@claude-flow/cli 3.71.4 → 3.72.1

package/bin/mcp-server.js

@@ -33,8 +33,11 @@ import {
   loadMcpPolicy,
   evaluateToolCall,
 } from '../dist/src/mcp-tools/policy-enforcer.js';
+// ADR-524: shared MCP revision handling (2026-07-28 + legacy initialize).
+import * as mcpProtocol from '../dist/src/mcp-protocol.js';
 
-const VERSION = '3.0.0';
+const MCP_CAPABILITIES = { tools: { listChanged: true }, resources: {} };
+const VERSION = mcpProtocol.defaultServerIdentity().version;
 const sessionId = `mcp-${Date.now()}-${randomUUID().slice(0, 8)}`;
 
 // Log to stderr (doesn't corrupt stdout for MCP protocol)
@@ -132,27 +135,19 @@ async function handleMessage(message) {
       error: { code: -32600, message: 'Invalid Request: missing method' },
     };
   }
+  const preflight = mcpProtocol.protocolPreflight(message, MCP_CAPABILITIES);
+  if (preflight.response) return preflight.response;
+  const response = await dispatchMessage(message, preflight.context);
+  return mcpProtocol.finalizeResponse(response, message.method, preflight.context);
+}
 
+async function dispatchMessage(message, protocol) {
   const params = message.params || {};
 
   try {
     switch (message.method) {
-      case 'initialize':
-        return {
-          jsonrpc: '2.0',
-          id: message.id,
-          result: {
-            protocolVersion: '2024-11-05',
-            serverInfo: { name: 'ruflo', version: VERSION },
-            capabilities: {
-              tools: { listChanged: true },
-              resources: {},
-            },
-          },
-        };
-
       case 'tools/list': {
-        const tools = listMCPTools();
+        const tools = mcpProtocol.sortToolsDeterministically(listMCPTools());
         return {
           jsonrpc: '2.0',
           id: message.id,
@@ -190,7 +185,7 @@ async function handleMessage(message) {
         }
 
         try {
-          const result = await callMCPTool(toolName, toolParams, { sessionId, transport: 'stdio' });
+          const result = await callMCPTool(toolName, toolParams, { sessionId, transport: 'stdio', ...mcpProtocol.traceContextFields(protocol) });
           return {
             jsonrpc: '2.0',
             id: message.id,
@@ -216,7 +211,7 @@ async function handleMessage(message) {
         return { jsonrpc: '2.0', id: message.id, result: { resourceTemplates: [] } };
 
       case 'resources/read':
-        return { jsonrpc: '2.0', id: message.id, error: { code: -32002, message: 'Resource not found' } };
+        return { jsonrpc: '2.0', id: message.id, error: { code: mcpProtocol.resourceNotFoundCode(protocol), message: 'Resource not found' } };
 
       case 'notifications/initialized':
         console.error(`[${new Date().toISOString()}] INFO [claude-flow-mcp] Client initialized`);

package/catalog-manifest.json

@@ -1,12 +1,12 @@
 {
   "schemaVersion": 1,
   "generation": 7,
-  "generatedAt": "2026-11-05T03:28:45.039Z",
-  "gitSha": "bf5d71a1",
+  "generatedAt": "2026-11-06T02:50:18.000Z",
+  "gitSha": "29b327ee",
   "catalog": {
     "agents": 177,
-    "tools": 450,
-    "skills": 34
+    "tools": 451,
+    "skills": 40
   },
   "benchmark": null
 }

package/dist/src/appliance/ruvllm-bridge.d.ts

@@ -90,8 +90,12 @@ export declare class RuvllmBridge {
     shutdown(): Promise<void>;
     private scanModelsDir;
     private tryImport;
-    /** Tier-1 Agent Booster: handle trivial transforms without any LLM. */
-    private tryAgentBooster;
+    /**
+     * Tier-1 codemod hint for trivial transforms, no LLM. Not agent-booster:
+     * that engine merges a code snippet into code (hooks_fast-apply) and cannot
+     * act on an instruction alone.
+     */
+    private tryCodemodHint;
 }
 /** Get or create the singleton RuvllmBridge. Config required on first call. */
 export declare function getRuvllmBridge(config?: RuvllmConfig): RuvllmBridge;

package/dist/src/appliance/ruvllm-bridge.js

@@ -135,10 +135,11 @@ export class RuvllmBridge {
     async generate(request) {
         const start = performance.now();
         const modelName = request.model ?? this.config.defaultModel ?? this.activeModel ?? '';
-        // Tier 1: Agent Booster
-        const booster = this.tryAgentBooster(request.prompt);
+        // Tier 1: deterministic codemod hint (ADR-143). The prompt carries no code,
+        // so nothing can be applied here; this points the caller at hooks_codemod.
+        const booster = this.tryCodemodHint(request.prompt);
         if (booster !== null) {
-            return { text: booster, model: 'agent-booster', tokensUsed: 0, latencyMs: performance.now() - start, tier: 1, cached: false };
+            return { text: booster, model: 'codemod', tokensUsed: 0, latencyMs: performance.now() - start, tier: 1, cached: false };
         }
         // Tier 2: Local model (GGUF engine preferred, then @ruvector/core)
         const info = this.models.get(modelName);
@@ -183,7 +184,7 @@ export class RuvllmBridge {
         const complexity = estimateComplexity(description);
         const words = description.split(/\s+/).length;
         if (words < 15 && complexity < 0.25)
-            return { tier: 1, model: 'agent-booster', confidence: 0.9 };
+            return { tier: 1, model: 'codemod', confidence: 0.9 };
         if (complexity < 0.55 && this.activeModel)
             return { tier: 2, model: this.activeModel, confidence: 0.7 };
         return { tier: 3, model: 'cloud', confidence: 0.6 };
@@ -252,17 +253,21 @@ export class RuvllmBridge {
             return null;
         }
     }
-    /** Tier-1 Agent Booster: handle trivial transforms without any LLM. */
-    tryAgentBooster(prompt) {
+    /**
+     * Tier-1 codemod hint for trivial transforms, no LLM. Not agent-booster:
+     * that engine merges a code snippet into code (hooks_fast-apply) and cannot
+     * act on an instruction alone.
+     */
+    tryCodemodHint(prompt) {
         const t = prompt.trim();
         if (t.length > 200)
             return null;
         if (/^(convert|change)\s+(var|let)\s+to\s+const$/i.test(t)) {
-            return 'Use the Edit tool to replace `var`/`let` declarations with `const`.';
+            return 'Call hooks_codemod with intent="var-to-const" (deterministic, $0), or use the Edit tool.';
         }
         if (/^remove\s+console\.(log|warn|error|debug|info)$/i.test(t)) {
             const m = t.toLowerCase().match(/console\.(\w+)/)?.[1] ?? 'log';
-            return `Use the Edit tool to remove all \`console.${m}\` calls.`;
+            return `Call hooks_codemod with intent="remove-console" (deterministic, $0), or use the Edit tool to remove all \`console.${m}\` calls.`;
         }
         return null;
     }

package/dist/src/appliance/rvfa-distribution.js

@@ -9,7 +9,7 @@
  */
 import { createHash, sign, verify as edVerify } from 'node:crypto';
 import { readFile, writeFile, rename, unlink, copyFile, mkdir } from 'node:fs/promises';
-import { dirname } from 'node:path';
+import { basename, dirname } from 'node:path';
 import { request as httpsRequest } from 'node:https';
 import { gzipSync, gunzipSync } from 'node:zlib';
 import { RvfaReader, RvfaWriter } from './rvfa-format.js';
@@ -324,7 +324,7 @@ export class RvfaPublisher {
     }
     async publish(rvfaPath, meta) {
         const data = await readFile(rvfaPath);
-        const name = meta?.name || rvfaPath.split('/').pop() || 'appliance.rvf';
+        const name = meta?.name || basename(rvfaPath) || 'appliance.rvf';
         return this.upload(name, data, {
             type: 'rvfa-appliance', version: meta?.version || '',
             profile: meta?.profile || '', description: meta?.description || '',

package/dist/src/benchmarks/gaia-critic.d.ts

@@ -10,8 +10,7 @@
  * without requiring better search backends.  Expected L1 lift: +3-5pp.
  *
  * Design:
- *  - NEW file only; NOT wired into gaia-bench.ts yet to avoid merge conflicts
- *    with in-flight iter 29/31/34 branches.  Wiring is a small follow-up PR.
+ *  - gaia-bench.ts loads the wrapper when critic review is enabled.
  *  - `criticReview()` — single Sonnet call, returns structured verdict.
  *  - `runGaiaAgentWithCritic()` — orchestration wrapper: runs agent, calls
  *    critic, retries once on "fail".  "uncertain" is treated as "pass" (don't
@@ -25,11 +24,6 @@
  *  - One critic call + one optional retry = max 2 extra Sonnet calls per Q.
  *  - Approximate extra cost per question: ~$0.003-0.005 (well within budget).
  *
- * Plugin sync TODO (follow-up PR after gaia-bench wiring):
- *  - Update plugins/ruflo-workflows/commands/gaia-run.md with --enable-critic flag.
- *  - Update plugins/ruflo-workflows/skills/gaia-debugging/SKILL.md: add critic
- *    as a recommended diagnostic step for wrong-answer analysis.
- *
  * Refs: ADR-135, ADR-133, iter 29 finding, #2156
  */
 import { GaiaQuestion } from './gaia-loader.js';

package/dist/src/benchmarks/gaia-critic.js

@@ -10,8 +10,7 @@
  * without requiring better search backends.  Expected L1 lift: +3-5pp.
  *
  * Design:
- *  - NEW file only; NOT wired into gaia-bench.ts yet to avoid merge conflicts
- *    with in-flight iter 29/31/34 branches.  Wiring is a small follow-up PR.
+ *  - gaia-bench.ts loads the wrapper when critic review is enabled.
  *  - `criticReview()` — single Sonnet call, returns structured verdict.
  *  - `runGaiaAgentWithCritic()` — orchestration wrapper: runs agent, calls
  *    critic, retries once on "fail".  "uncertain" is treated as "pass" (don't
@@ -25,11 +24,6 @@
  *  - One critic call + one optional retry = max 2 extra Sonnet calls per Q.
  *  - Approximate extra cost per question: ~$0.003-0.005 (well within budget).
  *
- * Plugin sync TODO (follow-up PR after gaia-bench wiring):
- *  - Update plugins/ruflo-workflows/commands/gaia-run.md with --enable-critic flag.
- *  - Update plugins/ruflo-workflows/skills/gaia-debugging/SKILL.md: add critic
- *    as a recommended diagnostic step for wrong-answer analysis.
- *
  * Refs: ADR-135, ADR-133, iter 29 finding, #2156
  */
 import { execSync } from 'node:child_process';

package/dist/src/benchmarks/gaia-decomposer.d.ts

@@ -11,9 +11,7 @@
  * Expected L1 lift: +5-10pp on multi-step questions (~30-40% of L1 set).
  *
  * Design:
- *  - NEW standalone file only; NOT wired into gaia-bench.ts to avoid merge
- *    conflicts with in-flight iter 29/31/34/35/36 branches.
- *    Wiring is a small follow-up PR.
+ *  - gaia-bench.ts loads the decomposer when decomposition is enabled.
  *  - `decomposeQuestion()` — Haiku-cheap classification + decomposition
  *    (~$0.0003 per question).
  *  - `synthesizeFromSubAnswers()` — Sonnet synthesis from sub-answers
@@ -26,11 +24,6 @@
  *  - Synthesis uses claude-sonnet-4-6 (~$0.002/question).
  *  - Total overhead per question (when decomposed): ~$0.002-0.003.
  *
- * Plugin sync TODO (follow-up PR after gaia-bench wiring):
- *  - Update plugins/ruflo-workflows/commands/gaia-run.md with --decompose flag.
- *  - Update plugins/ruflo-workflows/skills/gaia-debugging/SKILL.md: add
- *    decomposition as a recommended strategy for multi-step failures.
- *
  * Refs: ADR-135, ADR-133, iter 29 finding, #2156
  */
 export interface DecomposedQuestion {

package/dist/src/benchmarks/gaia-decomposer.js

@@ -11,9 +11,7 @@
  * Expected L1 lift: +5-10pp on multi-step questions (~30-40% of L1 set).
  *
  * Design:
- *  - NEW standalone file only; NOT wired into gaia-bench.ts to avoid merge
- *    conflicts with in-flight iter 29/31/34/35/36 branches.
- *    Wiring is a small follow-up PR.
+ *  - gaia-bench.ts loads the decomposer when decomposition is enabled.
  *  - `decomposeQuestion()` — Haiku-cheap classification + decomposition
  *    (~$0.0003 per question).
  *  - `synthesizeFromSubAnswers()` — Sonnet synthesis from sub-answers
@@ -26,11 +24,6 @@
  *  - Synthesis uses claude-sonnet-4-6 (~$0.002/question).
  *  - Total overhead per question (when decomposed): ~$0.002-0.003.
  *
- * Plugin sync TODO (follow-up PR after gaia-bench wiring):
- *  - Update plugins/ruflo-workflows/commands/gaia-run.md with --decompose flag.
- *  - Update plugins/ruflo-workflows/skills/gaia-debugging/SKILL.md: add
- *    decomposition as a recommended strategy for multi-step failures.
- *
  * Refs: ADR-135, ADR-133, iter 29 finding, #2156
  */
 import { execSync } from 'node:child_process';

package/dist/src/commands/agent-wasm.js

@@ -146,7 +146,7 @@ export const wasmCreateCommand = {
                 info = await wasm.createWasmAgent({
                     model: ctx.flags.model,
                     instructions: ctx.flags.instructions,
-                    maxTurns: ctx.flags['max-turns'],
+                    maxTurns: ctx.flags.maxTurns,
                 });
             }
             if (ctx.flags.format === 'json') {
@@ -201,7 +201,7 @@ export const wasmPromptCommand = {
         { command: 'claude-flow agent wasm-prompt -a wasm-agent-1-abc -i "Write a hello world"', description: 'Send prompt to WASM agent' },
     ],
     action: async (ctx) => {
-        const agentId = ctx.flags['agent-id'] || ctx.args[0];
+        const agentId = ctx.flags.agentId || ctx.args[0];
         const promptInput = ctx.flags.input || ctx.args[1];
         if (!agentId) {
             output.printError('Agent ID is required. Use --agent-id or -a');

package/dist/src/commands/analyze.js

@@ -1556,7 +1556,7 @@ const modulesCommand = {
         const targetDir = ctx.args[0] || ctx.cwd;
         const outputFile = ctx.flags.output;
         const format = ctx.flags.format || 'text';
-        const minSize = ctx.flags['min-size'] || 2;
+        const minSize = ctx.flags.minSize || 2;
         output.printInfo(`Detecting module communities in: ${output.highlight(targetDir)}`);
         output.writeln();
         const spinner = output.createSpinner({ text: 'Building dependency graph...', spinner: 'dots' });

package/dist/src/commands/daemon.js

@@ -1247,7 +1247,7 @@ const statusCommand = {
     ],
     action: async (ctx) => {
         const verbose = ctx.flags.verbose;
-        const showModes = ctx.flags['show-modes'];
+        const showModes = ctx.flags.showModes;
         // #2356: global view across every workspace, not just cwd.
         if (ctx.flags.all) {
             return renderAllDaemonsStatus();

package/dist/src/commands/doctor.js

@@ -7,6 +7,7 @@
 import { output } from '../output.js';
 import { existsSync, readFileSync, statSync, openSync, readSync, closeSync } from 'fs';
 import { join, dirname } from 'path';
+import { homedir } from 'node:os';
 import { fileURLToPath, pathToFileURL } from 'url';
 import { createHash } from 'crypto';
 import { ownInstallAncestors } from '../plugins/own-install.js';
@@ -182,7 +183,7 @@ async function checkStaleSettingsNpx() {
     // Look in both project-local and home-dir settings.
     const candidates = [
         join(process.cwd(), '.claude', 'settings.json'),
-        join(process.env.HOME ?? '', '.claude', 'settings.json'),
+        join(homedir(), '.claude', 'settings.json'),
     ].filter((p, i, a) => p && a.indexOf(p) === i);
     const offenders = [];
     for (const settingsPath of candidates) {
@@ -248,7 +249,7 @@ export async function checkHelperIntegrity(opts = {}) {
     const { verifyInstalledCriticalHelpers } = await import('../init/helper-integrity.js');
     const { CRITICAL_HELPERS, findPackageHelpersDir } = await import('../init/helper-refresh.js');
     const envLocked = /^(1|true|on|yes)$/i.test(String(process.env.RUFLO_HELPERS_LOCKED || ''));
-    const home = opts.homeDir ?? process.env.HOME ?? '';
+    const home = opts.homeDir ?? homedir();
     const dirs = [
         join(opts.cwd ?? process.cwd(), '.claude', 'helpers'),
         ...(home ? [join(home, '.claude', 'helpers')] : []),

package/dist/src/commands/guidance.js

@@ -34,7 +34,7 @@ const compileCommand = {
                 output.writeln(output.error(`Root guidance file not found: ${rootPath}`));
                 return { success: false, message: `File not found: ${rootPath}` };
             }
-            const modExport = ctx.flags['mod-projection'] === true;
+            const modExport = (ctx.flags.modProjection ?? ctx.flags['mod-projection']) === true;
             const checked = modExport ? await (await import('../guidance/mod-sources.js')).readModGuidanceSources({
                 rootPath, localPath, revision: String(ctx.flags.revision || ''),
             }) : undefined;
@@ -112,7 +112,7 @@ const retrieveCommand = {
         const task = ctx.flags.task;
         const rootPath = ctx.flags.root || './CLAUDE.md';
         const localPath = ctx.flags.local;
-        const maxShards = parseInt(ctx.flags['max-shards'] || '5', 10);
+        const maxShards = parseInt(String(ctx.flags.maxShards ?? ctx.flags['max-shards'] ?? 5), 10);
         const intentOverride = ctx.flags.intent;
         const jsonOutput = ctx.flags.json === true;
         if (!task) {
@@ -338,9 +338,9 @@ const optimizeCommand = {
         const rootPath = ctx.flags.root || './CLAUDE.md';
         const localPath = ctx.flags.local;
         const applyChanges = ctx.flags.apply === true;
-        const contextSize = (ctx.flags['context-size'] || 'standard');
-        const targetScore = parseInt(ctx.flags['target-score'] || '90', 10);
-        const maxIterations = parseInt(ctx.flags['max-iterations'] || '5', 10);
+        const contextSize = (ctx.flags.contextSize ?? ctx.flags['context-size'] ?? 'standard');
+        const targetScore = parseInt(String(ctx.flags.targetScore ?? ctx.flags['target-score'] ?? 90), 10);
+        const maxIterations = parseInt(String(ctx.flags.maxIterations ?? ctx.flags['max-iterations'] ?? 5), 10);
         const jsonOutput = ctx.flags.json === true;
         output.writeln();
         output.writeln(output.bold('Guidance Optimizer'));
@@ -437,10 +437,10 @@ const abTestCommand = {
         { command: 'claude-flow guidance ab-test --json', description: 'Output full report as JSON' },
     ],
     action: async (ctx) => {
-        const configAPath = ctx.flags['config-a'];
-        const configBPath = ctx.flags['config-b'] || './CLAUDE.md';
+        const configAPath = (ctx.flags.configA ?? ctx.flags['config-a']);
+        const configBPath = (ctx.flags.configB ?? ctx.flags['config-b'] ?? './CLAUDE.md');
         const tasksPath = ctx.flags.tasks;
-        const workDir = ctx.flags['work-dir'];
+        const workDir = (ctx.flags.workDir ?? ctx.flags['work-dir']);
         const jsonOutput = ctx.flags.json === true;
         output.writeln();
         output.writeln(output.bold('A/B Behavioral Benchmark'));
@@ -541,7 +541,7 @@ const modCandidatesCommand = {
     action: async (ctx) => {
         try {
             const { collectModCandidates } = await import('../guidance/mod-projection.js');
-            const data = await collectModCandidates(String(ctx.flags.directory || '.claude-flow/mods/guidance/observations'), ctx.flags['bundle-id']);
+            const data = await collectModCandidates(String(ctx.flags.directory || '.claude-flow/mods/guidance/observations'), (ctx.flags.bundleId ?? ctx.flags['bundle-id']));
             output.writeln(JSON.stringify(data, null, ctx.flags.json === true ? undefined : 2));
             return { success: true, data };
         }

package/dist/src/commands/hooks.js

@@ -2529,8 +2529,8 @@ const workerDetectCommand = {
     ],
     action: async (ctx) => {
         const prompt = ctx.flags['prompt'];
-        const autoDispatch = ctx.flags['auto-dispatch'];
-        const minConfidence = parseFloat(ctx.flags['min-confidence'] || '0.5');
+        const autoDispatch = (ctx.flags.autoDispatch ?? ctx.flags['auto-dispatch']);
+        const minConfidence = parseFloat(String(ctx.flags.minConfidence ?? ctx.flags['min-confidence'] ?? 0.5) || '0.5');
         if (!prompt) {
             output.printError('--prompt is required');
             return { success: false, exitCode: 1 };
@@ -2570,7 +2570,12 @@ const workerDetectCommand = {
             }
             if (result.autoDispatched && result.workerIds) {
                 output.writeln();
-                output.writeln(output.success('Workers auto-dispatched:'));
+                if (result.autoDispatchStatus === 'synthetic-completed') {
+                    output.printWarning(result.note ?? 'No executor ran. Worker records are synthetic placeholders.');
+                }
+                else {
+                    output.writeln(output.success('Workers auto-dispatched:'));
+                }
                 result.workerIds.forEach(id => {
                     output.writeln(`  - ${id}`);
                 });
@@ -3079,8 +3084,8 @@ const coverageGapsCommand = {
     ],
     action: async (ctx) => {
         const threshold = ctx.flags.threshold ?? 80;
-        const groupByAgent = ctx.flags['group-by-agent'] !== false;
-        const criticalOnly = ctx.flags['critical-only'] || false;
+        const groupByAgent = (ctx.flags.groupByAgent ?? ctx.flags['group-by-agent']) !== false;
+        const criticalOnly = (ctx.flags.criticalOnly ?? ctx.flags['critical-only']) === true;
         const spinner = output.createSpinner({ text: 'Analyzing project coverage gaps...' });
         spinner.start();
         // Try reading coverage from disk first
@@ -4161,7 +4166,7 @@ const modelRouteCommand = {
         { name: 'task', short: 't', type: 'string', description: 'Task description to route', required: true },
         { name: 'context', short: 'c', type: 'string', description: 'Additional context' },
         { name: 'prefer-cost', type: 'boolean', description: 'Prefer lower cost models' },
-        { name: 'prefer-quality', type: 'boolean', description: 'Prefer higher quality models' },
+        { name: 'prefer-speed', type: 'boolean', description: 'Prefer faster models when possible' },
     ],
     examples: [
         { command: 'claude-flow hooks model-route -t "fix typo"', description: 'Route simple task (likely haiku)' },
@@ -4178,8 +4183,8 @@ const modelRouteCommand = {
             const result = await callMCPTool('hooks_model-route', {
                 task,
                 context: ctx.flags.context,
-                preferCost: ctx.flags['prefer-cost'],
-                preferQuality: ctx.flags['prefer-quality'],
+                preferCost: ctx.flags.preferCost,
+                preferSpeed: ctx.flags.preferSpeed,
             });
             if (ctx.flags.format === 'json') {
                 output.printJson(result);

package/dist/src/commands/init.js

@@ -816,16 +816,22 @@ const initClaudeAction = async (ctx) => {
         if (startDaemon || startAll) {
             output.writeln();
             output.printInfo('Starting services...');
-            const { execSync } = await import('child_process');
+            const { execFileSync } = await import('child_process');
+            // #4770: drop stderr via stdio, not a shell redirect (breaks on cmd.exe).
+            // shell on win32 so npx.cmd resolves (#2770); args are fixed literals.
+            const runCli = (args) => {
+                execFileSync('npx', ['@claude-flow/cli@latest', ...args], {
+                    stdio: ['ignore', 'pipe', 'ignore'],
+                    cwd: ctx.cwd,
+                    timeout: 30000,
+                    shell: process.platform === 'win32',
+                });
+            };
             // Initialize memory database
             if (startAll) {
                 try {
                     output.writeln(output.dim('  Initializing memory database...'));
-                    execSync('npx @claude-flow/cli@latest memory init 2>/dev/null', {
-                        stdio: 'pipe',
-                        cwd: ctx.cwd,
-                        timeout: 30000
-                    });
+                    runCli(['memory', 'init']);
                     output.writeln(output.success('  ✓ Memory initialized'));
                 }
                 catch {
@@ -854,11 +860,7 @@ const initClaudeAction = async (ctx) => {
             if (startDaemon) {
                 try {
                     output.writeln(output.dim('  Starting daemon...'));
-                    execSync('npx @claude-flow/cli@latest daemon start 2>/dev/null', {
-                        stdio: 'pipe',
-                        cwd: ctx.cwd,
-                        timeout: 30000
-                    });
+                    runCli(['daemon', 'start']);
                     output.writeln(output.success('  ✓ Daemon started'));
                 }
                 catch {
@@ -872,11 +874,7 @@ const initClaudeAction = async (ctx) => {
             if (startAll) {
                 try {
                     output.writeln(output.dim('  Initializing swarm...'));
-                    execSync('npx @claude-flow/cli@latest swarm init --topology hierarchical 2>/dev/null', {
-                        stdio: 'pipe',
-                        cwd: ctx.cwd,
-                        timeout: 30000
-                    });
+                    runCli(['swarm', 'init', '--topology', 'hierarchical']);
                     output.writeln(output.success('  ✓ Swarm initialized'));
                 }
                 catch {
@@ -1357,6 +1355,7 @@ const skillsCommand = {
         { name: 'github', description: 'Install GitHub skills', type: 'boolean', default: false },
         { name: 'v3', description: 'Install V3 skills', type: 'boolean', default: false },
         { name: 'legacy', description: 'Install skills that document commands v3 does not ship (stream-chain, sparc)', type: 'boolean', default: false },
+        { name: 'ecosystem', description: 'Install ecosystem skills (vector quantization, graph min-cut, sublinear solving, injection defense, fast edits, LoRA learning)', type: 'boolean', default: true },
     ],
     action: async (ctx) => {
         const options = {
@@ -1384,6 +1383,7 @@ const skillsCommand = {
                 v3: ctx.flags.v3,
                 dualMode: false,
                 legacy: ctx.flags.legacy,
+                ecosystem: ctx.flags.ecosystem,
             },
         };
         const spinner = output.createSpinner({ text: 'Installing skills...' });