@claude-flow/cli 3.32.1 → 3.32.3

package/dist/src/commands/init.js

@@ -1,1297 +0,0 @@
-/**
- * V3 CLI Init Command
- * Comprehensive initialization for Claude Flow with Claude Code integration
- */
-import { output } from '../output.js';
-import { confirm, select, multiSelect, input } from '../prompt.js';
-import * as fs from 'fs';
-import * as path from 'path';
-import { spawnSync } from 'node:child_process';
-import { executeInit, executeUpgrade, executeUpgradeWithMissing, DEFAULT_INIT_OPTIONS, MINIMAL_INIT_OPTIONS, FULL_INIT_OPTIONS, } from '../init/index.js';
-import { ENROLLMENT_SCREEN, recordEnrollmentOutcome, shouldOfferEnrollment, } from '../funnel/enrollment.js';
-import { commandExists } from '../services/harness-hosts.js';
-/**
- * ADR-302 post-init capability enrollment. One-time, interactive-TTY-only,
- * skippable with --no-signup, auto-skipped in CI/automation. Never throws
- * and never affects init's exit code. Accepting records the `account`
- * consent receipt only — no other capability is enabled by this prompt.
- */
-async function offerCapabilityEnrollment(ctx) {
-    try {
-        const noSignup = Boolean(ctx.flags['no-signup'] || ctx.flags.noSignup);
-        if (ctx.flags.format === 'json')
-            return; // scripted output stays pure
-        if (!shouldOfferEnrollment({ noSignup, cwd: ctx.cwd }))
-            return;
-        output.writeln();
-        output.writeln(ENROLLMENT_SCREEN);
-        output.writeln();
-        const accepted = await confirm({
-            message: 'Create a free Cognitum account now?',
-            default: false,
-        });
-        recordEnrollmentOutcome(Boolean(accepted));
-        output.writeln();
-        if (accepted) {
-            output.printInfo('Create your free account at https://cognitum.one');
-            output.writeln(output.dim('  CLI sign-in (`ruflo auth login`) ships with the ADR-306 auth release.'));
-        }
-        else {
-            output.writeln(output.dim('You can enable later at https://cognitum.one — this prompt will not repeat.'));
-        }
-    }
-    catch {
-        // Enrollment is optional; init success is never affected.
-    }
-}
-async function resolveCodexInitializer(cwd) {
-    // Use a variable to prevent TypeScript from statically resolving the optional module
-    const codexModuleId = '@claude-flow/codex';
-    const resolutionStrategies = [
-        // Strategy 1: Direct import (works if installed as CLI dependency)
-        async () => (await import(codexModuleId)).CodexInitializer,
-        // Strategy 2: Project node_modules (works if installed in user's project)
-        async () => {
-            const projectPath = path.join(cwd, 'node_modules', '@claude-flow', 'codex', 'dist', 'index.js');
-            if (fs.existsSync(projectPath)) {
-                const mod = await import(`file://${projectPath}`);
-                return mod.CodexInitializer;
-            }
-            throw new Error('Not found in project');
-        },
-        // Strategy 3: Global node_modules
-        async () => {
-            const { execSync } = await import('child_process');
-            const globalPath = execSync('npm root -g', { encoding: 'utf-8' }).trim();
-            const codexPath = path.join(globalPath, '@claude-flow', 'codex', 'dist', 'index.js');
-            if (fs.existsSync(codexPath)) {
-                const mod = await import(`file://${codexPath}`);
-                return mod.CodexInitializer;
-            }
-            throw new Error('Not found globally');
-        },
-    ];
-    for (const strategy of resolutionStrategies) {
-        try {
-            const ctor = await strategy();
-            if (ctor)
-                return ctor;
-        }
-        catch {
-            // Try next strategy
-        }
-    }
-    return undefined;
-}
-// Keep Codex out of the CLI dependency graph so cold `npx ruflo --version`
-// remains fast (#2561). An explicit `init --codex` may fetch the small,
-// stable adapter on demand when it is not already installed by an umbrella
-// package, the current project, or the global npm prefix.
-export function runCodexInitializerCli(cwd, options) {
-    const npxArgs = [
-        '-y',
-        '@claude-flow/codex@latest',
-        'init',
-        '--template',
-        options.template,
-        ...(options.force ? ['--force'] : []),
-        ...(options.dual ? ['--dual'] : []),
-    ];
-    const result = process.platform === 'win32'
-        ? spawnSync(process.env.ComSpec || 'cmd.exe', ['/d', '/s', '/c', ['npx', ...npxArgs].join(' ')], { cwd, stdio: 'inherit', windowsHide: true })
-        : spawnSync('npx', npxArgs, { cwd, stdio: 'inherit' });
-    if (result.error)
-        throw result.error;
-    return result.status === 0;
-}
-// #2666-adjacent — quietly wire up Codex too when a plain `ruflo init` (no
-// --codex/--dual) runs on a machine that also has the OpenAI Codex CLI on
-// PATH: registers its MCP server and installs skills alongside the Claude
-// Code setup that just happened. Best-effort and silent-by-default — must
-// never fail or noisily interrupt a normal init. Opt out with
-// --no-codex-detect. Skipped entirely under --skip-claude (runtime-only
-// init) and scripted `--format json` output.
-async function maybeAutoDetectCodex(ctx, options) {
-    try {
-        if (ctx.flags['no-codex-detect'] === true)
-            return;
-        if (ctx.flags.format === 'json')
-            return; // scripted output stays pure
-        if (!commandExists('codex'))
-            return;
-        const CodexInitializer = await resolveCodexInitializer(ctx.cwd);
-        if (!CodexInitializer) {
-            output.writeln();
-            output.printInfo('Detected the OpenAI Codex CLI — install @claude-flow/codex to auto-configure its MCP server and skills:');
-            output.writeln(output.dim('  npm install @claude-flow/codex && ruflo init --codex'));
-            return;
-        }
-        const initializer = new CodexInitializer();
-        const result = await initializer.initialize({
-            projectPath: ctx.cwd,
-            template: (options.minimal ? 'minimal' : options.full ? 'full' : 'default'),
-            force: options.force,
-            dual: false, // Claude Code files were already written by the main init flow above
-        });
-        if (!result.success)
-            return; // best-effort — never fail the primary init over this
-        output.writeln();
-        output.printBox([
-            `AGENTS.md:            Codex project instructions`,
-            `.agents/config.toml:  MCP server + skills config`,
-            `.agents/skills/:      ${result.skillsGenerated.length} skills`,
-        ].join('\n'), 'OpenAI Codex detected — configured');
-    }
-    catch {
-        // Codex auto-detect is a bonus, never a requirement — swallow everything.
-    }
-}
-// Cross-agent skill registration via skills.sh. Runs `npx --yes skills add
-// ruvnet/ruflo --skill ruflo --yes` so the *single* canonical ruflo skill
-// (SKILL.md at the ruvnet/ruflo repo root — describes the platform + entry
-// points) reaches whatever agent the project uses (Claude Code, Cursor,
-// Copilot, Gemini, Cline, …). Users who want ALL 267 plugin-specific skills
-// can run `npx skills add ruvnet/ruflo --all` themselves. Best-effort — never
-// fails init. Opt-out: --no-skills-sh flag OR RUFLO_NO_SKILLS_SH=1. Skipped
-// under --skip-claude and scripted `--format json` output.
-//
-// windowsHide silences the console flash the npx child would otherwise produce
-// (anthropics/claude-code#14828 spawn hazard applies to hook-fired spawns,
-// but our own subprocess spawns should always set this).
-async function maybeInstallSkillsSh(ctx) {
-    try {
-        if (ctx.flags['no-skills-sh'] === true)
-            return;
-        if (ctx.flags.format === 'json')
-            return;
-        if (/^(1|true|on|yes)$/i.test(String(process.env.RUFLO_NO_SKILLS_SH || '')))
-            return;
-        // Idempotency gate: if this project has already registered ruflo with
-        // skills.sh, don't re-clone the repo + re-fire a fresh install telemetry
-        // event on every `ruflo init --force` / `init upgrade` / etc. Each install
-        // pings skills.sh's leaderboard AND clones the whole ruvnet/ruflo repo
-        // (~50MB) — re-running per-init would silently inflate our own metrics
-        // (GitHub unique-cloners, skills.sh rank) and waste user bandwidth. This
-        // check makes the registration once-per-project, matching the intent.
-        const nodePath = await import('path');
-        const nodeFs = await import('fs');
-        const marker = nodePath.join(ctx.cwd, '.agents', 'skills', 'ruflo');
-        if (nodeFs.existsSync(marker)) {
-            output.writeln();
-            output.writeln(output.dim('  skills.sh registration already present at .agents/skills/ruflo — skipping'));
-            return;
-        }
-        const npxCmd = process.platform === 'win32' ? 'npx.cmd' : 'npx';
-        if (!commandExists('npx'))
-            return;
-        output.writeln();
-        output.printInfo('Registering the core `ruflo` skill with skills.sh (cross-agent catalog)…');
-        const { spawnSync } = await import('child_process');
-        const result = spawnSync(npxCmd, ['--yes', 'skills', 'add', 'ruvnet/ruflo', '--skill', 'ruflo', '--yes'], { cwd: ctx.cwd, stdio: 'pipe', timeout: 60_000, windowsHide: true, encoding: 'utf-8' });
-        if (result.status === 0) {
-            output.writeln(output.success('  ✓ ruflo registered via skills.sh — the platform skill is available to any agent in this project'));
-            output.writeln(output.dim('    Want all 267 plugin skills? npx skills add ruvnet/ruflo --all'));
-            output.writeln(output.dim('    Opt out next time: --no-skills-sh or RUFLO_NO_SKILLS_SH=1'));
-        }
-        else {
-            // Common non-fatal reasons: offline, npx cache miss, skills CLI version
-            // mismatch, unknown package. Log a soft note; users can retry manually.
-            output.writeln(output.dim('  skills.sh registration skipped (network or npx cache) — retry with: npx skills add ruvnet/ruflo --skill ruflo --yes'));
-        }
-    }
-    catch {
-        // Skills.sh registration is a bonus, never a requirement — swallow everything.
-    }
-}
-// Codex initialization action
-async function initCodexAction(ctx, options) {
-    const { force, minimal, full, dualMode } = options;
-    output.writeln();
-    output.writeln(output.bold('Initializing RuFlo V3 for OpenAI Codex'));
-    output.writeln();
-    // Determine template
-    const template = minimal ? 'minimal' : full ? 'full' : 'default';
-    const spinner = output.createSpinner({ text: 'Initializing Codex project...' });
-    spinner.start();
-    try {
-        const CodexInitializer = await resolveCodexInitializer(ctx.cwd);
-        if (!CodexInitializer) {
-            spinner.stop();
-            output.printInfo('Fetching the stable Codex adapter for this initialization...');
-            const success = runCodexInitializerCli(ctx.cwd, { template, force, dual: dualMode });
-            if (!success) {
-                output.printError('Codex initialization failed while running @claude-flow/codex@latest.');
-                return { success: false, exitCode: 1 };
-            }
-            return { success: true, data: { adapter: '@claude-flow/codex@latest' } };
-        }
-        const initializer = new CodexInitializer();
-        const result = await initializer.initialize({
-            projectPath: ctx.cwd,
-            template: template,
-            force,
-            dual: dualMode,
-        });
-        if (!result.success) {
-            spinner.fail('Codex initialization failed');
-            if (result.errors) {
-                for (const error of result.errors) {
-                    output.printError(error);
-                }
-            }
-            return { success: false, exitCode: 1 };
-        }
-        spinner.succeed('Codex project initialized successfully!');
-        output.writeln();
-        // Display summary
-        const summary = [];
-        summary.push(`Files: ${result.filesCreated.length} created`);
-        summary.push(`Skills: ${result.skillsGenerated.length} installed`);
-        output.printBox(summary.join('\n'), 'Summary');
-        output.writeln();
-        // Show what was created
-        output.printBox([
-            `AGENTS.md:     Main project instructions`,
-            `.agents/config.toml: Project configuration`,
-            `.agents/skills/: ${result.skillsGenerated.length} skills`,
-            `.codex/: Local overrides (gitignored)`,
-            dualMode ? `CLAUDE.md: Claude Code compatibility` : '',
-        ].filter(Boolean).join('\n'), 'OpenAI Codex Integration');
-        output.writeln();
-        // Warnings
-        if (result.warnings && result.warnings.length > 0) {
-            output.printWarning('Warnings:');
-            for (const warning of result.warnings.slice(0, 5)) {
-                output.printInfo(`  • ${warning}`);
-            }
-            if (result.warnings.length > 5) {
-                output.printInfo(`  ... and ${result.warnings.length - 5} more`);
-            }
-            output.writeln();
-        }
-        // Next steps
-        output.writeln(output.bold('Next steps:'));
-        output.printList([
-            `Review ${output.highlight('AGENTS.md')} for project instructions`,
-            `Add skills with ${output.highlight('$skill-name')} syntax`,
-            `Configure ${output.highlight('.agents/config.toml')} for your project`,
-            dualMode ? `Claude Code users can use ${output.highlight('CLAUDE.md')}` : '',
-        ].filter(Boolean));
-        return { success: true, data: result };
-    }
-    catch (error) {
-        spinner.fail('Codex initialization failed');
-        const errorMessage = error instanceof Error ? error.message : String(error);
-        // Handle module not found error gracefully
-        if (errorMessage.includes('Cannot find module') || errorMessage.includes('@claude-flow/codex')) {
-            output.printError('The @claude-flow/codex package is not installed.');
-            output.printInfo('Install it with: npm install @claude-flow/codex');
-            output.writeln();
-            output.printInfo('Alternatively, copy skills manually from .claude/skills/ to .agents/skills/');
-        }
-        else {
-            output.printError(`Failed to initialize: ${errorMessage}`);
-        }
-        return { success: false, exitCode: 1 };
-    }
-}
-// Check if project is already initialized with ruflo.
-// #2207: .claude/settings.json alone is NOT a ruflo marker — it's created by
-// Claude Code itself and exists in every Claude Code project. We require a
-// ruflo-specific signal: either a claudeFlow section in settings.json, OR a
-// .mcp.json with a 'claude-flow' or 'ruflo' server key, OR the ruflo-only
-// .claude-flow/config.yaml. Using the bare file-existence check was causing
-// false-positives for new users whose only existing file was Claude Code's own
-// settings.json.
-function isInitialized(cwd) {
-    const claudeFlowPath = path.join(cwd, '.claude-flow', 'config.yaml');
-    const mcpJsonPath = path.join(cwd, '.mcp.json');
-    const settingsPath = path.join(cwd, '.claude', 'settings.json');
-    // Check .claude-flow/config.yaml — ruflo-specific, always reliable
-    const hasClaudeFlow = fs.existsSync(claudeFlowPath);
-    // Check .claude/settings.json for ruflo-specific content (claudeFlow section)
-    let hasRufloSettings = false;
-    if (fs.existsSync(settingsPath)) {
-        try {
-            const parsed = JSON.parse(fs.readFileSync(settingsPath, 'utf-8'));
-            hasRufloSettings =
-                parsed != null &&
-                    typeof parsed === 'object' &&
-                    'claudeFlow' in parsed;
-        }
-        catch { /* malformed — ignore */ }
-    }
-    // Check .mcp.json for ruflo/claude-flow server key
-    let hasRufloMcp = false;
-    if (fs.existsSync(mcpJsonPath)) {
-        try {
-            const parsed = JSON.parse(fs.readFileSync(mcpJsonPath, 'utf-8'));
-            hasRufloMcp =
-                parsed != null &&
-                    typeof parsed === 'object' &&
-                    parsed.mcpServers != null &&
-                    typeof parsed.mcpServers === 'object' &&
-                    ('claude-flow' in parsed.mcpServers ||
-                        'ruflo' in parsed.mcpServers);
-        }
-        catch { /* malformed — ignore */ }
-    }
-    return {
-        claude: hasRufloSettings || hasRufloMcp,
-        claudeFlow: hasClaudeFlow,
-    };
-}
-// Init subcommand (default)
-const initAction = async (ctx) => {
-    const force = ctx.flags.force;
-    const minimal = ctx.flags.minimal;
-    const full = ctx.flags.full;
-    const skipClaude = ctx.flags['skip-claude'];
-    const onlyClaude = ctx.flags['only-claude'];
-    // #2098A — the parser handles `--no-foo` by stripping the prefix and
-    // storing `flags.foo = false` (parser.ts:291-294), not by storing
-    // `flags['no-foo'] = true`. So `--no-global` lands as
-    // `ctx.flags.global === false`. The old read of `flags['no-global']`
-    // was always undefined and silently no-op'd — every user with the flag
-    // set still got `~/.claude/CLAUDE.md` modified. Read the real key.
-    const noGlobal = ctx.flags['no-global'] === true || ctx.flags['global'] === false;
-    const allAgents = ctx.flags['all-agents'];
-    const cloudMcp = ctx.flags['cloud-mcp'];
-    const codexMode = ctx.flags.codex;
-    const dualMode = ctx.flags.dual;
-    const cwd = ctx.cwd;
-    // If codex mode, use the Codex initializer
-    if (codexMode || dualMode) {
-        return initCodexAction(ctx, { codexMode, dualMode, force, minimal, full });
-    }
-    // Check if already initialized
-    const initialized = isInitialized(cwd);
-    const hasExisting = initialized.claude || initialized.claudeFlow;
-    if (hasExisting && !force) {
-        output.printWarning('RuFlo appears to be already initialized');
-        if (initialized.claude)
-            output.printInfo('  Found: .claude/settings.json');
-        if (initialized.claudeFlow)
-            output.printInfo('  Found: .claude-flow/config.yaml');
-        output.printInfo('Use --force to reinitialize');
-        if (ctx.interactive) {
-            const proceed = await confirm({
-                message: 'Do you want to reinitialize? This will overwrite existing configuration.',
-                default: false,
-            });
-            if (!proceed) {
-                return { success: true, message: 'Initialization cancelled' };
-            }
-        }
-        else {
-            return { success: false, exitCode: 1, message: 'Already initialized' };
-        }
-    }
-    output.writeln();
-    output.writeln(output.bold('Initializing RuFlo V3'));
-    output.writeln();
-    // Build init options based on flags
-    let options;
-    if (minimal) {
-        options = { ...MINIMAL_INIT_OPTIONS, targetDir: cwd, force };
-    }
-    else if (full) {
-        options = { ...FULL_INIT_OPTIONS, targetDir: cwd, force };
-        // #2356: keep auth-gated cloud MCP servers opt-in even under --full. They
-        // require a login, get committed into .mcp.json, and add per-session MCP
-        // tool-definition token cost. --cloud-mcp restores the all-three behavior.
-        if (!cloudMcp) {
-            options.mcp = { ...options.mcp, ruvSwarm: false, flowNexus: false };
-        }
-    }
-    else {
-        options = { ...DEFAULT_INIT_OPTIONS, targetDir: cwd, force };
-    }
-    // Handle --skip-claude and --only-claude flags
-    if (skipClaude) {
-        options.components.settings = false;
-        options.components.skills = false;
-        options.components.commands = false;
-        options.components.agents = false;
-        options.components.helpers = false;
-        options.components.statusline = false;
-        options.components.mcp = false;
-        options.components.claudeMd = false;
-    }
-    if (onlyClaude) {
-        options.components.runtime = false;
-    }
-    // ADR-128 Phase 3 — restore full agent set (98 agents) when user explicitly
-    // requests it. Default is the ~24-agent substrate (core, consensus, swarm,
-    // sparc, testing). Pass --all-agents to get the old behavior.
-    if (allAgents) {
-        options.agents.all = true;
-    }
-    // #1744 — opt-out of the user-global ~/.claude/CLAUDE.md "Ruflo Integration"
-    // pointer block. Default behavior (off) preserves current install for users
-    // who rely on it; opting in via --no-global keeps the global file pristine.
-    if (noGlobal) {
-        options.skipGlobalClaudeMd = true;
-    }
-    // Create spinner
-    const spinner = output.createSpinner({ text: 'Initializing...' });
-    spinner.start();
-    try {
-        // Execute initialization
-        const result = await executeInit(options);
-        if (!result.success) {
-            spinner.fail('Initialization failed');
-            for (const error of result.errors) {
-                output.printError(error);
-            }
-            return { success: false, exitCode: 1 };
-        }
-        spinner.succeed('RuFlo V3 initialized successfully!');
-        output.writeln();
-        // Display summary
-        const summary = [];
-        if (result.created.directories.length > 0) {
-            summary.push(`Directories: ${result.created.directories.length} created`);
-        }
-        if (result.created.files.length > 0) {
-            summary.push(`Files: ${result.created.files.length} created`);
-        }
-        if (result.skipped.length > 0) {
-            summary.push(`Skipped: ${result.skipped.length} (already exist)`);
-        }
-        output.printBox(summary.join('\n'), 'Summary');
-        output.writeln();
-        // Show what was created
-        if (options.components.claudeMd || options.components.settings || options.components.skills || options.components.commands || options.components.agents) {
-            output.printBox([
-                options.components.claudeMd ? `CLAUDE.md:   Swarm guidance & configuration` : '',
-                options.components.settings ? `Settings:    .claude/settings.json` : '',
-                options.components.skills ? `Skills:      .claude/skills/ (${result.summary.skillsCount} skills)` : '',
-                options.components.commands ? `Commands:    .claude/commands/ (${result.summary.commandsCount} commands)` : '',
-                options.components.agents ? `Agents:      .claude/agents/ (${result.summary.agentsCount} agents)` : '',
-                options.components.helpers ? `Helpers:     .claude/helpers/` : '',
-                options.components.mcp ? `MCP:         .mcp.json` : '',
-            ].filter(Boolean).join('\n'), 'Claude Code Integration');
-            output.writeln();
-        }
-        if (options.components.runtime) {
-            output.printBox([
-                `Config:      .claude-flow/config.yaml`,
-                `Data:        .claude-flow/data/`,
-                `Logs:        .claude-flow/logs/`,
-                `Sessions:    .claude-flow/sessions/`,
-            ].join('\n'), 'V3 Runtime');
-            output.writeln();
-        }
-        // Hooks summary
-        if (result.summary.hooksEnabled > 0) {
-            output.printInfo(`Hooks: ${result.summary.hooksEnabled} hook types enabled in settings.json`);
-            output.writeln();
-        }
-        // #2666-adjacent — auto-detect + configure OpenAI Codex CLI if present
-        if (!skipClaude) {
-            await maybeAutoDetectCodex(ctx, { force, minimal, full });
-            await maybeInstallSkillsSh(ctx);
-        }
-        // Handle --start-all or --start-daemon
-        const startAll = ctx.flags['start-all'] || ctx.flags.startAll;
-        const startDaemon = ctx.flags['start-daemon'] || ctx.flags.startDaemon || startAll;
-        if (startDaemon || startAll) {
-            output.writeln();
-            output.printInfo('Starting services...');
-            const { execSync } = await import('child_process');
-            // 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
-                    });
-                    output.writeln(output.success('  ✓ Memory initialized'));
-                }
-                catch {
-                    output.writeln(output.dim('  Memory database already exists'));
-                }
-            }
-            // Start daemon — #2407 fix
-            //
-            // The previous version used `daemon start ... &` (shell background)
-            // which made execSync return as soon as the shell forked, BEFORE the
-            // daemon process wrote its PID file. Concurrent init runs
-            // (devcontainer setup + VS Code task + MCP hook firing within ~500 ms)
-            // all saw an empty PID file via getBackgroundDaemonPid(), so
-            // daemon.ts:99-103's dedup short-circuit didn't fire — every caller
-            // spawned its own daemon. One incident accumulated 39 zombie daemons
-            // holding ~8.5 GiB resident, which together with macOS compressor
-            // pressure (27 GiB compressed) caused the configd watchdog timeout
-            // and the 2026-06-15 21:06 kernel panic.
-            //
-            // Fix: drop the shell `&`. `daemon start` (default non-foreground
-            // mode) already forks its own detached background process via
-            // startBackgroundDaemon() AND writes the PID file BEFORE returning,
-            // so execSync without `&` waits for the dedup-relevant PID-file
-            // write but does NOT wait for the daemon itself to exit. Timeout
-            // bumped to 30s for npx cold-cache scenarios.
-            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
-                    });
-                    output.writeln(output.success('  ✓ Daemon started'));
-                }
-                catch {
-                    // Daemon dedup hit (already running) OR spawn timed out.
-                    // Either way the worst case is a single retry on next init,
-                    // not a forked race producing N zombies.
-                    output.writeln(output.warning('  Daemon may already be running'));
-                }
-            }
-            // Initialize swarm
-            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
-                    });
-                    output.writeln(output.success('  ✓ Swarm initialized'));
-                }
-                catch {
-                    output.writeln(output.dim('  Swarm initialization skipped'));
-                }
-            }
-            output.writeln();
-            output.printSuccess('All services started');
-        }
-        // Handle --with-embeddings
-        const withEmbeddings = ctx.flags['with-embeddings'] || ctx.flags.withEmbeddings;
-        const embeddingModel = (ctx.flags['embedding-model'] || ctx.flags.embeddingModel || 'Xenova/all-MiniLM-L6-v2');
-        if (withEmbeddings) {
-            output.writeln();
-            output.printInfo('Initializing ONNX embedding subsystem...');
-            const { execFileSync: execFileInit } = await import('child_process');
-            // Validate embeddingModel: must match pattern org/model-name (CRIT-02)
-            if (!/^[a-zA-Z0-9_-]+\/[a-zA-Z0-9._-]+$/.test(embeddingModel)) {
-                throw new Error(`Invalid embedding model name: ${embeddingModel}`);
-            }
-            try {
-                output.writeln(output.dim(`  Model: ${embeddingModel}`));
-                output.writeln(output.dim('  Hyperbolic: Enabled (Poincaré ball)'));
-                execFileInit('npx', [
-                    '@claude-flow/cli@latest', 'embeddings', 'init',
-                    '--model', embeddingModel,
-                    '--no-download', '--force',
-                ], {
-                    stdio: 'pipe',
-                    cwd: ctx.cwd,
-                    timeout: 30000,
-                });
-                output.writeln(output.success('  ✓ Embeddings initialized'));
-                output.writeln(output.dim('    Run "embeddings init --download" to download model'));
-            }
-            catch (err) {
-                output.writeln(output.warning('  Embedding initialization skipped (run manually)'));
-            }
-        }
-        if (!startDaemon && !startAll) {
-            const bin = (process.argv[1] || '').includes('ruflo') ? 'ruflo' : 'claude-flow';
-            output.writeln(output.bold('Next steps:'));
-            output.printList([
-                `Run ${output.highlight(`${bin} daemon start`)} to start background workers`,
-                // Memory is initialized automatically during init (persistent by
-                // default — see executor.ts) — no separate `memory init` step needed
-                // unless the DB was skipped (MINIMAL_INIT_OPTIONS) or needs --force.
-                `Run ${output.highlight(`${bin} swarm init`)} to initialize a swarm`,
-                `Or use ${output.highlight(`${bin} init --start-all`)} to do all of the above`,
-                options.components.settings ? `Review ${output.highlight('.claude/settings.json')} for hook configurations` : '',
-                // ADR-150 — surface the new metaharness scorecard to every new user.
-                // Optional dep; the command degrades gracefully when not installed.
-                `Run ${output.highlight(`${bin} metaharness score`)} for a 5-dim harness readiness scorecard (ADR-150)`,
-            ].filter(Boolean));
-        }
-        if (ctx.flags.format === 'json') {
-            output.printJson(result);
-        }
-        await offerCapabilityEnrollment(ctx);
-        return { success: true, data: result };
-    }
-    catch (error) {
-        spinner.fail('Initialization failed');
-        output.printError(`Failed to initialize: ${error instanceof Error ? error.message : String(error)}`);
-        return { success: false, exitCode: 1 };
-    }
-};
-// Wizard subcommand for interactive setup
-const wizardCommand = {
-    name: 'wizard',
-    description: 'Interactive setup wizard for comprehensive configuration',
-    action: async (ctx) => {
-        output.writeln();
-        output.writeln(output.bold('RuFlo V3 Setup Wizard'));
-        output.writeln(output.dim('Answer questions to configure your project'));
-        output.writeln();
-        try {
-            // Start with base options
-            const options = { ...DEFAULT_INIT_OPTIONS, targetDir: ctx.cwd };
-            // Configuration preset
-            const preset = await select({
-                message: 'Select configuration preset:',
-                options: [
-                    { value: 'default', label: 'Default', hint: 'Recommended settings for most projects' },
-                    { value: 'minimal', label: 'Minimal', hint: 'Core features only' },
-                    { value: 'full', label: 'Full', hint: 'All features enabled' },
-                    { value: 'custom', label: 'Custom', hint: 'Choose each component' },
-                ],
-            });
-            if (preset === 'minimal') {
-                Object.assign(options, MINIMAL_INIT_OPTIONS);
-                options.targetDir = ctx.cwd;
-            }
-            else if (preset === 'full') {
-                Object.assign(options, FULL_INIT_OPTIONS);
-                options.targetDir = ctx.cwd;
-            }
-            else if (preset === 'custom') {
-                // Component selection
-                const components = await multiSelect({
-                    message: 'Select components to initialize:',
-                    options: [
-                        { value: 'claudeMd', label: 'CLAUDE.md', hint: 'Swarm guidance and project configuration', selected: true },
-                        { value: 'settings', label: 'settings.json', hint: 'Claude Code hooks configuration', selected: true },
-                        { value: 'skills', label: 'Skills', hint: 'Claude Code skills in .claude/skills/', selected: true },
-                        { value: 'commands', label: 'Commands', hint: 'Claude Code commands in .claude/commands/', selected: true },
-                        { value: 'agents', label: 'Agents', hint: 'Agent definitions in .claude/agents/', selected: true },
-                        { value: 'helpers', label: 'Helpers', hint: 'Utility scripts in .claude/helpers/', selected: true },
-                        { value: 'statusline', label: 'Statusline', hint: 'Shell statusline integration', selected: false },
-                        { value: 'mcp', label: 'MCP', hint: '.mcp.json for MCP server configuration', selected: true },
-                        { value: 'runtime', label: 'Runtime', hint: '.claude-flow/ directory for V3 runtime', selected: true },
-                    ],
-                });
-                options.components.claudeMd = components.includes('claudeMd');
-                options.components.settings = components.includes('settings');
-                options.components.skills = components.includes('skills');
-                options.components.commands = components.includes('commands');
-                options.components.agents = components.includes('agents');
-                options.components.helpers = components.includes('helpers');
-                options.components.statusline = components.includes('statusline');
-                options.components.mcp = components.includes('mcp');
-                options.components.runtime = components.includes('runtime');
-                // Skills selection
-                if (options.components.skills) {
-                    const skillSets = await multiSelect({
-                        message: 'Select skill sets:',
-                        options: [
-                            { value: 'core', label: 'Core', hint: 'Swarm, memory, SPARC skills', selected: true },
-                            { value: 'agentdb', label: 'AgentDB', hint: 'Vector database skills', selected: true },
-                            { value: 'github', label: 'GitHub', hint: 'GitHub integration skills', selected: true },
-                            { value: 'flowNexus', label: 'Flow Nexus', hint: 'Cloud platform skills', selected: false },
-                            { value: 'v3', label: 'V3', hint: 'V3 implementation skills', selected: true },
-                        ],
-                    });
-                    options.skills.core = skillSets.includes('core');
-                    options.skills.agentdb = skillSets.includes('agentdb');
-                    options.skills.github = skillSets.includes('github');
-                    options.skills.flowNexus = skillSets.includes('flowNexus');
-                    options.skills.v3 = skillSets.includes('v3');
-                }
-                // Hooks selection
-                if (options.components.settings) {
-                    const hooks = await multiSelect({
-                        message: 'Select hooks to enable:',
-                        options: [
-                            { value: 'preToolUse', label: 'PreToolUse', hint: 'Before tool execution', selected: true },
-                            { value: 'postToolUse', label: 'PostToolUse', hint: 'After tool execution', selected: true },
-                            { value: 'userPromptSubmit', label: 'UserPromptSubmit', hint: 'Task routing', selected: true },
-                            { value: 'sessionStart', label: 'SessionStart', hint: 'Session initialization', selected: true },
-                            { value: 'stop', label: 'Stop', hint: 'Task completion evaluation', selected: true },
-                            { value: 'notification', label: 'Notification', hint: 'Swarm notifications', selected: true },
-                            { value: 'permissionRequest', label: 'PermissionRequest', hint: 'Auto-allow claude-flow tools', selected: true },
-                        ],
-                    });
-                    options.hooks.preToolUse = hooks.includes('preToolUse');
-                    options.hooks.postToolUse = hooks.includes('postToolUse');
-                    options.hooks.userPromptSubmit = hooks.includes('userPromptSubmit');
-                    options.hooks.sessionStart = hooks.includes('sessionStart');
-                    options.hooks.stop = hooks.includes('stop');
-                    options.hooks.notification = hooks.includes('notification');
-                }
-            }
-            // Swarm topology (for all presets)
-            const topology = await select({
-                message: 'Select swarm topology:',
-                options: [
-                    { value: 'hierarchical-mesh', label: 'Hierarchical Mesh', hint: 'Best for complex projects (recommended)' },
-                    { value: 'mesh', label: 'Mesh', hint: 'Peer-to-peer coordination' },
-                    { value: 'hierarchical', label: 'Hierarchical', hint: 'Tree-based coordination' },
-                    { value: 'adaptive', label: 'Adaptive', hint: 'Dynamic topology switching' },
-                ],
-            });
-            options.runtime.topology = topology;
-            // Max agents
-            const maxAgents = await input({
-                message: 'Maximum concurrent agents:',
-                default: String(options.runtime.maxAgents),
-                validate: (v) => {
-                    const n = parseInt(v);
-                    return (!isNaN(n) && n > 0 && n <= 50) || 'Enter a number between 1 and 50';
-                },
-            });
-            options.runtime.maxAgents = parseInt(maxAgents);
-            // Memory backend
-            const memoryBackend = await select({
-                message: 'Select memory backend:',
-                options: [
-                    { value: 'hybrid', label: 'Hybrid', hint: 'SQLite + AgentDB (recommended)' },
-                    { value: 'agentdb', label: 'AgentDB', hint: '150x faster vector search' },
-                    { value: 'sqlite', label: 'SQLite', hint: 'Standard SQL storage' },
-                    { value: 'memory', label: 'In-Memory', hint: 'Fast but non-persistent' },
-                ],
-            });
-            options.runtime.memoryBackend = memoryBackend;
-            // HNSW indexing
-            if (memoryBackend === 'agentdb' || memoryBackend === 'hybrid') {
-                const enableHNSW = await confirm({
-                    message: 'Enable HNSW indexing for faster vector search?',
-                    default: true,
-                });
-                options.runtime.enableHNSW = enableHNSW;
-            }
-            // Neural learning
-            const enableNeural = await confirm({
-                message: 'Enable neural pattern learning?',
-                default: options.runtime.enableNeural,
-            });
-            options.runtime.enableNeural = enableNeural;
-            // ADR-049: Self-Learning Memory capabilities
-            if (memoryBackend === 'agentdb' || memoryBackend === 'hybrid') {
-                const enableSelfLearning = await confirm({
-                    message: 'Enable self-learning memory? (LearningBridge + Knowledge Graph + Agent Scopes)',
-                    default: true,
-                });
-                options.runtime.enableLearningBridge = enableSelfLearning && enableNeural;
-                options.runtime.enableMemoryGraph = enableSelfLearning;
-                options.runtime.enableAgentScopes = enableSelfLearning;
-            }
-            else {
-                options.runtime.enableLearningBridge = false;
-                options.runtime.enableMemoryGraph = false;
-                options.runtime.enableAgentScopes = false;
-            }
-            // Embeddings configuration
-            const enableEmbeddings = await confirm({
-                message: 'Enable ONNX embedding system with hyperbolic support?',
-                default: true,
-            });
-            let embeddingModel = 'Xenova/all-MiniLM-L6-v2';
-            if (enableEmbeddings) {
-                embeddingModel = await select({
-                    message: 'Select embedding model:',
-                    options: [
-                        { value: 'Xenova/all-MiniLM-L6-v2', label: 'MiniLM L6 (384d)', hint: 'Fast, good quality (recommended)' },
-                        { value: 'Xenova/all-mpnet-base-v2', label: 'MPNet Base (768d)', hint: 'Higher quality, more memory' },
-                    ],
-                });
-            }
-            // Execute initialization
-            output.writeln();
-            const spinner = output.createSpinner({ text: 'Initializing...' });
-            spinner.start();
-            const result = await executeInit(options);
-            if (!result.success) {
-                spinner.fail('Initialization failed');
-                for (const error of result.errors) {
-                    output.printError(error);
-                }
-                return { success: false, exitCode: 1 };
-            }
-            spinner.succeed('Setup complete!');
-            // Initialize embeddings if enabled
-            let embeddingsInitialized = false;
-            if (enableEmbeddings) {
-                output.writeln();
-                output.printInfo('Initializing ONNX embedding subsystem...');
-                const { execFileSync } = await import('child_process');
-                // Validate embeddingModel: must match pattern org/model-name (CRIT-02)
-                if (!/^[a-zA-Z0-9_-]+\/[a-zA-Z0-9._-]+$/.test(embeddingModel)) {
-                    throw new Error(`Invalid embedding model name: ${embeddingModel}`);
-                }
-                try {
-                    execFileSync('npx', [
-                        '@claude-flow/cli@latest', 'embeddings', 'init',
-                        '--model', embeddingModel,
-                        '--no-download', '--force',
-                    ], {
-                        stdio: 'pipe',
-                        cwd: ctx.cwd,
-                        timeout: 30000,
-                    });
-                    output.writeln(output.success('  ✓ Embeddings configured'));
-                    embeddingsInitialized = true;
-                }
-                catch {
-                    output.writeln(output.dim('  Embeddings will be configured on first use'));
-                }
-            }
-            output.writeln();
-            // Summary table
-            output.printTable({
-                columns: [
-                    { key: 'setting', header: 'Setting', width: 20 },
-                    { key: 'value', header: 'Value', width: 40 },
-                ],
-                data: [
-                    { setting: 'Preset', value: preset },
-                    { setting: 'Topology', value: options.runtime.topology },
-                    { setting: 'Max Agents', value: String(options.runtime.maxAgents) },
-                    { setting: 'Memory Backend', value: options.runtime.memoryBackend },
-                    { setting: 'HNSW Indexing', value: options.runtime.enableHNSW ? 'Enabled' : 'Disabled' },
-                    { setting: 'Neural Learning', value: options.runtime.enableNeural ? 'Enabled' : 'Disabled' },
-                    { setting: 'Self-Learning', value: options.runtime.enableLearningBridge ? 'LearningBridge + Graph + Scopes' : 'Disabled' },
-                    { setting: 'Embeddings', value: enableEmbeddings ? `${embeddingModel} (hyperbolic)` : 'Disabled' },
-                    { setting: 'Skills', value: `${result.summary.skillsCount} installed` },
-                    { setting: 'Commands', value: `${result.summary.commandsCount} installed` },
-                    { setting: 'Agents', value: `${result.summary.agentsCount} installed` },
-                    { setting: 'Hooks', value: `${result.summary.hooksEnabled} enabled` },
-                ],
-            });
-            await offerCapabilityEnrollment(ctx);
-            return { success: true, data: result };
-        }
-        catch (error) {
-            if (error instanceof Error && error.message === 'User cancelled') {
-                output.printInfo('Setup cancelled');
-                return { success: true };
-            }
-            throw error;
-        }
-    },
-};
-// Check subcommand
-const checkCommand = {
-    name: 'check',
-    description: 'Check if RuFlo is initialized',
-    action: async (ctx) => {
-        const initialized = isInitialized(ctx.cwd);
-        const result = {
-            initialized: initialized.claude || initialized.claudeFlow,
-            claude: initialized.claude,
-            claudeFlow: initialized.claudeFlow,
-            paths: {
-                claudeSettings: initialized.claude ? path.join(ctx.cwd, '.claude', 'settings.json') : null,
-                claudeFlowConfig: initialized.claudeFlow ? path.join(ctx.cwd, '.claude-flow', 'config.yaml') : null,
-            },
-        };
-        if (ctx.flags.format === 'json') {
-            output.printJson(result);
-            return { success: true, data: result };
-        }
-        if (result.initialized) {
-            output.printSuccess('RuFlo is initialized');
-            if (initialized.claude) {
-                output.printInfo(`  Claude Code: .claude/settings.json`);
-            }
-            if (initialized.claudeFlow) {
-                output.printInfo(`  V3 Runtime: .claude-flow/config.yaml`);
-            }
-        }
-        else {
-            output.printWarning('RuFlo is not initialized in this directory');
-            output.printInfo('Run "ruflo init" to initialize');
-        }
-        return { success: true, data: result };
-    },
-};
-// Skills subcommand
-const skillsCommand = {
-    name: 'skills',
-    description: 'Initialize only skills',
-    options: [
-        { name: 'all', description: 'Install all skills', type: 'boolean', default: false },
-        { name: 'core', description: 'Install core skills', type: 'boolean', default: true },
-        { name: 'agentdb', description: 'Install AgentDB skills', type: 'boolean', default: false },
-        { name: 'github', description: 'Install GitHub skills', type: 'boolean', default: false },
-        { name: 'v3', description: 'Install V3 skills', type: 'boolean', default: false },
-    ],
-    action: async (ctx) => {
-        const options = {
-            ...MINIMAL_INIT_OPTIONS,
-            targetDir: ctx.cwd,
-            force: ctx.flags.force,
-            components: {
-                settings: false,
-                skills: true,
-                commands: false,
-                agents: false,
-                helpers: false,
-                statusline: false,
-                mcp: false,
-                runtime: false,
-                claudeMd: false,
-            },
-            skills: {
-                all: ctx.flags.all,
-                core: ctx.flags.core,
-                agentdb: ctx.flags.agentdb,
-                github: ctx.flags.github,
-                flowNexus: false,
-                browser: false,
-                v3: ctx.flags.v3,
-                dualMode: false,
-            },
-        };
-        const spinner = output.createSpinner({ text: 'Installing skills...' });
-        spinner.start();
-        const result = await executeInit(options);
-        if (result.success) {
-            spinner.succeed(`Installed ${result.summary.skillsCount} skills`);
-        }
-        else {
-            spinner.fail('Failed to install skills');
-            for (const error of result.errors) {
-                output.printError(error);
-            }
-        }
-        return { success: result.success, data: result };
-    },
-};
-// Hooks subcommand
-const hooksCommand = {
-    name: 'hooks',
-    description: 'Initialize only hooks configuration',
-    options: [
-        { name: 'all', description: 'Enable all hooks', type: 'boolean', default: true },
-        { name: 'minimal', description: 'Enable only essential hooks', type: 'boolean', default: false },
-    ],
-    action: async (ctx) => {
-        const minimal = ctx.flags.minimal;
-        const options = {
-            ...DEFAULT_INIT_OPTIONS,
-            targetDir: ctx.cwd,
-            force: ctx.flags.force,
-            components: {
-                settings: true,
-                skills: false,
-                commands: false,
-                agents: false,
-                // #2350: helpers MUST ship with the hooks subcommand. The hook entries
-                // in settings.json point at `.claude/helpers/hook-handler.cjs`; if
-                // that file doesn't exist, settings-generator (#1744 fix) drops the
-                // hooks block entirely — so the one subcommand whose stated purpose
-                // is "Initialize only hooks configuration" produced settings.json
-                // with no `hooks` key while reporting "N hooks enabled".
-                helpers: true,
-                statusline: false,
-                mcp: false,
-                runtime: false,
-                claudeMd: false,
-            },
-            hooks: minimal
-                ? {
-                    preToolUse: true,
-                    postToolUse: true,
-                    userPromptSubmit: false,
-                    sessionStart: false,
-                    stop: false,
-                    preCompact: false,
-                    notification: false,
-                    teammateIdle: false,
-                    taskCompleted: false,
-                    timeout: 5000,
-                    continueOnError: true,
-                }
-                : DEFAULT_INIT_OPTIONS.hooks,
-        };
-        const spinner = output.createSpinner({ text: 'Creating hooks configuration...' });
-        spinner.start();
-        const result = await executeInit(options);
-        if (result.success) {
-            spinner.succeed(`Created settings.json with ${result.summary.hooksEnabled} hooks enabled`);
-        }
-        else {
-            spinner.fail('Failed to create hooks configuration');
-            for (const error of result.errors) {
-                output.printError(error);
-            }
-        }
-        return { success: result.success, data: result };
-    },
-};
-// Upgrade subcommand - updates helpers without losing user data
-const upgradeCommand = {
-    name: 'upgrade',
-    description: 'Update statusline and helpers while preserving existing data',
-    options: [
-        {
-            name: 'verbose',
-            short: 'v',
-            description: 'Show detailed output',
-            type: 'boolean',
-            default: false,
-        },
-        {
-            name: 'add-missing',
-            short: 'a',
-            description: 'Add any new skills, agents, and commands that are missing',
-            type: 'boolean',
-            default: false,
-        },
-        {
-            name: 'settings',
-            short: 's',
-            description: 'Merge new settings (Agent Teams, hooks) into existing settings.json',
-            type: 'boolean',
-            default: false,
-        },
-    ],
-    action: async (ctx) => {
-        const addMissing = (ctx.flags['add-missing'] || ctx.flags.addMissing);
-        const upgradeSettings = (ctx.flags.settings);
-        output.writeln();
-        output.writeln(output.bold('Upgrading RuFlo'));
-        if (addMissing && upgradeSettings) {
-            output.writeln(output.dim('Updates helpers, settings, and adds any missing skills/agents/commands'));
-        }
-        else if (addMissing) {
-            output.writeln(output.dim('Updates helpers and adds any missing skills/agents/commands'));
-        }
-        else if (upgradeSettings) {
-            output.writeln(output.dim('Updates helpers and merges new settings (Agent Teams, hooks)'));
-        }
-        else {
-            output.writeln(output.dim('Updates helpers while preserving your existing data'));
-        }
-        output.writeln();
-        const spinnerText = upgradeSettings
-            ? 'Upgrading helpers and settings...'
-            : (addMissing ? 'Upgrading and adding missing assets...' : 'Upgrading...');
-        const spinner = output.createSpinner({ text: spinnerText });
-        spinner.start();
-        try {
-            const result = addMissing
-                ? await executeUpgradeWithMissing(ctx.cwd, upgradeSettings)
-                : await executeUpgrade(ctx.cwd, upgradeSettings);
-            if (!result.success) {
-                spinner.fail('Upgrade failed');
-                for (const error of result.errors) {
-                    output.printError(error);
-                }
-                return { success: false, exitCode: 1 };
-            }
-            spinner.succeed('Upgrade complete!');
-            output.writeln();
-            // Show what was updated
-            if (result.updated.length > 0) {
-                output.printBox(result.updated.map(f => `✓ ${f}`).join('\n'), 'Updated (latest version)');
-                output.writeln();
-            }
-            // Show what was created
-            if (result.created.length > 0) {
-                output.printBox(result.created.map(f => `+ ${f}`).join('\n'), 'Created (new files)');
-                output.writeln();
-            }
-            // Show what was preserved
-            if (result.preserved.length > 0 && ctx.flags.verbose) {
-                output.printBox(result.preserved.map(f => `• ${f}`).join('\n'), 'Preserved (existing data kept)');
-                output.writeln();
-            }
-            else if (result.preserved.length > 0) {
-                output.printInfo(`Preserved ${result.preserved.length} existing data files`);
-                output.writeln();
-            }
-            // Show added assets (when --add-missing flag is used)
-            if (result.addedSkills && result.addedSkills.length > 0) {
-                output.printBox(result.addedSkills.map(s => `+ ${s}`).join('\n'), `Added Skills (${result.addedSkills.length} new)`);
-                output.writeln();
-            }
-            if (result.addedAgents && result.addedAgents.length > 0) {
-                output.printBox(result.addedAgents.map(a => `+ ${a}`).join('\n'), `Added Agents (${result.addedAgents.length} new)`);
-                output.writeln();
-            }
-            if (result.addedCommands && result.addedCommands.length > 0) {
-                output.printBox(result.addedCommands.map(c => `+ ${c}`).join('\n'), `Added Commands (${result.addedCommands.length} new)`);
-                output.writeln();
-            }
-            // Show settings updates
-            if (result.settingsUpdated && result.settingsUpdated.length > 0) {
-                output.printBox(result.settingsUpdated.map(s => `+ ${s}`).join('\n'), 'Settings Updated');
-                output.writeln();
-            }
-            output.printSuccess('Your statusline helper has been updated to the latest version');
-            output.printInfo('Existing metrics and learning data were preserved');
-            // Show settings summary
-            if (upgradeSettings && result.settingsUpdated && result.settingsUpdated.length > 0) {
-                output.printSuccess('Settings.json updated with new Agent Teams configuration');
-            }
-            // Show summary for --add-missing
-            if (addMissing) {
-                const totalAdded = (result.addedSkills?.length || 0) + (result.addedAgents?.length || 0) + (result.addedCommands?.length || 0);
-                if (totalAdded > 0) {
-                    output.printSuccess(`Added ${totalAdded} missing assets to your project`);
-                }
-                else {
-                    output.printInfo('All skills, agents, and commands are already up to date');
-                }
-            }
-            if (ctx.flags.format === 'json') {
-                output.printJson(result);
-            }
-            return { success: true, data: result };
-        }
-        catch (error) {
-            spinner.fail('Upgrade failed');
-            output.printError(`Failed to upgrade: ${error instanceof Error ? error.message : String(error)}`);
-            return { success: false, exitCode: 1 };
-        }
-    },
-};
-// Main init command
-export const initCommand = {
-    name: 'init',
-    description: 'Initialize RuFlo in the current directory',
-    subcommands: [wizardCommand, checkCommand, skillsCommand, hooksCommand, upgradeCommand],
-    options: [
-        {
-            name: 'force',
-            short: 'f',
-            description: 'Overwrite existing configuration',
-            type: 'boolean',
-            default: false,
-        },
-        {
-            name: 'minimal',
-            short: 'm',
-            description: 'Create minimal configuration',
-            type: 'boolean',
-            default: false,
-        },
-        {
-            name: 'full',
-            description: 'Create full configuration with all components',
-            type: 'boolean',
-            default: false,
-        },
-        {
-            // #2356: under --full, the auth-gated cloud MCP servers (ruv-swarm,
-            // flow-nexus) get written into a committed .mcp.json and add MCP
-            // tool-definition token cost every session. Keep them opt-in even with
-            // --full; pass --cloud-mcp to register them.
-            name: 'cloud-mcp',
-            description: 'Register auth-gated cloud MCP servers (ruv-swarm, flow-nexus) in .mcp.json (only relevant with --full)',
-            type: 'boolean',
-            default: false,
-        },
-        {
-            name: 'skip-claude',
-            description: 'Skip .claude/ directory creation (runtime only)',
-            type: 'boolean',
-            default: false,
-        },
-        {
-            // ADR-302 — skip the one-time post-init capability enrollment prompt.
-            name: 'no-signup',
-            description: 'Skip the post-init Cognitum capability enrollment prompt',
-            type: 'boolean',
-            default: false,
-        },
-        {
-            name: 'only-claude',
-            description: 'Only create .claude/ directory (skip runtime)',
-            type: 'boolean',
-            default: false,
-        },
-        {
-            name: 'no-global',
-            description: 'Skip the ~/.claude/CLAUDE.md "Ruflo Integration" pointer block (#1744)',
-            type: 'boolean',
-            default: false,
-        },
-        {
-            name: 'start-all',
-            description: 'Auto-start daemon, memory, and swarm after init',
-            type: 'boolean',
-            default: false,
-        },
-        {
-            name: 'start-daemon',
-            description: 'Auto-start daemon after init',
-            type: 'boolean',
-            default: false,
-        },
-        {
-            name: 'with-embeddings',
-            description: 'Initialize ONNX embedding subsystem with hyperbolic support',
-            type: 'boolean',
-            default: false,
-        },
-        {
-            name: 'embedding-model',
-            description: 'ONNX embedding model to use',
-            type: 'string',
-            default: 'Xenova/all-MiniLM-L6-v2',
-            choices: ['Xenova/all-MiniLM-L6-v2', 'Xenova/all-mpnet-base-v2'],
-        },
-        {
-            name: 'codex',
-            description: 'Initialize for OpenAI Codex CLI (creates AGENTS.md, .agents/)',
-            type: 'boolean',
-            default: false,
-        },
-        {
-            name: 'dual',
-            description: 'Initialize for both Claude Code and OpenAI Codex',
-            type: 'boolean',
-            default: false,
-        },
-        {
-            name: 'no-codex-detect',
-            description: 'Skip auto-detecting the OpenAI Codex CLI and configuring its MCP server + skills',
-            type: 'boolean',
-            default: false,
-        },
-        {
-            name: 'no-skills-sh',
-            description: 'Skip the post-init `npx skills add ruvnet/ruflo` registration (also honored via RUFLO_NO_SKILLS_SH=1)',
-            type: 'boolean',
-            default: false,
-        },
-        {
-            name: 'all-agents',
-            description: 'Install all agent categories (ADR-128: default is ~24 substrate agents; this restores the full set of ~89)',
-            type: 'boolean',
-            default: false,
-        },
-    ],
-    examples: [
-        { command: 'claude-flow init', description: 'Initialize with default configuration' },
-        { command: 'claude-flow init --start-all', description: 'Initialize and start daemon, memory, swarm' },
-        { command: 'claude-flow init --start-daemon', description: 'Initialize and start daemon only' },
-        { command: 'claude-flow init --minimal', description: 'Initialize with minimal configuration' },
-        { command: 'claude-flow init --full', description: 'Initialize with all components' },
-        { command: 'claude-flow init --force', description: 'Reinitialize and overwrite existing config' },
-        { command: 'claude-flow init --only-claude', description: 'Only create Claude Code integration' },
-        { command: 'claude-flow init --skip-claude', description: 'Only create V3 runtime' },
-        { command: 'claude-flow init wizard', description: 'Interactive setup wizard' },
-        { command: 'claude-flow init --with-embeddings', description: 'Initialize with ONNX embeddings' },
-        { command: 'claude-flow init --with-embeddings --embedding-model Xenova/all-mpnet-base-v2', description: 'Use larger embedding model' },
-        { command: 'claude-flow init skills --all', description: 'Install all available skills' },
-        { command: 'claude-flow init hooks --minimal', description: 'Create minimal hooks configuration' },
-        { command: 'claude-flow init upgrade', description: 'Update helpers while preserving data' },
-        { command: 'claude-flow init upgrade --settings', description: 'Update helpers and merge new settings (Agent Teams)' },
-        { command: 'claude-flow init upgrade --verbose', description: 'Show detailed upgrade info' },
-        { command: 'claude-flow init --codex', description: 'Initialize for OpenAI Codex (AGENTS.md)' },
-        { command: 'claude-flow init --codex --full', description: 'Codex init with all 137+ skills' },
-        { command: 'claude-flow init --dual', description: 'Initialize for both Claude Code and Codex' },
-        { command: 'claude-flow init --no-codex-detect', description: 'Skip auto-configuring OpenAI Codex even if it is installed' },
-        { command: 'claude-flow init --no-skills-sh', description: 'Skip the post-init skills.sh registration' },
-        { command: 'claude-flow init --all-agents', description: 'Install all agent categories (~89 agents; ADR-128 opt-in)' },
-    ],
-    action: initAction,
-};
-export default initCommand;
-//# sourceMappingURL=init.js.map