moflo 4.8.10 → 4.8.12

package/src/@claude-flow/cli/dist/src/init/moflo-init.js

@@ -1,224 +1,275 @@
-/**
- * MoFlo Project Initializer
- *
- * One-stop setup that makes MoFlo work out of the box:
- * 1. Generate moflo.yaml (project config)
- * 2. Set up .claude/settings.json hooks
- * 3. Create .claude/skills/flo/ skill (with /fl alias)
- * 4. Append MoFlo section to CLAUDE.md
- * 5. Initialize memory DB
- * 6. Auto-index guidance + code map
- */
-import * as fs from 'fs';
-import * as path from 'path';
-import { fileURLToPath } from 'url';
-// ============================================================================
-// Init
-// ============================================================================
-/**
- * Discover guidance directories by checking top-level candidates AND walking
- * the project tree for subproject .claude/guidance dirs (monorepo support).
- */
-function discoverGuidanceDirs(root) {
-    const TOP_LEVEL = ['.claude/guidance', 'docs/guides', 'docs', 'architecture', 'adr', '.cursor/rules'];
-    const found = TOP_LEVEL.filter(d => fs.existsSync(path.join(root, d)));
-    // Walk up to 3 levels deep looking for .claude/guidance in subprojects
-    const SKIP = new Set(['node_modules', '.git', 'dist', 'build', 'coverage', '.next', '.reports', '.swarm', '.claude-flow', 'packages']);
-    function walk(dir, depth) {
-        if (depth > 3)
-            return;
-        try {
-            const entries = fs.readdirSync(path.join(root, dir), { withFileTypes: true });
-            for (const entry of entries) {
-                if (!entry.isDirectory() || SKIP.has(entry.name))
-                    continue;
-                const rel = dir ? `${dir}/${entry.name}` : entry.name;
-                const guidancePath = `${rel}/.claude/guidance`;
-                if (fs.existsSync(path.join(root, guidancePath))) {
-                    // Verify it has .md files
-                    try {
-                        const files = fs.readdirSync(path.join(root, guidancePath));
-                        if (files.some(f => f.endsWith('.md')))
-                            found.push(guidancePath);
-                    }
-                    catch { /* skip unreadable */ }
-                }
-                else {
-                    walk(rel, depth + 1);
-                }
-            }
-        }
-        catch { /* skip unreadable directories */ }
-    }
-    walk('', 0);
-    return found;
-}
-/**
- * Discover source directories by walking the project tree.
- * Finds directories named 'src' (or top-level 'packages', 'lib', etc.)
- * that contain .ts/.tsx/.js/.jsx files. Skips node_modules, dist, etc.
- */
-function discoverSrcDirs(root) {
-    const SKIP = new Set(['node_modules', '.git', 'dist', 'build', 'coverage', '.next', '.reports', '.swarm', '.claude-flow']);
-    // Top-level candidates that are always source roots if they exist
-    const TOP_LEVEL = ['packages', 'lib', 'app', 'apps', 'services', 'server', 'client'];
-    const found = [];
-    // Add top-level candidates first
-    for (const d of TOP_LEVEL) {
-        if (fs.existsSync(path.join(root, d)))
-            found.push(d);
-    }
-    // Walk up to 3 levels deep looking for 'src' and 'migrations' directories
-    const SRC_NAMES = new Set(['src', 'migrations']);
-    function walk(dir, depth) {
-        if (depth > 3)
-            return;
-        try {
-            const entries = fs.readdirSync(path.join(root, dir), { withFileTypes: true });
-            for (const entry of entries) {
-                if (!entry.isDirectory() || SKIP.has(entry.name))
-                    continue;
-                const rel = dir ? `${dir}/${entry.name}` : entry.name;
-                if (SRC_NAMES.has(entry.name)) {
-                    // Check it actually has source files
-                    try {
-                        const files = fs.readdirSync(path.join(root, rel));
-                        const hasSource = files.some(f => /\.(ts|tsx|js|jsx)$/.test(f));
-                        if (hasSource)
-                            found.push(rel);
-                    }
-                    catch { /* skip unreadable */ }
-                }
-                else {
-                    walk(rel, depth + 1);
-                }
-            }
-        }
-        catch { /* skip unreadable directories */ }
-    }
-    walk('', 0);
-    // Deduplicate: if 'packages' is found, don't also include 'packages/foo/src'
-    // since the code-map walker handles subdirs
-    return found.filter(d => {
-        return !found.some(other => other !== d && d.startsWith(other + '/'));
-    });
-}
-/**
- * Run interactive wizard to collect user preferences.
- */
-async function runWizard(root) {
-    const { confirm, input } = await import('../prompt.js');
-    // Detect project structure
-    const detectedGuidance = discoverGuidanceDirs(root);
-    const detectedSrc = discoverSrcDirs(root);
-    // Ask questions
-    const guidance = await confirm({
-        message: detectedGuidance.length > 0
-            ? `Found guidance docs in ${detectedGuidance.join(', ')}. Enable guidance indexing?`
-            : 'Do you have project guidance/documentation to index?',
-        default: true,
-    });
-    let guidanceDirs = detectedGuidance.length > 0 ? detectedGuidance : ['.claude/guidance'];
-    if (guidance) {
-        const answer = await input({
-            message: 'Guidance directories (comma-separated):',
-            default: guidanceDirs.join(', '),
-        });
-        guidanceDirs = answer.split(',').map((d) => d.trim()).filter(Boolean);
-    }
-    const codeMap = await confirm({
-        message: detectedSrc.length > 0
-            ? `Found source in ${detectedSrc.join(', ')}. Enable code map for navigation?`
-            : 'Enable code map for codebase navigation?',
-        default: true,
-    });
-    let srcDirs = detectedSrc.length > 0 ? detectedSrc : ['src'];
-    if (codeMap) {
-        const answer = await input({
-            message: 'Source directories (comma-separated):',
-            default: srcDirs.join(', '),
-        });
-        srcDirs = answer.split(',').map((d) => d.trim()).filter(Boolean);
-    }
-    const gates = await confirm({
-        message: 'Enable workflow gates (memory-first, task-create-before-agents)?',
-        default: true,
-    });
-    const stopHook = await confirm({
-        message: 'Enable session-end hook (saves session state)?',
-        default: true,
-    });
-    return { guidance, guidanceDirs, codeMap, srcDirs, gates, stopHook };
-}
-/**
- * Get default answers (--yes mode).
- */
-function defaultAnswers(root) {
-    const guidanceDirs = discoverGuidanceDirs(root);
-    if (guidanceDirs.length === 0)
-        guidanceDirs.push('.claude/guidance');
-    const srcDirs = discoverSrcDirs(root);
-    if (srcDirs.length === 0)
-        srcDirs.push('src');
-    return { guidance: true, guidanceDirs, codeMap: true, srcDirs, gates: true, stopHook: true };
-}
-/**
- * Get minimal answers (--minimal mode).
- */
-function minimalAnswers() {
-    return { guidance: false, guidanceDirs: [], codeMap: false, srcDirs: [], gates: false, stopHook: false };
-}
-export async function initMoflo(options) {
-    const { projectRoot, force, interactive, minimal } = options;
-    const steps = [];
-    // Collect answers based on mode
-    const answers = minimal
-        ? minimalAnswers()
-        : interactive
-            ? await runWizard(projectRoot)
-            : defaultAnswers(projectRoot);
-    // Step 1: moflo.yaml
-    steps.push(generateConfig(projectRoot, force, answers));
-    // Step 2: .claude/settings.json hooks
-    steps.push(generateHooks(projectRoot, force, answers));
-    // Step 3: .claude/skills/flo/ (with /fl alias)
-    steps.push(generateSkill(projectRoot, force));
-    // Step 4: CLAUDE.md MoFlo section
-    steps.push(generateClaudeMd(projectRoot, force));
-    // Step 5: .claude/scripts/ from moflo bin/
-    steps.push(syncScripts(projectRoot, force));
-    // Step 6: .gitignore entries
-    steps.push(updateGitignore(projectRoot));
-    // Step 7: .claude/guidance/moflo-bootstrap.md (subagent bootstrap protocol)
-    steps.push(syncBootstrapGuidance(projectRoot, force));
-    return { steps };
-}
-// ============================================================================
-// Step 1: moflo.yaml
-// ============================================================================
-function generateConfig(root, force, answers) {
-    const configPath = path.join(root, 'moflo.yaml');
-    if (fs.existsSync(configPath) && !force) {
-        return { name: 'moflo.yaml', status: 'skipped', detail: 'Already exists (use --force to overwrite)' };
-    }
-    const projectName = path.basename(root);
-    const guidanceDirs = answers?.guidanceDirs ?? ['.claude/guidance'];
-    const srcDirs = answers?.srcDirs ?? ['src'];
-    const gatesEnabled = answers?.gates ?? true;
-    // Detect languages
-    const extensions = new Set();
-    for (const dir of srcDirs) {
-        const fullDir = path.join(root, dir);
-        if (fs.existsSync(fullDir)) {
-            try {
-                scanExtensions(fullDir, extensions, 0, 3);
-            }
-            catch { /* skip */ }
-        }
-    }
-    const detectedExts = extensions.size > 0
-        ? [...extensions].sort()
-        : ['.ts', '.tsx', '.js', '.jsx'];
+/**
+ * MoFlo Project Initializer
+ *
+ * One-stop setup that makes MoFlo work out of the box:
+ * 1. Generate moflo.yaml (project config)
+ * 2. Set up .claude/settings.json hooks
+ * 3. Create .claude/skills/flo/ skill (with /fl alias)
+ * 4. Append MoFlo section to CLAUDE.md
+ * 5. Initialize memory DB
+ * 6. Auto-index guidance + code map
+ */
+import * as fs from 'fs';
+import * as path from 'path';
+import { fileURLToPath } from 'url';
+// ============================================================================
+// Init
+// ============================================================================
+/**
+ * Discover guidance directories by checking top-level candidates AND walking
+ * the project tree for subproject .claude/guidance dirs (monorepo support).
+ */
+function discoverGuidanceDirs(root) {
+    const TOP_LEVEL = ['.claude/guidance', 'docs/guides', 'docs', 'architecture', 'adr', '.cursor/rules'];
+    const found = TOP_LEVEL.filter(d => fs.existsSync(path.join(root, d)));
+    // Walk up to 3 levels deep looking for .claude/guidance in subprojects
+    const SKIP = new Set(['node_modules', '.git', 'dist', 'build', 'coverage', '.next', '.reports', '.swarm', '.claude-flow', 'packages']);
+    function walk(dir, depth) {
+        if (depth > 3)
+            return;
+        try {
+            const entries = fs.readdirSync(path.join(root, dir), { withFileTypes: true });
+            for (const entry of entries) {
+                if (!entry.isDirectory() || SKIP.has(entry.name))
+                    continue;
+                const rel = dir ? `${dir}/${entry.name}` : entry.name;
+                const guidancePath = `${rel}/.claude/guidance`;
+                if (fs.existsSync(path.join(root, guidancePath))) {
+                    // Verify it has .md files
+                    try {
+                        const files = fs.readdirSync(path.join(root, guidancePath));
+                        if (files.some(f => f.endsWith('.md')))
+                            found.push(guidancePath);
+                    }
+                    catch { /* skip unreadable */ }
+                }
+                else {
+                    walk(rel, depth + 1);
+                }
+            }
+        }
+        catch { /* skip unreadable directories */ }
+    }
+    walk('', 0);
+    return found;
+}
+/**
+ * Discover test directories by checking common locations and walking for
+ * colocated __tests__ dirs. Returns relative paths.
+ */
+export function discoverTestDirs(root) {
+    const TOP_LEVEL = ['tests', 'test', '__tests__', 'spec', 'e2e'];
+    const found = TOP_LEVEL.filter(d => fs.existsSync(path.join(root, d)));
+    // Walk up to 3 levels deep looking for __tests__ dirs inside src
+    const SKIP = new Set(['node_modules', '.git', 'dist', 'build', 'coverage', '.next', '.reports', '.swarm', '.claude-flow']);
+    function walk(dir, depth) {
+        if (depth > 3)
+            return;
+        try {
+            const entries = fs.readdirSync(path.join(root, dir), { withFileTypes: true });
+            for (const entry of entries) {
+                if (!entry.isDirectory() || SKIP.has(entry.name))
+                    continue;
+                const rel = dir ? `${dir}/${entry.name}` : entry.name;
+                if (entry.name === '__tests__') {
+                    found.push(rel);
+                }
+                else {
+                    walk(rel, depth + 1);
+                }
+            }
+        }
+        catch { /* skip unreadable directories */ }
+    }
+    walk('', 0);
+    return found;
+}
+/**
+ * Discover source directories by walking the project tree.
+ * Finds directories named 'src' (or top-level 'packages', 'lib', etc.)
+ * that contain .ts/.tsx/.js/.jsx files. Skips node_modules, dist, etc.
+ */
+function discoverSrcDirs(root) {
+    const SKIP = new Set(['node_modules', '.git', 'dist', 'build', 'coverage', '.next', '.reports', '.swarm', '.claude-flow']);
+    // Top-level candidates that are always source roots if they exist
+    const TOP_LEVEL = ['packages', 'lib', 'app', 'apps', 'services', 'server', 'client'];
+    const found = [];
+    // Add top-level candidates first
+    for (const d of TOP_LEVEL) {
+        if (fs.existsSync(path.join(root, d)))
+            found.push(d);
+    }
+    // Walk up to 3 levels deep looking for 'src' and 'migrations' directories
+    const SRC_NAMES = new Set(['src', 'migrations']);
+    function walk(dir, depth) {
+        if (depth > 3)
+            return;
+        try {
+            const entries = fs.readdirSync(path.join(root, dir), { withFileTypes: true });
+            for (const entry of entries) {
+                if (!entry.isDirectory() || SKIP.has(entry.name))
+                    continue;
+                const rel = dir ? `${dir}/${entry.name}` : entry.name;
+                if (SRC_NAMES.has(entry.name)) {
+                    // Check it actually has source files
+                    try {
+                        const files = fs.readdirSync(path.join(root, rel));
+                        const hasSource = files.some(f => /\.(ts|tsx|js|jsx)$/.test(f));
+                        if (hasSource)
+                            found.push(rel);
+                    }
+                    catch { /* skip unreadable */ }
+                }
+                else {
+                    walk(rel, depth + 1);
+                }
+            }
+        }
+        catch { /* skip unreadable directories */ }
+    }
+    walk('', 0);
+    // Deduplicate: if 'packages' is found, don't also include 'packages/foo/src'
+    // since the code-map walker handles subdirs
+    return found.filter(d => {
+        return !found.some(other => other !== d && d.startsWith(other + '/'));
+    });
+}
+/**
+ * Run interactive wizard to collect user preferences.
+ */
+async function runWizard(root) {
+    const { confirm, input } = await import('../prompt.js');
+    // Detect project structure
+    const detectedGuidance = discoverGuidanceDirs(root);
+    const detectedSrc = discoverSrcDirs(root);
+    // Ask questions
+    const guidance = await confirm({
+        message: detectedGuidance.length > 0
+            ? `Found guidance docs in ${detectedGuidance.join(', ')}. Enable guidance indexing?`
+            : 'Do you have project guidance/documentation to index?',
+        default: true,
+    });
+    let guidanceDirs = detectedGuidance.length > 0 ? detectedGuidance : ['.claude/guidance'];
+    if (guidance) {
+        const answer = await input({
+            message: 'Guidance directories (comma-separated):',
+            default: guidanceDirs.join(', '),
+        });
+        guidanceDirs = answer.split(',').map((d) => d.trim()).filter(Boolean);
+    }
+    const codeMap = await confirm({
+        message: detectedSrc.length > 0
+            ? `Found source in ${detectedSrc.join(', ')}. Enable code map for navigation?`
+            : 'Enable code map for codebase navigation?',
+        default: true,
+    });
+    let srcDirs = detectedSrc.length > 0 ? detectedSrc : ['src'];
+    if (codeMap) {
+        const answer = await input({
+            message: 'Source directories (comma-separated):',
+            default: srcDirs.join(', '),
+        });
+        srcDirs = answer.split(',').map((d) => d.trim()).filter(Boolean);
+    }
+    // Detect test directories
+    const detectedTests = discoverTestDirs(root);
+    const tests = await confirm({
+        message: detectedTests.length > 0
+            ? `Found tests in ${detectedTests.join(', ')}. Enable test file indexing?`
+            : 'Enable test file indexing?',
+        default: true,
+    });
+    let testDirs = detectedTests.length > 0 ? detectedTests : ['tests'];
+    if (tests) {
+        const answer = await input({
+            message: 'Test directories (comma-separated):',
+            default: testDirs.join(', '),
+        });
+        testDirs = answer.split(',').map((d) => d.trim()).filter(Boolean);
+    }
+    const gates = await confirm({
+        message: 'Enable workflow gates (memory-first, task-create-before-agents)?',
+        default: true,
+    });
+    const stopHook = await confirm({
+        message: 'Enable session-end hook (saves session state)?',
+        default: true,
+    });
+    return { guidance, guidanceDirs, codeMap, srcDirs, tests, testDirs, gates, stopHook };
+}
+/**
+ * Get default answers (--yes mode).
+ */
+function defaultAnswers(root) {
+    const guidanceDirs = discoverGuidanceDirs(root);
+    if (guidanceDirs.length === 0)
+        guidanceDirs.push('.claude/guidance');
+    const srcDirs = discoverSrcDirs(root);
+    if (srcDirs.length === 0)
+        srcDirs.push('src');
+    const testDirs = discoverTestDirs(root);
+    if (testDirs.length === 0)
+        testDirs.push('tests');
+    return { guidance: true, guidanceDirs, codeMap: true, srcDirs, tests: true, testDirs, gates: true, stopHook: true };
+}
+/**
+ * Get minimal answers (--minimal mode).
+ */
+function minimalAnswers() {
+    return { guidance: false, guidanceDirs: [], codeMap: false, srcDirs: [], tests: false, testDirs: [], gates: false, stopHook: false };
+}
+export async function initMoflo(options) {
+    const { projectRoot, force, interactive, minimal } = options;
+    const steps = [];
+    // Collect answers based on mode
+    const answers = minimal
+        ? minimalAnswers()
+        : interactive
+            ? await runWizard(projectRoot)
+            : defaultAnswers(projectRoot);
+    // Step 1: moflo.yaml
+    steps.push(generateConfig(projectRoot, force, answers));
+    // Step 2: .claude/settings.json hooks
+    steps.push(generateHooks(projectRoot, force, answers));
+    // Step 3: .claude/skills/flo/ (with /fl alias)
+    steps.push(generateSkill(projectRoot, force));
+    // Step 4: CLAUDE.md MoFlo section
+    steps.push(generateClaudeMd(projectRoot, force));
+    // Step 5: .claude/scripts/ from moflo bin/
+    steps.push(syncScripts(projectRoot, force));
+    // Step 6: .gitignore entries
+    steps.push(updateGitignore(projectRoot));
+    // Step 7: .claude/guidance/moflo-bootstrap.md (subagent bootstrap protocol)
+    steps.push(syncBootstrapGuidance(projectRoot, force));
+    return { steps };
+}
+// ============================================================================
+// Step 1: moflo.yaml
+// ============================================================================
+function generateConfig(root, force, answers) {
+    const configPath = path.join(root, 'moflo.yaml');
+    if (fs.existsSync(configPath) && !force) {
+        return { name: 'moflo.yaml', status: 'skipped', detail: 'Already exists (use --force to overwrite)' };
+    }
+    const projectName = path.basename(root);
+    const guidanceDirs = answers?.guidanceDirs ?? ['.claude/guidance'];
+    const srcDirs = answers?.srcDirs ?? ['src'];
+    const testDirs = answers?.testDirs ?? ['tests'];
+    const gatesEnabled = answers?.gates ?? true;
+    // Detect languages
+    const extensions = new Set();
+    for (const dir of srcDirs) {
+        const fullDir = path.join(root, dir);
+        if (fs.existsSync(fullDir)) {
+            try {
+                scanExtensions(fullDir, extensions, 0, 3);
+            }
+            catch { /* skip */ }
+        }
+    }
+    const detectedExts = extensions.size > 0
+        ? [...extensions].sort()
+        : ['.ts', '.tsx', '.js', '.jsx'];
     const yaml = `# MoFlo — Project Configuration
 # Generated by: moflo init
 # Docs: https://github.com/eric-cielo/moflo
@@ -240,6 +291,15 @@ ${srcDirs.map(d => `    - ${d}`).join('\n')}
   exclude: [node_modules, dist, .next, coverage, build, __pycache__, target, .git]
   namespace: code-map
 
+# Test file discovery and indexing
+tests:
+  directories:
+${testDirs.map(d => `    - ${d}`).join('\n')}
+  patterns: ["*.test.*", "*.spec.*", "*.test-*"]
+  extensions: [".ts", ".tsx", ".js", ".jsx"]
+  exclude: [node_modules, coverage, dist]
+  namespace: tests
+
 # Workflow gates (enforced via Claude Code hooks)
 gates:
   memory_first: ${gatesEnabled}
@@ -250,6 +310,7 @@ gates:
 auto_index:
   guidance: ${answers?.guidance ?? true}
   code_map: ${answers?.codeMap ?? true}
+  tests: ${answers?.tests ?? true}
 
 # Memory backend
 memory:
@@ -305,280 +366,290 @@ model_routing:
   # agent_overrides:
   #   security-architect: opus     # Always use opus for security
   #   researcher: sonnet           # Pin research to sonnet
-`;
-    fs.writeFileSync(configPath, yaml, 'utf-8');
-    return { name: 'moflo.yaml', status: 'created', detail: `Detected: ${srcDirs.join(', ')} | ${detectedExts.join(', ')}` };
-}
-function scanExtensions(dir, extensions, depth, maxDepth) {
-    if (depth > maxDepth)
-        return;
-    const entries = fs.readdirSync(dir, { withFileTypes: true });
-    for (const entry of entries.slice(0, 100)) {
-        if (entry.isDirectory() && !['node_modules', '.git', 'dist', 'build'].includes(entry.name)) {
-            scanExtensions(path.join(dir, entry.name), extensions, depth + 1, maxDepth);
-        }
-        else if (entry.isFile()) {
-            const ext = path.extname(entry.name);
-            if (['.ts', '.tsx', '.js', '.jsx', '.py', '.go', '.rs', '.java', '.kt', '.swift', '.rb', '.cs'].includes(ext)) {
-                extensions.add(ext);
-            }
-        }
-    }
-}
-// ============================================================================
-// Step 2: .claude/settings.json hooks
-// ============================================================================
-function generateHooks(root, force, answers) {
-    const settingsPath = path.join(root, '.claude', 'settings.json');
-    const settingsDir = path.dirname(settingsPath);
-    if (!fs.existsSync(settingsDir)) {
-        fs.mkdirSync(settingsDir, { recursive: true });
-    }
-    let existing = {};
-    if (fs.existsSync(settingsPath)) {
-        try {
-            existing = JSON.parse(fs.readFileSync(settingsPath, 'utf-8'));
-        }
-        catch { /* start fresh */ }
-        // Check if MoFlo hooks already set up
-        const settingsStr = JSON.stringify(existing);
-        const hasGateHooks = settingsStr.includes('flo gate') || settingsStr.includes('moflo gate');
-        if (hasGateHooks && !force) {
-            return { name: '.claude/settings.json', status: 'skipped', detail: 'MoFlo hooks already configured' };
-        }
-    }
-    // Build hooks config — all on by default (opinionated pit-of-success)
-    const hooks = {
-        "PreToolUse": [
-            {
-                "matcher": "^(Write|Edit|MultiEdit)$",
-                "hooks": [{
-                        "type": "command",
-                        "command": "npx flo hooks pre-edit",
-                        "timeout": 5000
-                    }]
-            },
-            {
-                "matcher": "^(Glob|Grep)$",
-                "hooks": [{
-                        "type": "command",
-                        "command": "npx flo gate check-before-scan",
-                        "timeout": 3000
-                    }]
-            },
-            {
-                "matcher": "^Read$",
-                "hooks": [{
-                        "type": "command",
-                        "command": "npx flo gate check-before-read",
-                        "timeout": 3000
-                    }]
-            },
-            {
-                "matcher": "^Task$",
-                "hooks": [
-                    {
-                        "type": "command",
-                        "command": "npx flo gate check-before-agent",
-                        "timeout": 3000
-                    },
-                    {
-                        "type": "command",
-                        "command": "npx flo hooks pre-task",
-                        "timeout": 5000
-                    }
-                ]
-            },
-            {
-                "matcher": "^Bash$",
-                "hooks": [{
-                        "type": "command",
-                        "command": "npx flo gate check-dangerous-command",
-                        "timeout": 2000
-                    }]
-            }
-        ],
-        "PostToolUse": [
-            {
-                "matcher": "^(Write|Edit|MultiEdit)$",
-                "hooks": [{
-                        "type": "command",
-                        "command": "npx flo hooks post-edit",
-                        "timeout": 5000
-                    }]
-            },
-            {
-                "matcher": "^Task$",
-                "hooks": [{
-                        "type": "command",
-                        "command": "npx flo hooks post-task",
-                        "timeout": 5000
-                    }]
-            },
-            {
-                "matcher": "^TaskCreate$",
-                "hooks": [{
-                        "type": "command",
-                        "command": "npx flo gate record-task-created",
-                        "timeout": 2000
-                    }]
-            },
-            {
-                "matcher": "^Bash$",
-                "hooks": [{
-                        "type": "command",
-                        "command": "npx flo gate check-bash-memory",
-                        "timeout": 2000
-                    }]
-            },
-            {
-                "matcher": "^mcp__claude-flow__memory_(search|retrieve)$",
-                "hooks": [{
-                        "type": "command",
-                        "command": "npx flo gate record-memory-searched",
-                        "timeout": 2000
-                    }]
-            }
-        ],
-        "UserPromptSubmit": [
-            {
-                "hooks": [
-                    {
-                        "type": "command",
-                        "command": "npx flo gate prompt-reminder",
-                        "timeout": 2000
-                    },
-                    {
-                        "type": "command",
-                        "command": "npx flo hooks route",
-                        "timeout": 5000
-                    }
-                ]
-            }
-        ],
-        "SessionStart": [
-            {
-                "hooks": [
-                    {
-                        "type": "command",
-                        "command": "node \"$CLAUDE_PROJECT_DIR/.claude/scripts/session-start-launcher.mjs\"",
-                        "timeout": 3000
-                    }
-                ]
-            }
-        ],
-        "Stop": [
-            {
-                "hooks": [{
-                        "type": "command",
-                        "command": "npx flo hooks session-end",
-                        "timeout": 5000
-                    }]
-            }
-        ],
-        "PreCompact": [
-            {
-                "hooks": [{
-                        "type": "command",
-                        "command": "npx flo gate compact-guidance",
-                        "timeout": 3000
-                    }]
-            }
-        ],
-        "Notification": [
-            {
-                "hooks": [{
-                        "type": "command",
-                        "command": "npx flo hooks notification",
-                        "timeout": 3000
-                    }]
-            }
-        ]
-    };
-    // Merge: preserve existing non-MoFlo hooks, add MoFlo hooks
-    existing.hooks = hooks;
-    fs.writeFileSync(settingsPath, JSON.stringify(existing, null, 2), 'utf-8');
-    return { name: '.claude/settings.json', status: existing.hooks ? 'updated' : 'created', detail: '14 hooks configured (gates, lifecycle, routing, session)' };
-}
-// ============================================================================
-// Step 3: .claude/skills/flo/ skill (with /fl alias)
-// ============================================================================
-function generateSkill(root, force) {
-    const skillDir = path.join(root, '.claude', 'skills', 'flo');
-    const skillFile = path.join(skillDir, 'SKILL.md');
-    const aliasDir = path.join(root, '.claude', 'skills', 'fl');
-    const aliasFile = path.join(aliasDir, 'SKILL.md');
-    if (fs.existsSync(skillFile) && !force) {
-        return { name: '.claude/skills/flo/', status: 'skipped', detail: 'Already exists' };
-    }
-    if (!fs.existsSync(skillDir)) {
-        fs.mkdirSync(skillDir, { recursive: true });
-    }
-    // Copy static SKILL.md from moflo package instead of generating it
-    let skillContent = '';
-    // Resolve this file's directory in ESM-safe way
-    let thisDir;
-    try {
-        thisDir = path.dirname(fileURLToPath(import.meta.url));
-    }
-    catch {
-        // Fallback for CJS or environments where import.meta.url is unavailable
-        thisDir = typeof __dirname !== 'undefined' ? __dirname : '';
-    }
-    const staticSkillCandidates = [
-        // Installed via npm (most common)
-        path.join(root, 'node_modules', 'moflo', '.claude', 'skills', 'flo', 'SKILL.md'),
-        // Running from moflo repo itself (dev)
-        ...(thisDir ? [path.join(thisDir, '..', '..', '..', '..', '.claude', 'skills', 'flo', 'SKILL.md')] : []),
-    ];
-    for (const candidate of staticSkillCandidates) {
-        try {
-            if (fs.existsSync(candidate)) {
-                skillContent = fs.readFileSync(candidate, 'utf-8');
-                break;
-            }
-        }
-        catch { /* skip inaccessible paths */ }
-    }
-    if (!skillContent) {
-        return { name: '.claude/skills/flo/', status: 'error', detail: 'Could not find SKILL.md in moflo package' };
-    }
-    fs.writeFileSync(skillFile, skillContent, 'utf-8');
-    // Create /fl alias (same content)
-    if (!fs.existsSync(aliasDir)) {
-        fs.mkdirSync(aliasDir, { recursive: true });
-    }
-    fs.writeFileSync(aliasFile, skillContent.replace('name: flo', 'name: fl'), 'utf-8');
-    // Clean up old /mf skill directory if it exists
-    const oldSkillDir = path.join(root, '.claude', 'skills', 'mf');
-    if (fs.existsSync(oldSkillDir)) {
-        fs.rmSync(oldSkillDir, { recursive: true });
-    }
-    return { name: '.claude/skills/flo/', status: 'created', detail: '/flo skill ready (alias: /fl)' };
-}
-// ============================================================================
-// Step 4: CLAUDE.md MoFlo section
-// ============================================================================
-const MOFLO_MARKER = '<!-- MOFLO:START -->';
-const MOFLO_MARKER_END = '<!-- MOFLO:END -->';
-function generateClaudeMd(root, force) {
-    const claudeMdPath = path.join(root, 'CLAUDE.md');
-    let existing = '';
-    if (fs.existsSync(claudeMdPath)) {
-        existing = fs.readFileSync(claudeMdPath, 'utf-8');
-        // Check if MoFlo section already exists
-        if (existing.includes(MOFLO_MARKER)) {
-            if (!force) {
-                return { name: 'CLAUDE.md', status: 'skipped', detail: 'MoFlo section already present' };
-            }
-            // Remove existing MoFlo section for replacement
-            const startIdx = existing.indexOf(MOFLO_MARKER);
-            const endIdx = existing.indexOf(MOFLO_MARKER_END);
-            if (endIdx > startIdx) {
-                existing = existing.substring(0, startIdx) + existing.substring(endIdx + MOFLO_MARKER_END.length);
-            }
-        }
-    }
+`;
+    fs.writeFileSync(configPath, yaml, 'utf-8');
+    return { name: 'moflo.yaml', status: 'created', detail: `Detected: ${srcDirs.join(', ')} | ${detectedExts.join(', ')}` };
+}
+function scanExtensions(dir, extensions, depth, maxDepth) {
+    if (depth > maxDepth)
+        return;
+    const entries = fs.readdirSync(dir, { withFileTypes: true });
+    for (const entry of entries.slice(0, 100)) {
+        if (entry.isDirectory() && !['node_modules', '.git', 'dist', 'build'].includes(entry.name)) {
+            scanExtensions(path.join(dir, entry.name), extensions, depth + 1, maxDepth);
+        }
+        else if (entry.isFile()) {
+            const ext = path.extname(entry.name);
+            if (['.ts', '.tsx', '.js', '.jsx', '.py', '.go', '.rs', '.java', '.kt', '.swift', '.rb', '.cs'].includes(ext)) {
+                extensions.add(ext);
+            }
+        }
+    }
+}
+// ============================================================================
+// Step 2: .claude/settings.json hooks
+// ============================================================================
+function generateHooks(root, force, answers) {
+    const settingsPath = path.join(root, '.claude', 'settings.json');
+    const settingsDir = path.dirname(settingsPath);
+    if (!fs.existsSync(settingsDir)) {
+        fs.mkdirSync(settingsDir, { recursive: true });
+    }
+    let existing = {};
+    if (fs.existsSync(settingsPath)) {
+        try {
+            existing = JSON.parse(fs.readFileSync(settingsPath, 'utf-8'));
+        }
+        catch { /* start fresh */ }
+        // Check if MoFlo hooks already set up
+        const settingsStr = JSON.stringify(existing);
+        const hasGateHooks = settingsStr.includes('flo gate') || settingsStr.includes('moflo gate');
+        if (hasGateHooks && !force) {
+            return { name: '.claude/settings.json', status: 'skipped', detail: 'MoFlo hooks already configured' };
+        }
+    }
+    // Build hooks config — all on by default (opinionated pit-of-success)
+    const hooks = {
+        "PreToolUse": [
+            {
+                "matcher": "^(Write|Edit|MultiEdit)$",
+                "hooks": [{
+                        "type": "command",
+                        "command": "npx flo hooks pre-edit",
+                        "timeout": 5000
+                    }]
+            },
+            {
+                "matcher": "^(Glob|Grep)$",
+                "hooks": [{
+                        "type": "command",
+                        "command": "npx flo gate check-before-scan",
+                        "timeout": 3000
+                    }]
+            },
+            {
+                "matcher": "^Read$",
+                "hooks": [{
+                        "type": "command",
+                        "command": "npx flo gate check-before-read",
+                        "timeout": 3000
+                    }]
+            },
+            {
+                "matcher": "^Task$",
+                "hooks": [
+                    {
+                        "type": "command",
+                        "command": "npx flo gate check-before-agent",
+                        "timeout": 3000
+                    },
+                    {
+                        "type": "command",
+                        "command": "npx flo hooks pre-task",
+                        "timeout": 5000
+                    }
+                ]
+            },
+            {
+                "matcher": "^Bash$",
+                "hooks": [{
+                        "type": "command",
+                        "command": "npx flo gate check-dangerous-command",
+                        "timeout": 2000
+                    }]
+            }
+        ],
+        "PostToolUse": [
+            {
+                "matcher": "^(Write|Edit|MultiEdit)$",
+                "hooks": [{
+                        "type": "command",
+                        "command": "npx flo hooks post-edit",
+                        "timeout": 5000
+                    }]
+            },
+            {
+                "matcher": "^Task$",
+                "hooks": [{
+                        "type": "command",
+                        "command": "npx flo hooks post-task",
+                        "timeout": 5000
+                    }]
+            },
+            {
+                "matcher": "^TaskCreate$",
+                "hooks": [{
+                        "type": "command",
+                        "command": "npx flo gate record-task-created",
+                        "timeout": 2000
+                    }]
+            },
+            {
+                "matcher": "^Bash$",
+                "hooks": [{
+                        "type": "command",
+                        "command": "npx flo gate check-bash-memory",
+                        "timeout": 2000
+                    }]
+            },
+            {
+                "matcher": "^mcp__moflo__memory_(search|retrieve)$",
+                "hooks": [{
+                        "type": "command",
+                        "command": "npx flo gate record-memory-searched",
+                        "timeout": 2000
+                    }]
+            }
+        ],
+        "UserPromptSubmit": [
+            {
+                "hooks": [
+                    {
+                        "type": "command",
+                        "command": "npx flo gate prompt-reminder",
+                        "timeout": 2000
+                    },
+                    {
+                        "type": "command",
+                        "command": "npx flo hooks route",
+                        "timeout": 5000
+                    }
+                ]
+            }
+        ],
+        "SessionStart": [
+            {
+                "hooks": [
+                    {
+                        "type": "command",
+                        "command": "node \"$CLAUDE_PROJECT_DIR/.claude/scripts/session-start-launcher.mjs\"",
+                        "timeout": 3000
+                    }
+                ]
+            }
+        ],
+        "Stop": [
+            {
+                "hooks": [{
+                        "type": "command",
+                        "command": "npx flo hooks session-end",
+                        "timeout": 5000
+                    }]
+            }
+        ],
+        "PreCompact": [
+            {
+                "hooks": [{
+                        "type": "command",
+                        "command": "npx flo gate compact-guidance",
+                        "timeout": 3000
+                    }]
+            }
+        ],
+        "Notification": [
+            {
+                "hooks": [{
+                        "type": "command",
+                        "command": "npx flo hooks notification",
+                        "timeout": 3000
+                    }]
+            }
+        ]
+    };
+    // Merge: preserve existing non-MoFlo hooks, add MoFlo hooks
+    existing.hooks = hooks;
+    fs.writeFileSync(settingsPath, JSON.stringify(existing, null, 2), 'utf-8');
+    return { name: '.claude/settings.json', status: existing.hooks ? 'updated' : 'created', detail: '14 hooks configured (gates, lifecycle, routing, session)' };
+}
+// ============================================================================
+// Step 3: .claude/skills/flo/ skill (with /fl alias)
+// ============================================================================
+function generateSkill(root, force) {
+    const skillDir = path.join(root, '.claude', 'skills', 'flo');
+    const skillFile = path.join(skillDir, 'SKILL.md');
+    const aliasDir = path.join(root, '.claude', 'skills', 'fl');
+    const aliasFile = path.join(aliasDir, 'SKILL.md');
+    if (fs.existsSync(skillFile) && !force) {
+        return { name: '.claude/skills/flo/', status: 'skipped', detail: 'Already exists' };
+    }
+    if (!fs.existsSync(skillDir)) {
+        fs.mkdirSync(skillDir, { recursive: true });
+    }
+    // Copy static SKILL.md from moflo package instead of generating it
+    let skillContent = '';
+    // Resolve this file's directory in ESM-safe way
+    let thisDir;
+    try {
+        thisDir = path.dirname(fileURLToPath(import.meta.url));
+    }
+    catch {
+        // Fallback for CJS or environments where import.meta.url is unavailable
+        thisDir = typeof __dirname !== 'undefined' ? __dirname : '';
+    }
+    const staticSkillCandidates = [
+        // Installed via npm (most common)
+        path.join(root, 'node_modules', 'moflo', '.claude', 'skills', 'flo', 'SKILL.md'),
+        // Running from moflo repo itself (dev)
+        ...(thisDir ? [path.join(thisDir, '..', '..', '..', '..', '.claude', 'skills', 'flo', 'SKILL.md')] : []),
+    ];
+    for (const candidate of staticSkillCandidates) {
+        try {
+            if (fs.existsSync(candidate)) {
+                skillContent = fs.readFileSync(candidate, 'utf-8');
+                break;
+            }
+        }
+        catch { /* skip inaccessible paths */ }
+    }
+    if (!skillContent) {
+        return { name: '.claude/skills/flo/', status: 'error', detail: 'Could not find SKILL.md in moflo package' };
+    }
+    fs.writeFileSync(skillFile, skillContent, 'utf-8');
+    // Create /fl alias (same content)
+    if (!fs.existsSync(aliasDir)) {
+        fs.mkdirSync(aliasDir, { recursive: true });
+    }
+    fs.writeFileSync(aliasFile, skillContent.replace('name: flo', 'name: fl'), 'utf-8');
+    // Clean up old /mf skill directory if it exists
+    const oldSkillDir = path.join(root, '.claude', 'skills', 'mf');
+    if (fs.existsSync(oldSkillDir)) {
+        fs.rmSync(oldSkillDir, { recursive: true });
+    }
+    return { name: '.claude/skills/flo/', status: 'created', detail: '/flo skill ready (alias: /fl)' };
+}
+// ============================================================================
+// Step 4: CLAUDE.md MoFlo section
+// ============================================================================
+// Markers for idempotent CLAUDE.md injection — keep in sync with claudemd-generator.ts
+const MOFLO_MARKER = '<!-- MOFLO:INJECTED:START -->';
+const MOFLO_MARKER_END = '<!-- MOFLO:INJECTED:END -->';
+// Also detect legacy markers so we can replace them
+const LEGACY_MARKERS = ['<!-- MOFLO:START -->', '<!-- MOFLO:SUBAGENT-PROTOCOL:START -->'];
+const LEGACY_MARKERS_END = ['<!-- MOFLO:END -->', '<!-- MOFLO:SUBAGENT-PROTOCOL:END -->'];
+function generateClaudeMd(root, force) {
+    const claudeMdPath = path.join(root, 'CLAUDE.md');
+    let existing = '';
+    if (fs.existsSync(claudeMdPath)) {
+        existing = fs.readFileSync(claudeMdPath, 'utf-8');
+        // Check for current or legacy markers
+        const allStartMarkers = [MOFLO_MARKER, ...LEGACY_MARKERS];
+        const allEndMarkers = [MOFLO_MARKER_END, ...LEGACY_MARKERS_END];
+        for (let i = 0; i < allStartMarkers.length; i++) {
+            if (existing.includes(allStartMarkers[i])) {
+                if (!force && allStartMarkers[i] === MOFLO_MARKER) {
+                    return { name: 'CLAUDE.md', status: 'skipped', detail: 'MoFlo section already present' };
+                }
+                // Remove existing section for replacement
+                const startIdx = existing.indexOf(allStartMarkers[i]);
+                const endIdx = existing.indexOf(allEndMarkers[i]);
+                if (endIdx > startIdx) {
+                    existing = existing.substring(0, startIdx) + existing.substring(endIdx + allEndMarkers[i].length);
+                }
+            }
+        }
+    }
+    // Minimal injection — just enough for Claude to work with moflo.
+    // All detailed docs live in .claude/guidance/shipped/moflo.md.
     const mofloSection = `
 ${MOFLO_MARKER}
 ## MoFlo — AI Agent Orchestration
@@ -590,194 +661,180 @@ This project uses [MoFlo](https://github.com/eric-cielo/moflo) for AI-assisted d
 Your first tool call for every new user prompt MUST be a memory search. Do this BEFORE Glob, Grep, Read, or any file exploration.
 
 \`\`\`
-mcp__claude-flow__memory_search  — query: "<task description>", namespace: "guidance" or "patterns" or "knowledge" or "code-map"
+mcp__moflo__memory_search — query: "<task description>", namespace: "guidance" or "patterns" or "code-map"
 \`\`\`
 
-For codebase navigation, search the \`code-map\` namespace first. For patterns and domain knowledge, search \`patterns\`, \`knowledge\`, and \`guidance\`.
-When the user asks you to remember something, store it: \`memory store --namespace knowledge --key "[topic]" --value "[what to remember]"\`
+Search \`guidance\` and \`patterns\` namespaces on every prompt. Search \`code-map\` when navigating the codebase.
+When the user asks you to remember something: \`mcp__moflo__memory_store\` with namespace \`knowledge\`.
 
 ### Workflow Gates (enforced automatically)
 
-These are enforced by hooks — you cannot bypass them:
-- **Memory-first**: Must search memory before Glob/Grep/Read on guidance files
+- **Memory-first**: Must search memory before Glob/Grep/Read
 - **TaskCreate-first**: Must call TaskCreate before spawning Agent tool
-- **Context tracking**: Session tracked as FRESH → MODERATE → DEPLETED → CRITICAL
-
-### /flo Skill — Issue Execution
 
-Use \`/flo <issue-number>\` (or \`/fl\`) to execute GitHub issues through the full workflow:
-Research → Enhance → Implement → Test → Simplify → PR
-
-### MCP Tools Reference
+### MCP Tools (preferred over CLI)
 
 | Tool | Purpose |
 |------|---------|
-| \`mcp__claude-flow__memory_search\` | Semantic search across indexed knowledge |
-| \`mcp__claude-flow__memory_store\` | Store patterns and decisions |
-| \`mcp__claude-flow__hooks_route\` | Route task to optimal agent type |
-| \`mcp__claude-flow__hooks_pre-task\` | Record task start |
-| \`mcp__claude-flow__hooks_post-task\` | Record task completion for learning |
+| \`mcp__moflo__memory_search\` | Semantic search across indexed knowledge |
+| \`mcp__moflo__memory_store\` | Store patterns and decisions |
+| \`mcp__moflo__hooks_route\` | Route task to optimal agent type |
+| \`mcp__moflo__hooks_pre-task\` | Record task start |
+| \`mcp__moflo__hooks_post-task\` | Record task completion for learning |
 
-### Agent Icon Mapping
+### CLI Fallback
 
-| Icon | Agent Type | Use For |
-|------|------------|---------|
-| 🔍 | Explore | Research, codebase exploration |
-| 📐 | Plan | Architecture, design |
-| ⚙️ | General | General coding tasks |
-| 🧪 | Test | Writing tests |
-| 🔬 | Analyzer | Code review, analysis |
-| 🔧 | Backend | API implementation |
+\`\`\`bash
+npx flo-search "[query]" --namespace guidance   # Semantic search
+npx flo doctor --fix                             # Health check
+\`\`\`
 
-### Non-Trivial Task Workflow
+### Full Reference
 
-For any task beyond a single-line fix:
-1. Search memory first (mandatory gate)
-2. Create tasks with TaskCreate (mandatory gate)
-3. Spawn agents in waves (Explore first, then Implement + Test)
-4. Update task status as you go
-5. Store learnings after completion
+For CLI commands, hooks, agents, swarm config, memory commands, and moflo.yaml options, see:
+\`.claude/guidance/shipped/moflo.md\`
 ${MOFLO_MARKER_END}
-`;
-    const finalContent = existing.trimEnd() + '\n' + mofloSection;
-    fs.writeFileSync(claudeMdPath, finalContent, 'utf-8');
-    return {
-        name: 'CLAUDE.md',
-        status: existing ? 'updated' : 'created',
-        detail: 'MoFlo workflow section appended',
-    };
-}
-// ============================================================================
-// Step 5: .claude/scripts/ — sync from moflo bin/
-// These scripts are used by session-start hooks for indexing, code map, etc.
-// Always overwrite to keep them in sync with the installed moflo version.
-// ============================================================================
-const SCRIPT_MAP = {
-    'hooks.mjs': 'hooks.mjs',
-    'session-start-launcher.mjs': 'session-start-launcher.mjs',
-    'index-guidance.mjs': 'index-guidance.mjs',
-    'build-embeddings.mjs': 'build-embeddings.mjs',
-    'generate-code-map.mjs': 'generate-code-map.mjs',
-    'semantic-search.mjs': 'semantic-search.mjs',
-};
-function syncScripts(root, force) {
-    const scriptsDir = path.join(root, '.claude', 'scripts');
-    if (!fs.existsSync(scriptsDir)) {
-        fs.mkdirSync(scriptsDir, { recursive: true });
-    }
-    // Find moflo bin/ directory
-    let syncThisDir;
-    try {
-        syncThisDir = path.dirname(fileURLToPath(import.meta.url));
-    }
-    catch {
-        syncThisDir = typeof __dirname !== 'undefined' ? __dirname : '';
-    }
-    const candidates = [
-        path.join(root, 'node_modules', 'moflo', 'bin'),
-        // When running from moflo repo itself
-        ...(syncThisDir ? [path.join(syncThisDir, '..', '..', '..', '..', 'bin')] : []),
-    ];
-    const binDir = candidates.find(d => { try {
-        return fs.existsSync(d);
-    }
-    catch {
-        return false;
-    } });
-    if (!binDir) {
-        return { name: '.claude/scripts/', status: 'skipped', detail: 'moflo bin/ not found' };
-    }
-    let copied = 0;
-    for (const [dest, src] of Object.entries(SCRIPT_MAP)) {
-        const srcPath = path.join(binDir, src);
-        const destPath = path.join(scriptsDir, dest);
-        if (!fs.existsSync(srcPath))
-            continue;
-        // Always overwrite scripts to keep in sync (they're derived, not user-edited)
-        if (!fs.existsSync(destPath) || force || isStale(srcPath, destPath)) {
-            fs.copyFileSync(srcPath, destPath);
-            copied++;
-        }
-    }
-    if (copied === 0) {
-        return { name: '.claude/scripts/', status: 'skipped', detail: 'Scripts already up to date' };
-    }
-    return { name: '.claude/scripts/', status: 'updated', detail: `${copied} scripts synced from moflo` };
-}
-function isStale(srcPath, destPath) {
-    try {
-        return fs.statSync(srcPath).mtimeMs > fs.statSync(destPath).mtimeMs;
-    }
-    catch {
-        return true;
-    }
-}
-// ============================================================================
-// Step 6: .gitignore
-// ============================================================================
-function updateGitignore(root) {
-    const gitignorePath = path.join(root, '.gitignore');
-    const entries = ['.claude-orc/', '.swarm/', '.moflo/'];
-    if (!fs.existsSync(gitignorePath)) {
-        // Create .gitignore with common defaults + MoFlo entries
-        const defaultEntries = ['node_modules/', 'dist/', '.env', '.env.*', ''];
-        const content = '# Dependencies\n' + defaultEntries.join('\n') + '\n# MoFlo state\n' + entries.join('\n') + '\n';
-        fs.writeFileSync(gitignorePath, content, 'utf-8');
-        return { name: '.gitignore', status: 'created', detail: 'Created with node_modules, .env, and MoFlo entries' };
-    }
-    const existing = fs.readFileSync(gitignorePath, 'utf-8');
-    const toAdd = entries.filter(e => !existing.includes(e));
-    if (toAdd.length === 0) {
-        return { name: '.gitignore', status: 'skipped', detail: 'Entries already present' };
-    }
-    fs.appendFileSync(gitignorePath, '\n# MoFlo state (gitignored)\n' + toAdd.join('\n') + '\n');
-    return { name: '.gitignore', status: 'updated', detail: `Added: ${toAdd.join(', ')}` };
-}
-// ============================================================================
-// Step 7: .claude/guidance/moflo-bootstrap.md
-// Copies the agent bootstrap guidance to the project so subagents can read it
-// from disk without requiring memory search.
-// ============================================================================
-function syncBootstrapGuidance(root, force) {
-    const guidanceDir = path.join(root, '.claude', 'guidance');
-    const targetFile = path.join(guidanceDir, 'moflo-bootstrap.md');
-    // Find the source bootstrap file from the moflo package
-    let sourceDir;
-    try {
-        sourceDir = path.dirname(fileURLToPath(import.meta.url));
-    }
-    catch {
-        sourceDir = typeof __dirname !== 'undefined' ? __dirname : '';
-    }
-    const candidates = [
-        path.join(root, 'node_modules', 'moflo', '.claude', 'guidance', 'agent-bootstrap.md'),
-        // When running from moflo repo itself
-        ...(sourceDir ? [path.join(sourceDir, '..', '..', '..', '..', '.claude', 'guidance', 'agent-bootstrap.md')] : []),
-    ];
-    const sourceFile = candidates.find(f => { try {
-        return fs.existsSync(f);
-    }
-    catch {
-        return false;
-    } });
-    if (!sourceFile) {
-        return { name: 'guidance/moflo-bootstrap.md', status: 'skipped', detail: 'Source bootstrap not found' };
-    }
-    // Check if target exists and is up to date
-    if (fs.existsSync(targetFile) && !force) {
-        if (!isStale(sourceFile, targetFile)) {
-            return { name: 'guidance/moflo-bootstrap.md', status: 'skipped', detail: 'Already up to date' };
-        }
-    }
-    // Read source and prepend header
-    const content = fs.readFileSync(sourceFile, 'utf-8');
-    const header = `<!-- AUTO-GENERATED by moflo init. Do not edit — changes will be overwritten on next init. -->\n<!-- Source: moflo/.claude/guidance/agent-bootstrap.md -->\n<!-- To customize, create .claude/guidance/agent-bootstrap.md for project-specific rules. -->\n\n`;
-    fs.mkdirSync(guidanceDir, { recursive: true });
-    fs.writeFileSync(targetFile, header + content, 'utf-8');
-    return {
-        name: 'guidance/moflo-bootstrap.md',
-        status: fs.existsSync(targetFile) ? 'updated' : 'created',
-        detail: 'Subagent bootstrap protocol'
-    };
-}
+`;
+    const finalContent = existing.trimEnd() + '\n' + mofloSection;
+    fs.writeFileSync(claudeMdPath, finalContent, 'utf-8');
+    return {
+        name: 'CLAUDE.md',
+        status: existing ? 'updated' : 'created',
+        detail: 'MoFlo section injected (~35 lines)',
+    };
+}
+// ============================================================================
+// Step 5: .claude/scripts/ — sync from moflo bin/
+// These scripts are used by session-start hooks for indexing, code map, etc.
+// Always overwrite to keep them in sync with the installed moflo version.
+// ============================================================================
+const SCRIPT_MAP = {
+    'hooks.mjs': 'hooks.mjs',
+    'session-start-launcher.mjs': 'session-start-launcher.mjs',
+    'index-guidance.mjs': 'index-guidance.mjs',
+    'build-embeddings.mjs': 'build-embeddings.mjs',
+    'generate-code-map.mjs': 'generate-code-map.mjs',
+    'semantic-search.mjs': 'semantic-search.mjs',
+    'index-tests.mjs': 'index-tests.mjs',
+};
+function syncScripts(root, force) {
+    const scriptsDir = path.join(root, '.claude', 'scripts');
+    if (!fs.existsSync(scriptsDir)) {
+        fs.mkdirSync(scriptsDir, { recursive: true });
+    }
+    // Find moflo bin/ directory
+    let syncThisDir;
+    try {
+        syncThisDir = path.dirname(fileURLToPath(import.meta.url));
+    }
+    catch {
+        syncThisDir = typeof __dirname !== 'undefined' ? __dirname : '';
+    }
+    const candidates = [
+        path.join(root, 'node_modules', 'moflo', 'bin'),
+        // When running from moflo repo itself
+        ...(syncThisDir ? [path.join(syncThisDir, '..', '..', '..', '..', 'bin')] : []),
+    ];
+    const binDir = candidates.find(d => { try {
+        return fs.existsSync(d);
+    }
+    catch {
+        return false;
+    } });
+    if (!binDir) {
+        return { name: '.claude/scripts/', status: 'skipped', detail: 'moflo bin/ not found' };
+    }
+    let copied = 0;
+    for (const [dest, src] of Object.entries(SCRIPT_MAP)) {
+        const srcPath = path.join(binDir, src);
+        const destPath = path.join(scriptsDir, dest);
+        if (!fs.existsSync(srcPath))
+            continue;
+        // Always overwrite scripts to keep in sync (they're derived, not user-edited)
+        if (!fs.existsSync(destPath) || force || isStale(srcPath, destPath)) {
+            fs.copyFileSync(srcPath, destPath);
+            copied++;
+        }
+    }
+    if (copied === 0) {
+        return { name: '.claude/scripts/', status: 'skipped', detail: 'Scripts already up to date' };
+    }
+    return { name: '.claude/scripts/', status: 'updated', detail: `${copied} scripts synced from moflo` };
+}
+function isStale(srcPath, destPath) {
+    try {
+        return fs.statSync(srcPath).mtimeMs > fs.statSync(destPath).mtimeMs;
+    }
+    catch {
+        return true;
+    }
+}
+// ============================================================================
+// Step 6: .gitignore
+// ============================================================================
+function updateGitignore(root) {
+    const gitignorePath = path.join(root, '.gitignore');
+    const entries = ['.claude-orc/', '.swarm/', '.moflo/'];
+    if (!fs.existsSync(gitignorePath)) {
+        // Create .gitignore with common defaults + MoFlo entries
+        const defaultEntries = ['node_modules/', 'dist/', '.env', '.env.*', ''];
+        const content = '# Dependencies\n' + defaultEntries.join('\n') + '\n# MoFlo state\n' + entries.join('\n') + '\n';
+        fs.writeFileSync(gitignorePath, content, 'utf-8');
+        return { name: '.gitignore', status: 'created', detail: 'Created with node_modules, .env, and MoFlo entries' };
+    }
+    const existing = fs.readFileSync(gitignorePath, 'utf-8');
+    const toAdd = entries.filter(e => !existing.includes(e));
+    if (toAdd.length === 0) {
+        return { name: '.gitignore', status: 'skipped', detail: 'Entries already present' };
+    }
+    fs.appendFileSync(gitignorePath, '\n# MoFlo state (gitignored)\n' + toAdd.join('\n') + '\n');
+    return { name: '.gitignore', status: 'updated', detail: `Added: ${toAdd.join(', ')}` };
+}
+// ============================================================================
+// Step 7: .claude/guidance/moflo-bootstrap.md
+// Copies the agent bootstrap guidance to the project so subagents can read it
+// from disk without requiring memory search.
+// ============================================================================
+function syncBootstrapGuidance(root, force) {
+    const guidanceDir = path.join(root, '.claude', 'guidance');
+    const targetFile = path.join(guidanceDir, 'moflo-bootstrap.md');
+    // Find the source bootstrap file from the moflo package
+    let sourceDir;
+    try {
+        sourceDir = path.dirname(fileURLToPath(import.meta.url));
+    }
+    catch {
+        sourceDir = typeof __dirname !== 'undefined' ? __dirname : '';
+    }
+    const candidates = [
+        path.join(root, 'node_modules', 'moflo', '.claude', 'guidance', 'agent-bootstrap.md'),
+        // When running from moflo repo itself
+        ...(sourceDir ? [path.join(sourceDir, '..', '..', '..', '..', '.claude', 'guidance', 'agent-bootstrap.md')] : []),
+    ];
+    const sourceFile = candidates.find(f => { try {
+        return fs.existsSync(f);
+    }
+    catch {
+        return false;
+    } });
+    if (!sourceFile) {
+        return { name: 'guidance/moflo-bootstrap.md', status: 'skipped', detail: 'Source bootstrap not found' };
+    }
+    // Check if target exists and is up to date
+    if (fs.existsSync(targetFile) && !force) {
+        if (!isStale(sourceFile, targetFile)) {
+            return { name: 'guidance/moflo-bootstrap.md', status: 'skipped', detail: 'Already up to date' };
+        }
+    }
+    // Read source and prepend header
+    const content = fs.readFileSync(sourceFile, 'utf-8');
+    const header = `<!-- AUTO-GENERATED by moflo init. Do not edit — changes will be overwritten on next init. -->\n<!-- Source: moflo/.claude/guidance/agent-bootstrap.md -->\n<!-- To customize, create .claude/guidance/agent-bootstrap.md for project-specific rules. -->\n\n`;
+    fs.mkdirSync(guidanceDir, { recursive: true });
+    fs.writeFileSync(targetFile, header + content, 'utf-8');
+    return {
+        name: 'guidance/moflo-bootstrap.md',
+        status: fs.existsSync(targetFile) ? 'updated' : 'created',
+        detail: 'Subagent bootstrap protocol'
+    };
+}
 //# sourceMappingURL=moflo-init.js.map