@aigentic/claude-flow 3.7.0-alpha.69

package/v3/@claude-flow/cli/dist/src/commands/doctor.js

@@ -0,0 +1,885 @@
+/**
+ * V3 CLI Doctor Command
+ * System diagnostics, dependency checks, config validation
+ *
+ * Created with ruv.io
+ */
+import { output } from '../output.js';
+import { existsSync, readFileSync, statSync } from 'fs';
+import { join, dirname } from 'path';
+import { fileURLToPath } from 'url';
+import { createHash } from 'crypto';
+import { execSync, exec } from 'child_process';
+import { promisify } from 'util';
+import { decodeKey, isEncryptionEnabled } from '../encryption/vault.js';
+import { isEncryptedBlob } from '../encryption/vault.js';
+// Promisified exec with proper shell and env inheritance for cross-platform support
+const execAsync = promisify(exec);
+/**
+ * Execute command asynchronously with proper environment inheritance
+ * Critical for Windows where PATH may not be inherited properly
+ */
+async function runCommand(command, timeoutMs = 5000) {
+    const { stdout } = await execAsync(command, {
+        encoding: 'utf8',
+        timeout: timeoutMs,
+        shell: process.platform === 'win32' ? 'cmd.exe' : '/bin/sh', // Use proper shell per platform
+        env: { ...process.env }, // Explicitly inherit full environment
+        windowsHide: true, // Hide window on Windows
+    });
+    return stdout.trim();
+}
+// Check Node.js version
+async function checkNodeVersion() {
+    const requiredMajor = 20;
+    const version = process.version;
+    const major = parseInt(version.slice(1).split('.')[0], 10);
+    if (major >= requiredMajor) {
+        return { name: 'Node.js Version', status: 'pass', message: `${version} (>= ${requiredMajor} required)` };
+    }
+    else if (major >= 18) {
+        return { name: 'Node.js Version', status: 'warn', message: `${version} (>= ${requiredMajor} recommended)`, fix: 'nvm install 20 && nvm use 20' };
+    }
+    else {
+        return { name: 'Node.js Version', status: 'fail', message: `${version} (>= ${requiredMajor} required)`, fix: 'nvm install 20 && nvm use 20' };
+    }
+}
+// Check npm version (async with proper env inheritance)
+async function checkNpmVersion() {
+    try {
+        const version = await runCommand('npm --version');
+        const major = parseInt(version.split('.')[0], 10);
+        if (major >= 9) {
+            return { name: 'npm Version', status: 'pass', message: `v${version}` };
+        }
+        else {
+            return { name: 'npm Version', status: 'warn', message: `v${version} (>= 9 recommended)`, fix: 'npm install -g npm@latest' };
+        }
+    }
+    catch {
+        return { name: 'npm Version', status: 'fail', message: 'npm not found', fix: 'Install Node.js from https://nodejs.org' };
+    }
+}
+// Check config file
+async function checkConfigFile() {
+    // JSON configs (parse-validated). The first three are LEGACY shapes from
+    // pre-v3 init flows; v3 init writes only `.claude-flow/config.yaml`.
+    const jsonPaths = [
+        '.claude-flow/config.json',
+        'claude-flow.config.json',
+        '.claude-flow.json'
+    ];
+    // YAML configs (existence-checked only — no heavy yaml parser dependency).
+    const yamlPaths = [
+        '.claude-flow/config.yaml',
+        '.claude-flow/config.yml',
+        'claude-flow.config.yaml'
+    ];
+    // #1798 — collect ALL configs that exist instead of returning at the first
+    // hit. The previous early-return masked silent collisions: if both a v2
+    // JSON and a v3 YAML existed, doctor reported only the JSON while the
+    // daemon was actually reading from the YAML. Surfacing both lets the user
+    // see and resolve the disagreement.
+    const foundJson = [];
+    const invalidJson = [];
+    for (const configPath of jsonPaths) {
+        if (!existsSync(configPath))
+            continue;
+        try {
+            JSON.parse(readFileSync(configPath, 'utf8'));
+            foundJson.push(configPath);
+        }
+        catch {
+            invalidJson.push(configPath);
+        }
+    }
+    const foundYaml = yamlPaths.filter(p => existsSync(p));
+    // Hard failures first: malformed JSON wins.
+    if (invalidJson.length > 0) {
+        return { name: 'Config File', status: 'fail', message: `Invalid JSON: ${invalidJson.join(', ')}`, fix: 'Fix JSON syntax in config file' };
+    }
+    // #1798 — collision: legacy JSON + new YAML both present. Subsystems can
+    // disagree on which to read; surface this as a warn with the recommended
+    // resolution (keep the YAML, archive the JSON).
+    if (foundJson.length > 0 && foundYaml.length > 0) {
+        return {
+            name: 'Config File',
+            status: 'warn',
+            message: `Config collision: legacy ${foundJson.join(', ')} + ${foundYaml.join(', ')} — subsystems may disagree silently`,
+            fix: `Archive the legacy JSON (mv ${foundJson[0]} ${foundJson[0]}.bak) and keep ${foundYaml[0]} as the canonical config`,
+        };
+    }
+    if (foundYaml.length > 0) {
+        return { name: 'Config File', status: 'pass', message: `Found: ${foundYaml[0]}` };
+    }
+    if (foundJson.length > 0) {
+        return { name: 'Config File', status: 'pass', message: `Found: ${foundJson[0]}` };
+    }
+    return { name: 'Config File', status: 'warn', message: 'No config file (using defaults)', fix: 'claude-flow config init' };
+}
+// Check daemon status
+async function checkDaemonStatus() {
+    try {
+        const pidFile = '.claude-flow/daemon.pid';
+        if (existsSync(pidFile)) {
+            const pid = readFileSync(pidFile, 'utf8').trim();
+            try {
+                process.kill(parseInt(pid, 10), 0); // Check if process exists
+                return { name: 'Daemon Status', status: 'pass', message: `Running (PID: ${pid})` };
+            }
+            catch {
+                return { name: 'Daemon Status', status: 'warn', message: 'Stale PID file', fix: 'rm .claude-flow/daemon.pid && claude-flow daemon start' };
+            }
+        }
+        return { name: 'Daemon Status', status: 'warn', message: 'Not running', fix: 'claude-flow daemon start' };
+    }
+    catch {
+        return { name: 'Daemon Status', status: 'warn', message: 'Unable to check', fix: 'claude-flow daemon status' };
+    }
+}
+// Check memory database
+async function checkMemoryDatabase() {
+    // Authoritative path comes from `getMemoryRoot()` (honors
+    // `CLAUDE_FLOW_MEMORY_PATH`, claude-flow.config.json's `memory.persistPath`,
+    // then defaults to `.swarm/`). #1946: the previous hard-coded list missed
+    // `data/memory/memory.db` (a common config) and ignored the env var
+    // entirely, so doctor reported "Not initialized" on perfectly-init'd DBs.
+    // Try the configured path first, then fall back to the historic candidates.
+    const candidates = [];
+    try {
+        const { getMemoryRoot } = await import('../memory/memory-initializer.js');
+        candidates.push(join(getMemoryRoot(), 'memory.db'));
+    }
+    catch {
+        /* memory-initializer not available — fall through to legacy candidates */
+    }
+    candidates.push('.swarm/memory.db', '.claude-flow/memory.db', 'data/memory/memory.db', // matches `CLAUDE_FLOW_MEMORY_PATH=data/memory`
+    'data/memory.db');
+    for (const dbPath of candidates) {
+        if (existsSync(dbPath)) {
+            try {
+                const stats = statSync(dbPath);
+                const sizeMB = (stats.size / 1024 / 1024).toFixed(2);
+                return { name: 'Memory Database', status: 'pass', message: `${dbPath} (${sizeMB} MB)` };
+            }
+            catch {
+                return { name: 'Memory Database', status: 'warn', message: `${dbPath} (unable to stat)` };
+            }
+        }
+    }
+    return { name: 'Memory Database', status: 'warn', message: 'Not initialized', fix: 'claude-flow memory configure --backend hybrid' };
+}
+// Check API keys
+async function checkApiKeys() {
+    const keys = ['ANTHROPIC_API_KEY', 'CLAUDE_API_KEY', 'OPENAI_API_KEY'];
+    const found = [];
+    for (const key of keys) {
+        if (process.env[key]) {
+            found.push(key);
+        }
+    }
+    // Detect Claude Code environment — API keys are managed internally
+    const inClaudeCode = !!(process.env.CLAUDE_CODE || process.env.CLAUDE_PROJECT_DIR || process.env.MCP_SESSION_ID);
+    if (found.includes('ANTHROPIC_API_KEY') || found.includes('CLAUDE_API_KEY')) {
+        return { name: 'API Keys', status: 'pass', message: `Found: ${found.join(', ')}` };
+    }
+    else if (inClaudeCode) {
+        return { name: 'API Keys', status: 'pass', message: 'Claude Code (managed internally)' };
+    }
+    else if (found.length > 0) {
+        return { name: 'API Keys', status: 'warn', message: `Found: ${found.join(', ')} (no Claude key)`, fix: 'export ANTHROPIC_API_KEY=your_key' };
+    }
+    else {
+        return { name: 'API Keys', status: 'warn', message: 'No API keys found', fix: 'export ANTHROPIC_API_KEY=your_key' };
+    }
+}
+// Check git (async with proper env inheritance)
+async function checkGit() {
+    try {
+        const version = await runCommand('git --version');
+        return { name: 'Git', status: 'pass', message: version.replace('git version ', 'v') };
+    }
+    catch {
+        return { name: 'Git', status: 'warn', message: 'Not installed', fix: 'Install git from https://git-scm.com' };
+    }
+}
+// Check if in git repo (async with proper env inheritance)
+//
+// #1791.7 — `git rev-parse` was reported as failing on hosts where `.git`
+// clearly exists in cwd (linux-arm64 daemon contexts). Treat the git binary
+// as authoritative when it succeeds, but fall back to a `.git` walk-up so a
+// present repository is recognized even when the git invocation fails for
+// environment reasons (PATH, broken global config, EBADCWD, etc.).
+async function checkGitRepo() {
+    try {
+        await runCommand('git rev-parse --is-inside-work-tree');
+        return { name: 'Git Repository', status: 'pass', message: 'In a git repository' };
+    }
+    catch {
+        // Walk parents of cwd for a .git directory before reporting "not a repo"
+        let dir = process.cwd();
+        while (true) {
+            if (existsSync(join(dir, '.git'))) {
+                return {
+                    name: 'Git Repository',
+                    status: 'warn',
+                    message: `Repo detected on disk (${join(dir, '.git')}) but \`git rev-parse\` failed — check git installation and PATH`,
+                    fix: 'Verify git is on PATH (try `git --version`) and that the working tree is not corrupted',
+                };
+            }
+            const parent = dirname(dir);
+            if (parent === dir)
+                break;
+            dir = parent;
+        }
+        return { name: 'Git Repository', status: 'warn', message: 'Not a git repository', fix: 'git init' };
+    }
+}
+// Check AIDefence package availability (#1807)
+//
+// `aidefence_*` MCP tools (scan, analyze, has_pii, stats, learn) require
+// `@claude-flow/aidefence` to be installed and loadable. The package is an
+// optional dependency — present in some installs (project-local) but
+// missing in others (npm-global of `claude-flow`). Without it, every
+// aidefence MCP call fails at runtime with "Cannot find module".
+//
+// Surface that state in `doctor` so operators know BEFORE they rely on
+// AI-defence scanning. The probe is the same dynamic `import()` the MCP
+// tool's handler uses, so a `pass` here means the actual tools will work.
+async function checkAIDefence() {
+    try {
+        // eslint-disable-next-line @typescript-eslint/no-var-requires
+        await import('@claude-flow/aidefence');
+        return {
+            name: 'AIDefence',
+            status: 'pass',
+            message: '@claude-flow/aidefence loadable — aidefence_* MCP tools functional',
+        };
+    }
+    catch {
+        return {
+            name: 'AIDefence',
+            status: 'warn',
+            message: '@claude-flow/aidefence not loadable — aidefence_* MCP tools will fail (optional package)',
+            fix: 'npm install --save @claude-flow/aidefence  (in your project), or run `claude-flow mcp start` from a directory that has it installed',
+        };
+    }
+}
+/**
+ * ADR-097 Phase 4: federation peer-state surface for doctor.
+ *
+ * Probes the federation plugin loadability + asserts the breaker entity
+ * layer is present in the installed version. Without the plugin
+ * installed this is a "not configured" pass — federation is opt-in.
+ *
+ * Live coordinator state (per-peer counts) requires a running MCP server
+ * with `federation_init` called; operators inspect that via the
+ * `federation_breaker_status` MCP tool, not the doctor (which is a
+ * one-shot CLI process with no coordinator session).
+ */
+async function checkFederationBreaker() {
+    try {
+        // Optional plugin — not a hard dep of @claude-flow/cli. Build the
+        // module specifier dynamically so TypeScript cannot statically
+        // resolve it (which would emit TS2307); at runtime the import
+        // either resolves (plugin installed) or throws (handled below).
+        const specifier = ['@claude-flow', 'plugin-agent-federation'].join('/');
+        const mod = await import(specifier);
+        if (!mod.FederationNodeState) {
+            return {
+                name: 'Federation Breaker',
+                status: 'warn',
+                message: '@claude-flow/plugin-agent-federation loaded but FederationNodeState export missing — version older than ADR-097 Phase 2',
+                fix: 'Upgrade: npm install @claude-flow/plugin-agent-federation@alpha',
+            };
+        }
+        return {
+            name: 'Federation Breaker',
+            status: 'pass',
+            message: 'ADR-097 breaker loadable — federation_breaker_status / federation_evict / federation_reactivate MCP tools available',
+        };
+    }
+    catch {
+        return {
+            name: 'Federation Breaker',
+            status: 'pass',
+            message: 'Federation plugin not installed (optional) — install only if you need cross-installation peering',
+            fix: 'npm install --save @claude-flow/plugin-agent-federation@alpha',
+        };
+    }
+}
+// Check MCP servers
+async function checkMcpServers() {
+    const home = process.env.HOME || process.env.USERPROFILE || '';
+    // #1842: ~/.claude.json holds project-scoped registrations under
+    // parsed.projects[<projectPath>].mcpServers.ruflo, in addition to any
+    // top-level mcpServers. Check both shapes plus the legacy desktop and
+    // local .mcp.json paths.
+    const mcpConfigPaths = [
+        join(home, '.claude.json'),
+        join(home, '.claude/claude_desktop_config.json'),
+        join(home, '.config/claude/mcp.json'),
+        '.mcp.json',
+    ];
+    const isRufloKey = (k) => k === 'ruflo' || k === 'ruflo_alpha' || k === 'claude-flow' || k === 'claude-flow_alpha';
+    for (const configPath of mcpConfigPaths) {
+        if (!existsSync(configPath))
+            continue;
+        try {
+            const content = JSON.parse(readFileSync(configPath, 'utf8'));
+            // Top-level mcpServers (legacy / desktop form)
+            const topServers = content.mcpServers || content.servers || {};
+            const topServerKeys = Object.keys(topServers);
+            const topHasRuflo = topServerKeys.some(isRufloKey);
+            // Project-scoped (Claude Code shape): projects[*].mcpServers.ruflo
+            let projectHits = 0;
+            let projectScannedServers = 0;
+            if (content.projects && typeof content.projects === 'object') {
+                for (const projectVal of Object.values(content.projects)) {
+                    const pm = projectVal?.mcpServers;
+                    if (pm && typeof pm === 'object') {
+                        const keys = Object.keys(pm);
+                        projectScannedServers += keys.length;
+                        if (keys.some(isRufloKey))
+                            projectHits += 1;
+                    }
+                }
+            }
+            const totalServers = topServerKeys.length + projectScannedServers;
+            if (topHasRuflo || projectHits > 0) {
+                const where = topHasRuflo
+                    ? 'top-level'
+                    : `${projectHits} project-scoped`;
+                return {
+                    name: 'MCP Servers',
+                    status: 'pass',
+                    message: `${totalServers} servers (ruflo configured: ${where})`,
+                };
+            }
+            if (totalServers > 0) {
+                return {
+                    name: 'MCP Servers',
+                    status: 'warn',
+                    message: `${totalServers} servers (ruflo not found)`,
+                    fix: 'claude mcp add ruflo -- npx -y ruflo@latest mcp start',
+                };
+            }
+        }
+        catch {
+            // continue to next path
+        }
+    }
+    return {
+        name: 'MCP Servers',
+        status: 'warn',
+        message: 'No MCP config found',
+        fix: 'claude mcp add ruflo -- npx -y ruflo@latest mcp start',
+    };
+}
+// Check disk space (async with proper env inheritance)
+async function checkDiskSpace() {
+    try {
+        if (process.platform === 'win32') {
+            return { name: 'Disk Space', status: 'pass', message: 'Check skipped on Windows' };
+        }
+        // Use df -Ph for POSIX mode (guarantees single-line output even with long device names)
+        const output_str = await runCommand('df -Ph . | tail -1');
+        const parts = output_str.split(/\s+/);
+        // POSIX format: Filesystem Size Used Avail Capacity Mounted
+        const available = parts[3];
+        const usePercent = parseInt(parts[4]?.replace('%', '') || '0', 10);
+        if (isNaN(usePercent)) {
+            return { name: 'Disk Space', status: 'warn', message: `${available || 'unknown'} available (unable to parse usage)` };
+        }
+        if (usePercent > 90) {
+            return { name: 'Disk Space', status: 'fail', message: `${available} available (${usePercent}% used)`, fix: 'Free up disk space' };
+        }
+        else if (usePercent > 80) {
+            return { name: 'Disk Space', status: 'warn', message: `${available} available (${usePercent}% used)` };
+        }
+        return { name: 'Disk Space', status: 'pass', message: `${available} available` };
+    }
+    catch {
+        return { name: 'Disk Space', status: 'warn', message: 'Unable to check' };
+    }
+}
+// Check TypeScript/build (async with proper env inheritance)
+async function checkBuildTools() {
+    try {
+        const tscVersion = await runCommand('npx tsc --version', 10000); // tsc can be slow
+        if (!tscVersion || tscVersion.includes('not found')) {
+            return { name: 'TypeScript', status: 'warn', message: 'Not installed locally', fix: 'npm install -D typescript' };
+        }
+        return { name: 'TypeScript', status: 'pass', message: tscVersion.replace('Version ', 'v') };
+    }
+    catch {
+        return { name: 'TypeScript', status: 'warn', message: 'Not installed locally', fix: 'npm install -D typescript' };
+    }
+}
+// Check for stale npx cache (version freshness)
+async function checkVersionFreshness() {
+    try {
+        // Get current CLI version from package.json
+        // Use import.meta.url to reliably locate our own package.json,
+        // regardless of how deep the compiled file sits (e.g. dist/src/commands/).
+        let currentVersion = '0.0.0';
+        try {
+            const thisFile = fileURLToPath(import.meta.url);
+            let dir = dirname(thisFile);
+            // Walk up from the current file's directory until we find the
+            // package.json that belongs to @claude-flow/cli (or claude-flow/cli).
+            // Walk until dirname(dir) === dir (filesystem root on any platform).
+            for (;;) {
+                const candidate = join(dir, 'package.json');
+                try {
+                    if (existsSync(candidate)) {
+                        const pkg = JSON.parse(readFileSync(candidate, 'utf8'));
+                        if (pkg.version &&
+                            typeof pkg.name === 'string' &&
+                            (pkg.name === '@claude-flow/cli' || pkg.name === 'claude-flow' || pkg.name === 'ruflo')) {
+                            currentVersion = pkg.version;
+                            break;
+                        }
+                    }
+                }
+                catch {
+                    // Unreadable/invalid JSON -- skip and keep walking up
+                }
+                const parent = dirname(dir);
+                if (parent === dir)
+                    break; // reached root
+                dir = parent;
+            }
+        }
+        catch {
+            // Fall back to a default
+            currentVersion = '0.0.0';
+        }
+        // Check if running via npx (look for _npx in process path or argv)
+        const isNpx = process.argv[1]?.includes('_npx') ||
+            process.env.npm_execpath?.includes('npx') ||
+            process.cwd().includes('_npx');
+        // Query npm for latest version (using alpha tag since that's what we publish to)
+        let latestVersion = currentVersion;
+        try {
+            const npmInfo = await runCommand('npm view @claude-flow/cli@alpha version', 5000);
+            latestVersion = npmInfo.trim();
+        }
+        catch {
+            // Can't reach npm registry - skip check
+            return {
+                name: 'Version Freshness',
+                status: 'warn',
+                message: `v${currentVersion} (cannot check registry)`
+            };
+        }
+        // Parse version numbers for comparison (handle prerelease like 3.0.0-alpha.84)
+        const parseVersion = (v) => {
+            const match = v.match(/^(\d+)\.(\d+)\.(\d+)(?:-[a-zA-Z]+\.(\d+))?/);
+            if (!match)
+                return { major: 0, minor: 0, patch: 0, prerelease: 0 };
+            return {
+                major: parseInt(match[1], 10) || 0,
+                minor: parseInt(match[2], 10) || 0,
+                patch: parseInt(match[3], 10) || 0,
+                prerelease: parseInt(match[4], 10) || 0
+            };
+        };
+        const current = parseVersion(currentVersion);
+        const latest = parseVersion(latestVersion);
+        // Compare versions (including prerelease number)
+        const isOutdated = (latest.major > current.major ||
+            (latest.major === current.major && latest.minor > current.minor) ||
+            (latest.major === current.major && latest.minor === current.minor && latest.patch > current.patch) ||
+            (latest.major === current.major && latest.minor === current.minor && latest.patch === current.patch && latest.prerelease > current.prerelease));
+        if (isOutdated) {
+            const fix = isNpx
+                ? 'rm -rf ~/.npm/_npx/* && npx -y @claude-flow/cli@latest'
+                : 'npm update @claude-flow/cli';
+            return {
+                name: 'Version Freshness',
+                status: 'warn',
+                message: `v${currentVersion} (latest: v${latestVersion})${isNpx ? ' [npx cache stale]' : ''}`,
+                fix
+            };
+        }
+        return {
+            name: 'Version Freshness',
+            status: 'pass',
+            message: `v${currentVersion} (up to date)`
+        };
+    }
+    catch (error) {
+        return {
+            name: 'Version Freshness',
+            status: 'warn',
+            message: 'Unable to check version freshness'
+        };
+    }
+}
+// Check Claude Code CLI (async with proper env inheritance)
+async function checkClaudeCode() {
+    try {
+        const version = await runCommand('claude --version');
+        // Parse version from output like "claude 1.0.0" or "Claude Code v1.0.0"
+        const versionMatch = version.match(/v?(\d+\.\d+\.\d+)/);
+        const versionStr = versionMatch ? `v${versionMatch[1]}` : version;
+        return { name: 'Claude Code CLI', status: 'pass', message: versionStr };
+    }
+    catch {
+        return {
+            name: 'Claude Code CLI',
+            status: 'warn',
+            message: 'Not installed',
+            fix: 'npm install -g @anthropic-ai/claude-code'
+        };
+    }
+}
+// Install Claude Code CLI
+async function installClaudeCode() {
+    try {
+        output.writeln();
+        output.writeln(output.bold('Installing Claude Code CLI...'));
+        execSync('npm install -g @anthropic-ai/claude-code', {
+            encoding: 'utf8',
+            stdio: 'inherit'
+        });
+        output.writeln(output.success('Claude Code CLI installed successfully!'));
+        return true;
+    }
+    catch (error) {
+        output.writeln(output.error('Failed to install Claude Code CLI'));
+        if (error instanceof Error) {
+            output.writeln(output.dim(error.message));
+        }
+        return false;
+    }
+}
+// Check agentic-flow v3 integration (filesystem-based to avoid slow WASM/DB init)
+async function checkAgenticFlow() {
+    try {
+        // Walk common node_modules paths to find agentic-flow/package.json
+        const candidates = [
+            join(process.cwd(), 'node_modules', 'agentic-flow', 'package.json'),
+            join(process.cwd(), '..', 'node_modules', 'agentic-flow', 'package.json'),
+        ];
+        let pkgJsonPath = null;
+        for (const p of candidates) {
+            if (existsSync(p)) {
+                pkgJsonPath = p;
+                break;
+            }
+        }
+        if (!pkgJsonPath) {
+            return {
+                name: 'agentic-flow',
+                status: 'warn',
+                message: 'Not installed (optional — embeddings/routing will use fallbacks)',
+                fix: 'npm install agentic-flow@latest'
+            };
+        }
+        const pkg = JSON.parse(readFileSync(pkgJsonPath, 'utf-8'));
+        const version = pkg.version || 'unknown';
+        const exports = pkg.exports || {};
+        const features = [
+            exports['./reasoningbank'] ? 'ReasoningBank' : null,
+            exports['./router'] ? 'Router' : null,
+            exports['./transport/quic'] ? 'QUIC' : null,
+        ].filter(Boolean);
+        return {
+            name: 'agentic-flow',
+            status: 'pass',
+            message: `v${version} (${features.join(', ')})`
+        };
+    }
+    catch {
+        return { name: 'agentic-flow', status: 'warn', message: 'Check failed' };
+    }
+}
+// Check encryption-at-rest status (ADR-096 Phase 5)
+//
+// Reports four facets without disclosing the key itself:
+//   1. Gate status — is CLAUDE_FLOW_ENCRYPT_AT_REST set?
+//   2. Key resolution — does CLAUDE_FLOW_ENCRYPTION_KEY resolve to a valid
+//      32-byte key (env-var path only; keychain/passphrase are deferred)?
+//   3. Key fingerprint — first 16 hex chars of sha256(key) so users can
+//      sanity-check across machines without ever logging the key bytes.
+//   4. High-tier store presence — for sessions/, terminals/, .swarm/memory.db
+//      report whether on-disk bytes carry the RFE1 magic (encrypted) or not.
+async function checkEncryptionAtRest() {
+    if (!isEncryptionEnabled()) {
+        return {
+            name: 'Encryption at Rest',
+            status: 'warn',
+            message: 'Off — session/terminal/memory stores are plaintext (mode 0600 only)',
+            fix: 'export CLAUDE_FLOW_ENCRYPT_AT_REST=1 && export CLAUDE_FLOW_ENCRYPTION_KEY=<64-char-hex>',
+        };
+    }
+    // Gate is on — try to resolve the key. Fail-closed if missing or malformed.
+    const rawKey = process.env.CLAUDE_FLOW_ENCRYPTION_KEY;
+    if (!rawKey) {
+        return {
+            name: 'Encryption at Rest',
+            status: 'fail',
+            message: 'Gate is on but CLAUDE_FLOW_ENCRYPTION_KEY is unset (fail-closed)',
+            fix: 'Generate a key: openssl rand -hex 32 → export CLAUDE_FLOW_ENCRYPTION_KEY=<value>',
+        };
+    }
+    let keyFingerprint;
+    try {
+        const key = decodeKey(rawKey);
+        keyFingerprint = createHash('sha256').update(key).digest('hex').slice(0, 16);
+    }
+    catch (err) {
+        return {
+            name: 'Encryption at Rest',
+            status: 'fail',
+            message: `CLAUDE_FLOW_ENCRYPTION_KEY invalid: ${err instanceof Error ? err.message : String(err)}`,
+            fix: 'Provide a 64-char hex or 44-char base64 key (32 bytes)',
+        };
+    }
+    // Check the three high-tier store paths for RFE1 magic
+    const cwd = process.cwd();
+    const stores = [
+        { label: 'sessions/', path: join(cwd, '.claude-flow', 'sessions') },
+        { label: 'terminals', path: join(cwd, '.claude-flow', 'terminals', 'store.json') },
+        { label: 'memory.db', path: join(cwd, '.swarm', 'memory.db') },
+    ];
+    const status = [];
+    for (const s of stores) {
+        if (!existsSync(s.path)) {
+            status.push(`${s.label}=∅`);
+            continue;
+        }
+        try {
+            const stat = statSync(s.path);
+            if (stat.isDirectory()) {
+                // Sessions: probe the first .json file
+                const { readdirSync } = await import('fs');
+                const files = readdirSync(s.path).filter(f => f.endsWith('.json'));
+                if (files.length === 0) {
+                    status.push(`${s.label}=∅`);
+                    continue;
+                }
+                const first = readFileSync(join(s.path, files[0]));
+                status.push(`${s.label}=${isEncryptedBlob(first) ? 'enc' : 'plain'}`);
+            }
+            else {
+                const buf = readFileSync(s.path);
+                status.push(`${s.label}=${isEncryptedBlob(buf) ? 'enc' : 'plain'}`);
+            }
+        }
+        catch {
+            status.push(`${s.label}=err`);
+        }
+    }
+    return {
+        name: 'Encryption at Rest',
+        status: 'pass',
+        message: `On — key fp:${keyFingerprint}… (${status.join(' ')})`,
+    };
+}
+// Format health check result
+function formatCheck(check) {
+    const icon = check.status === 'pass' ? output.success('✓') :
+        check.status === 'warn' ? output.warning('⚠') :
+            output.error('✗');
+    return `${icon} ${check.name}: ${check.message}`;
+}
+// Main doctor command
+export const doctorCommand = {
+    name: 'doctor',
+    description: 'System diagnostics and health checks',
+    options: [
+        {
+            name: 'fix',
+            short: 'f',
+            // #1791.5 — flag name was misleading: it does NOT auto-apply fixes,
+            // it only prints the suggested commands so the user can run them
+            // themselves. Make that explicit in the help output.
+            description: 'Print suggested fix commands (does not auto-apply — copy/paste them yourself)',
+            type: 'boolean',
+            default: false
+        },
+        {
+            name: 'install',
+            short: 'i',
+            description: 'Auto-install missing dependencies (Claude Code CLI)',
+            type: 'boolean',
+            default: false
+        },
+        {
+            name: 'component',
+            short: 'c',
+            description: 'Check specific component (version, node, npm, config, daemon, memory, api, git, mcp, claude, disk, typescript)',
+            type: 'string'
+        },
+        {
+            name: 'verbose',
+            short: 'v',
+            description: 'Verbose output',
+            type: 'boolean',
+            default: false
+        }
+    ],
+    examples: [
+        { command: 'claude-flow doctor', description: 'Run full health check' },
+        { command: 'claude-flow doctor --fix', description: 'Print suggested fix commands (does not auto-apply)' },
+        { command: 'claude-flow doctor --install', description: 'Auto-install missing dependencies' },
+        { command: 'claude-flow doctor -c version', description: 'Check for stale npx cache' },
+        { command: 'claude-flow doctor -c claude', description: 'Check Claude Code CLI only' }
+    ],
+    action: async (ctx) => {
+        const showFix = ctx.flags.fix;
+        const autoInstall = ctx.flags.install;
+        const component = ctx.flags.component;
+        const verbose = ctx.flags.verbose;
+        output.writeln();
+        output.writeln(output.bold('RuFlo Doctor'));
+        output.writeln(output.dim('System diagnostics and health check'));
+        output.writeln(output.dim('─'.repeat(50)));
+        output.writeln();
+        const allChecks = [
+            checkVersionFreshness,
+            checkNodeVersion,
+            checkNpmVersion,
+            checkClaudeCode,
+            checkGit,
+            checkGitRepo,
+            checkConfigFile,
+            checkDaemonStatus,
+            checkMemoryDatabase,
+            checkApiKeys,
+            checkMcpServers,
+            checkAIDefence, // #1807
+            checkDiskSpace,
+            checkBuildTools,
+            checkAgenticFlow,
+            checkEncryptionAtRest, // ADR-096 Phase 5
+            checkFederationBreaker, // ADR-097 Phase 4
+        ];
+        const componentMap = {
+            'version': checkVersionFreshness,
+            'freshness': checkVersionFreshness,
+            'node': checkNodeVersion,
+            'npm': checkNpmVersion,
+            'claude': checkClaudeCode,
+            'config': checkConfigFile,
+            'daemon': checkDaemonStatus,
+            'memory': checkMemoryDatabase,
+            'api': checkApiKeys,
+            'git': checkGit,
+            'mcp': checkMcpServers,
+            'aidefence': checkAIDefence, // #1807
+            'disk': checkDiskSpace,
+            'typescript': checkBuildTools,
+            'agentic-flow': checkAgenticFlow,
+            'encryption': checkEncryptionAtRest, // ADR-096 Phase 5
+            'federation': checkFederationBreaker, // ADR-097 Phase 4
+        };
+        let checksToRun = allChecks;
+        if (component && componentMap[component]) {
+            checksToRun = [componentMap[component]];
+        }
+        const results = [];
+        const fixes = [];
+        // OPTIMIZATION: Run all checks in parallel for 3-5x faster execution
+        const spinner = output.createSpinner({ text: 'Running health checks in parallel...', spinner: 'dots' });
+        spinner.start();
+        try {
+            // Execute all checks concurrently
+            const checkResults = await Promise.allSettled(checksToRun.map(check => check()));
+            spinner.stop();
+            // Process results in order
+            for (const settledResult of checkResults) {
+                if (settledResult.status === 'fulfilled') {
+                    const result = settledResult.value;
+                    results.push(result);
+                    output.writeln(formatCheck(result));
+                    if (result.fix && (result.status === 'fail' || result.status === 'warn')) {
+                        fixes.push(`${result.name}: ${result.fix}`);
+                    }
+                }
+                else {
+                    const errorResult = {
+                        name: 'Check',
+                        status: 'fail',
+                        message: settledResult.reason?.message || 'Unknown error'
+                    };
+                    results.push(errorResult);
+                    output.writeln(formatCheck(errorResult));
+                }
+            }
+        }
+        catch (error) {
+            spinner.stop();
+            output.writeln(output.error('Failed to run health checks'));
+        }
+        // Auto-install missing dependencies if requested
+        if (autoInstall) {
+            const claudeCodeResult = results.find(r => r.name === 'Claude Code CLI');
+            if (claudeCodeResult && claudeCodeResult.status !== 'pass') {
+                const installed = await installClaudeCode();
+                if (installed) {
+                    // Re-check Claude Code after installation
+                    const newCheck = await checkClaudeCode();
+                    const idx = results.findIndex(r => r.name === 'Claude Code CLI');
+                    if (idx !== -1) {
+                        results[idx] = newCheck;
+                        // Update fixes list
+                        const fixIdx = fixes.findIndex(f => f.startsWith('Claude Code CLI:'));
+                        if (fixIdx !== -1 && newCheck.status === 'pass') {
+                            fixes.splice(fixIdx, 1);
+                        }
+                    }
+                    output.writeln(formatCheck(newCheck));
+                }
+            }
+        }
+        // Summary
+        const passed = results.filter(r => r.status === 'pass').length;
+        const warnings = results.filter(r => r.status === 'warn').length;
+        const failed = results.filter(r => r.status === 'fail').length;
+        output.writeln();
+        output.writeln(output.dim('─'.repeat(50)));
+        output.writeln();
+        const summaryParts = [
+            output.success(`${passed} passed`),
+            warnings > 0 ? output.warning(`${warnings} warnings`) : null,
+            failed > 0 ? output.error(`${failed} failed`) : null
+        ].filter(Boolean);
+        output.writeln(`Summary: ${summaryParts.join(', ')}`);
+        // Show fixes — #1791.5: header makes it explicit these are commands you
+        // run yourself, not actions doctor took.
+        if (showFix && fixes.length > 0) {
+            output.writeln();
+            output.writeln(output.bold('Suggested commands (run them yourself):'));
+            output.writeln();
+            for (const fix of fixes) {
+                output.writeln(output.dim(`  ${fix}`));
+            }
+        }
+        else if (fixes.length > 0 && !showFix) {
+            output.writeln();
+            output.writeln(output.dim(`Run with --fix to see ${fixes.length} suggested command${fixes.length > 1 ? 's' : ''} (does not auto-apply)`));
+        }
+        // Overall result
+        if (failed > 0) {
+            output.writeln();
+            output.writeln(output.error('Some checks failed. Please address the issues above.'));
+            return { success: false, exitCode: 1, data: { passed, warnings, failed, results } };
+        }
+        else if (warnings > 0) {
+            output.writeln();
+            output.writeln(output.warning('All checks passed with some warnings.'));
+            return { success: true, data: { passed, warnings, failed, results } };
+        }
+        else {
+            output.writeln();
+            output.writeln(output.success('All checks passed! System is healthy.'));
+            return { success: true, data: { passed, warnings, failed, results } };
+        }
+    }
+};
+export default doctorCommand;
+//# sourceMappingURL=doctor.js.map