false;
+  try {
+    execSync('git --version', { encoding: 'utf8', timeout: 5000, stdio: 'pipe' });
+    worktreeAvailable = true;
+  } catch { /* no git at all */ }
+
+  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';
+      try {
+        const manifest = fs.readFileSync(manifestPath, 'utf8');
+        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;
+      } catch { /* best-effort */ }
+      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: ${wsPath}`);
+  }
+
+  // Parse manifest for repo info
+  const repos = [];
+  let strategy = 'unknown';
+  if (fs.existsSync(manifestPath)) {
+    try {
+      const manifest = fs.readFileSync(manifestPath, 'utf8');
+      const strategyMatch = manifest.match(/^Strategy:\s*(.+)$/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;
+    try {
+      const status = execSync('git status --porcelain', { cwd: repoPath, encoding: 'utf8', timeout: 5000, stdio: 'pipe' });
+      if (status.trim().length > 0) {
+        dirtyRepos.push(repo.name);
+      }
+    } catch { /* best-effort */ }
+  }
+
+  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');
+
+  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;
+
+    // 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(skillPath);
+  }
+
+  if (validPaths.length === 0) return '';
+
+  const lines = validPaths.map(p => `- @${p}/SKILL.md`).join('\n');
+  return `<agent_skills>\nRead these user-configured skills:\n${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);
+}
+
 module.exports = {
   cmdInitExecutePhase,
   cmdInitPlanPhase,
@@ -707,4 +1512,11 @@ module.exports = {
   cmdInitMilestoneOp,
   cmdInitMapCodebase,
   cmdInitProgress,
+  cmdInitManager,
+  cmdInitNewWorkspace,
+  cmdInitListWorkspaces,
+  cmdInitRemoveWorkspace,
+  detectChildRepos,
+  buildAgentSkillsBlock,
+  cmdAgentSkills,
 };