@claude-flow/cli 3.32.3 → 3.32.5

package/dist/src/commands/doctor.js

@@ -0,0 +1,1902 @@
+/**
+ * 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';
+import { resolveMemoryPackageFromProject, readMemoryPackageVersion, recordMemoryPackagePath, } from '../init/memory-package-resolver.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
+/**
+ * #2448 — Detect the runaway `npx @claude-flow/cli@latest` statusLine / hook
+ * commands left over in `.claude/settings.json` from pre-#2337 installs.
+ *
+ * These fire on every Claude Code event (statusLine refires every few hundred
+ * ms, hooks fire per tool-use), each spawning a cold Node process + npm
+ * registry round-trip. On the reporter's 48 GB macOS box this produced
+ * load average 49, jetsam, and a kernel watchdog panic two minutes after
+ * boot. Severity is CRITICAL when present; users who installed before #2337
+ * and never re-ran `ruflo init` still have it.
+ *
+ * Detection only — does not modify settings. Fix path is `ruflo init` (the
+ * executor's migration logic, also patched in #2448, will now regenerate
+ * the broken commands).
+ */
+async function checkStaleSettingsNpx() {
+    // Same regex pattern the executor migration uses — kept in sync. Flag-list
+    // repetition bounded at 10 (CodeQL js/redos — unbounded `*` here is
+    // exponential-backtracking-prone on a crafted settings.json).
+    const BROKEN_RE = /npx\s+(?:--?\S+\s+){0,10}@?claude-flow\/cli@latest\s+hooks\s+(?:statusline|\S+)/;
+    // Look in both project-local and home-dir settings.
+    const candidates = [
+        join(process.cwd(), '.claude', 'settings.json'),
+        join(process.env.HOME ?? '', '.claude', 'settings.json'),
+    ].filter((p, i, a) => p && a.indexOf(p) === i);
+    const offenders = [];
+    for (const settingsPath of candidates) {
+        if (!existsSync(settingsPath))
+            continue;
+        let settings;
+        try {
+            settings = JSON.parse(readFileSync(settingsPath, 'utf8'));
+        }
+        catch {
+            continue; // checkConfigFile reports JSON errors separately
+        }
+        // statusLine.command
+        const sl = settings.statusLine;
+        if (sl?.command && BROKEN_RE.test(sl.command)) {
+            offenders.push({ path: settingsPath, where: 'statusLine' });
+        }
+        // hooks.<event>[].hooks[].command
+        const hooks = settings.hooks;
+        if (hooks) {
+            for (const [eventName, groups] of Object.entries(hooks)) {
+                if (!Array.isArray(groups))
+                    continue;
+                for (const group of groups) {
+                    if (!Array.isArray(group.hooks))
+                        continue;
+                    for (const h of group.hooks) {
+                        if (typeof h?.command === 'string' && BROKEN_RE.test(h.command)) {
+                            offenders.push({ path: settingsPath, where: `hooks.${eventName}` });
+                        }
+                    }
+                }
+            }
+        }
+    }
+    if (offenders.length === 0) {
+        return { name: 'Stale npx@latest in settings (#2448)', status: 'pass', message: 'no runaway commands detected' };
+    }
+    // Group by file for readable output
+    const byFile = offenders.reduce((acc, o) => {
+        (acc[o.path] ??= []).push(o.where);
+        return acc;
+    }, {});
+    const summary = Object.entries(byFile)
+        .map(([p, wheres]) => `${p} [${[...new Set(wheres)].join(', ')}]`)
+        .join('; ');
+    return {
+        name: 'Stale npx@latest in settings (#2448)',
+        status: 'fail',
+        message: `CRITICAL — runaway \`npx @claude-flow/cli@latest\` commands detected: ${summary}`,
+        fix: 'Re-run `npx ruflo init` to migrate (the v3.13.3+ init migrator regenerates these to local-helper form). On macOS this prevents the process-storm / kernel-panic class reported in #2448.',
+    };
+}
+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' };
+}
+// ═══════════════════════════════════════════════════════════════════════════
+// #2677 — memory doctor: functional checks (stuinfla)
+//
+// The existing `checkMemoryDatabase` above asserts existence + statability
+// only, so it CANNOT distinguish a healthy DB from a 99.97%-empty or
+// SQLite-malformed one. Stuinfla reported both cases live (81-store fleet).
+// The three checks below layer functional assertions on top, ordered so
+// the earliest chain-break is always the first red the user sees:
+//   1. Integrity          — can sql.js open it AND does PRAGMA integrity_check pass?
+//   2. Content            — do most memory_entries rows carry non-empty content?
+//   3. Embedding coverage — do most rows have a vector? (unembedded rows are
+//                           both unrecallable AND undistillable per ADR-174)
+// Ordering matters: content ratio is meaningless on a DB that can't open;
+// embedding coverage is meaningless on rows with no content. First red wins.
+//
+// Recall probe (stuinfla check 4) requires actual write+search+delete round
+// trips through the CLI's own memory pipeline — deferred to a follow-up PR
+// to keep this one purely additive and safe.
+//
+// Design rules (also from stuinfla's report):
+//   - "A check that cannot fail protects nothing" — every check has a
+//     demonstrable red state.
+//   - "UNKNOWN is never PASS" — if the check can't RUN, report warn/fail,
+//     never a reassuring pass. Encrypted-DB case gets warn with the caveat
+//     spelled out; corruption gets fail.
+//   - "Print the measurement, not a checkmark" — messages include the
+//     ratios so operators see the shape of the problem.
+/** Resolve the same DB path checkMemoryDatabase above uses. Returns null
+ * if no candidate exists (in which case none of these checks should
+ * fire — checkMemoryDatabase will already have surfaced the missing DB). */
+async function resolveMemoryDbPath() {
+    const candidates = [];
+    try {
+        const { getMemoryRoot } = await import('../memory/memory-initializer.js');
+        candidates.push(join(getMemoryRoot(), 'memory.db'));
+    }
+    catch { /* fall through to legacy candidates */ }
+    candidates.push('.swarm/memory.db', '.claude-flow/memory.db', 'data/memory/memory.db', 'data/memory.db');
+    for (const p of candidates)
+        if (existsSync(p))
+            return p;
+    return null;
+}
+/** Open a sql.js Database over an on-disk file, returning null when the
+ * file can't be opened as a SQLite database (encrypted / corrupted / not
+ * a database). Callers decide whether that's warn or fail. */
+async function tryOpenSqlJs(dbPath) {
+    try {
+        const initSqlJs = (await import('sql.js')).default ?? (await import('sql.js'));
+        const SQL = await (typeof initSqlJs === 'function' ? initSqlJs() : initSqlJs.default());
+        const { readFileSync } = await import('fs');
+        const buf = readFileSync(dbPath);
+        return new SQL.Database(new Uint8Array(buf));
+    }
+    catch {
+        return null;
+    }
+}
+// Check 1 — sql.js can open it AND PRAGMA integrity_check returns 'ok'.
+// Two fail modes handled distinctly per "UNKNOWN is never PASS":
+//   - Open fails: warn ("cannot open; encrypted DB or corrupt — doctor
+//     can't distinguish from this side")
+//   - Open succeeds but pragma != 'ok': fail (definite corruption)
+async function checkMemoryIntegrity() {
+    const dbPath = await resolveMemoryDbPath();
+    if (!dbPath)
+        return { name: 'Memory Integrity', status: 'warn', message: 'no memory.db found (see Memory Database check above)' };
+    const db = await tryOpenSqlJs(dbPath);
+    if (!db) {
+        return {
+            name: 'Memory Integrity',
+            status: 'warn',
+            message: `${dbPath} — sql.js can't open (encrypted DB or corrupt; doctor can't tell which from outside)`,
+            fix: 'if encrypted: expected. if not: back up + `claude-flow memory init --force` to rebuild',
+        };
+    }
+    try {
+        const res = db.exec('PRAGMA integrity_check');
+        const rows = res[0]?.values?.map((v) => String(v[0])) ?? [];
+        if (rows.length === 1 && rows[0] === 'ok') {
+            return { name: 'Memory Integrity', status: 'pass', message: `${dbPath} — PRAGMA integrity_check: ok` };
+        }
+        return {
+            name: 'Memory Integrity',
+            status: 'fail',
+            message: `${dbPath} — PRAGMA integrity_check: ${rows.slice(0, 3).join('; ')}${rows.length > 3 ? ` (+${rows.length - 3} more)` : ''}`,
+            fix: 'back up .swarm/memory.db then `claude-flow memory init --force`',
+        };
+    }
+    catch (e) {
+        const msg = e.message || String(e);
+        const encryptedOrCorrupt = msg.includes('file is not a database') || msg.includes('malformed');
+        return {
+            name: 'Memory Integrity',
+            status: 'warn',
+            message: encryptedOrCorrupt
+                ? `${dbPath} — DB refused query: ${msg} (encrypted DB or corruption; see Memory Integrity above)`
+                : `${dbPath} — probe threw: ${msg}`,
+        };
+    }
+    finally {
+        try {
+            db.close();
+        }
+        catch { /* best-effort */ }
+    }
+}
+// Check 2 — memory_entries rows should mostly carry non-empty content.
+// Stuinfla's live case: 11,133 rows, 3 with content (0.03%). Threshold 95%
+// is the number he proposed. Values below → fail with the exact ratio in
+// the message ("Print the measurement, not a checkmark").
+async function checkMemoryContent() {
+    const dbPath = await resolveMemoryDbPath();
+    if (!dbPath)
+        return { name: 'Memory Content', status: 'warn', message: 'no memory.db found' };
+    const db = await tryOpenSqlJs(dbPath);
+    if (!db)
+        return { name: 'Memory Content', status: 'warn', message: 'DB unreadable (see Memory Integrity)' };
+    try {
+        const tables = db.exec("SELECT name FROM sqlite_master WHERE type='table' AND name='memory_entries'")[0]?.values?.map((v) => String(v[0])) ?? [];
+        if (tables.length === 0)
+            return { name: 'Memory Content', status: 'warn', message: 'no memory_entries table in DB — schema mismatch or empty init' };
+        const r = db.exec("SELECT count(*), sum(CASE WHEN length(trim(coalesce(content,'')))>0 THEN 1 ELSE 0 END) FROM memory_entries");
+        const total = Number(r[0]?.values?.[0]?.[0] ?? 0);
+        const populated = Number(r[0]?.values?.[0]?.[1] ?? 0);
+        if (total === 0)
+            return { name: 'Memory Content', status: 'pass', message: `${dbPath} — 0 rows (fresh DB, expected)` };
+        const ratio = populated / total;
+        const pct = (ratio * 100).toFixed(2);
+        const detail = `content ${populated}/${total} (${pct}%)`;
+        if (ratio < 0.95) {
+            return {
+                name: 'Memory Content',
+                status: 'fail',
+                message: `${dbPath} — ${detail} below 95% floor`,
+                fix: 'schema drift likely (rename of value→content or similar). check migration state via `claude-flow migrate status`',
+            };
+        }
+        return { name: 'Memory Content', status: 'pass', message: `${dbPath} — ${detail}` };
+    }
+    catch (e) {
+        const msg = e.message || String(e);
+        const encryptedOrCorrupt = msg.includes('file is not a database') || msg.includes('malformed');
+        return {
+            name: 'Memory Content',
+            status: 'warn',
+            message: encryptedOrCorrupt
+                ? `${dbPath} — DB refused query: ${msg} (encrypted DB or corruption; see Memory Integrity above)`
+                : `${dbPath} — probe threw: ${msg}`,
+        };
+    }
+    finally {
+        try {
+            db.close();
+        }
+        catch { /* best-effort */ }
+    }
+}
+// Check 3 — most memory_entries with content should also carry an embedding
+// vector. Rows without a vector are BOTH unrecallable (no similarity search
+// can find them) AND undistillable (ADR-174's distill skips rows with no
+// parseable vector). Same 95% threshold + fail-with-ratio pattern as check 2.
+//
+// Embedding storage varies across ruflo installs (agentdb migrations, HNSW
+// index vs inline vector column). Discovers the shape via schema probes,
+// falls back to warn if the schema is unrecognized (better than a false
+// pass, per "UNKNOWN is never PASS").
+async function checkMemoryEmbeddingCoverage() {
+    const dbPath = await resolveMemoryDbPath();
+    if (!dbPath)
+        return { name: 'Memory Embedding Coverage', status: 'warn', message: 'no memory.db found' };
+    const db = await tryOpenSqlJs(dbPath);
+    if (!db)
+        return { name: 'Memory Embedding Coverage', status: 'warn', message: 'DB unreadable (see Memory Integrity)' };
+    try {
+        // Schema-shape discovery. Three candidate columns / tables we've seen
+        // across the agentdb / ruvector history — first match wins.
+        const cols = db.exec("PRAGMA table_info(memory_entries)");
+        const colNames = new Set((cols[0]?.values ?? []).map((v) => String(v[1])));
+        let vectorPredicate = null;
+        if (colNames.has('embedding'))
+            vectorPredicate = "embedding IS NOT NULL AND length(embedding) > 0";
+        else if (colNames.has('vector'))
+            vectorPredicate = "vector IS NOT NULL AND length(vector) > 0";
+        if (!vectorPredicate) {
+            const otherTables = db.exec("SELECT name FROM sqlite_master WHERE type='table' AND name IN ('vector_indexes','embeddings','memory_embeddings')")[0]?.values?.map((v) => String(v[0])) ?? [];
+            if (otherTables.length === 0) {
+                return {
+                    name: 'Memory Embedding Coverage',
+                    status: 'warn',
+                    message: 'no embedding column/table recognized (agentdb schema mismatch or older format) — doctor cannot measure',
+                };
+            }
+            const tbl = otherTables[0];
+            const r = db.exec(`SELECT count(*) FROM memory_entries m WHERE EXISTS (SELECT 1 FROM ${tbl} e WHERE e.memory_id = m.id OR e.entry_id = m.id OR e.id = m.id)`);
+            const withEmbedding = Number(r[0]?.values?.[0]?.[0] ?? 0);
+            const total = Number(db.exec("SELECT count(*) FROM memory_entries WHERE length(trim(coalesce(content,'')))>0")[0]?.values?.[0]?.[0] ?? 0);
+            if (total === 0)
+                return { name: 'Memory Embedding Coverage', status: 'pass', message: `${dbPath} — 0 content rows (nothing to embed)` };
+            const ratio = withEmbedding / total;
+            const pct = (ratio * 100).toFixed(2);
+            const detail = `embedded ${withEmbedding}/${total} (${pct}%) via ${tbl}`;
+            if (ratio < 0.95)
+                return { name: 'Memory Embedding Coverage', status: 'fail', message: `${dbPath} — ${detail} below 95% floor`, fix: 'unembedded rows are unrecallable + undistillable — re-run `claude-flow memory embed --namespace <name>` for populated namespaces' };
+            return { name: 'Memory Embedding Coverage', status: 'pass', message: `${dbPath} — ${detail}` };
+        }
+        // Inline embedding column
+        const r = db.exec(`SELECT count(*), sum(CASE WHEN ${vectorPredicate} THEN 1 ELSE 0 END) FROM memory_entries WHERE length(trim(coalesce(content,'')))>0`);
+        const total = Number(r[0]?.values?.[0]?.[0] ?? 0);
+        const withEmb = Number(r[0]?.values?.[0]?.[1] ?? 0);
+        if (total === 0)
+            return { name: 'Memory Embedding Coverage', status: 'pass', message: `${dbPath} — 0 content rows (nothing to embed)` };
+        const ratio = withEmb / total;
+        const pct = (ratio * 100).toFixed(2);
+        const detail = `embedded ${withEmb}/${total} (${pct}%)`;
+        if (ratio < 0.95) {
+            return { name: 'Memory Embedding Coverage', status: 'fail', message: `${dbPath} — ${detail} below 95% floor`, fix: 'unembedded rows are unrecallable + undistillable — re-run `claude-flow memory embed --namespace <name>` for populated namespaces' };
+        }
+        return { name: 'Memory Embedding Coverage', status: 'pass', message: `${dbPath} — ${detail}` };
+    }
+    catch (e) {
+        const msg = e.message || String(e);
+        const encryptedOrCorrupt = msg.includes('file is not a database') || msg.includes('malformed');
+        return {
+            name: 'Memory Embedding Coverage',
+            status: 'warn',
+            message: encryptedOrCorrupt
+                ? `${dbPath} — DB refused query: ${msg} (encrypted DB or corruption; see Memory Integrity above)`
+                : `${dbPath} — probe threw: ${msg}`,
+        };
+    }
+    finally {
+        try {
+            db.close();
+        }
+        catch { /* best-effort */ }
+    }
+}
+// #2545: Check that the self-learning bridge can actually load @claude-flow/memory
+// the SAME way the SessionStart auto-memory hook does. On the documented `npx ruflo`
+// path the package lands in the npx cache — unreachable from the project — so the
+// hook silently no-op'd with no signal anywhere. This surfaces it.
+async function checkLearningBridge() {
+    const cwd = process.cwd();
+    const hookPath = join(cwd, '.claude', 'helpers', 'auto-memory-hook.mjs');
+    // Only relevant once init has deployed the hook; otherwise stay quiet.
+    if (!existsSync(hookPath)) {
+        return {
+            name: 'Learning Bridge',
+            status: 'pass',
+            message: 'auto-memory hook not installed (run: npx ruflo@latest init)',
+        };
+    }
+    const distPath = resolveMemoryPackageFromProject(cwd);
+    if (distPath) {
+        const version = readMemoryPackageVersion(distPath);
+        return {
+            name: 'Learning Bridge',
+            status: 'pass',
+            message: `@claude-flow/memory resolvable${version ? ` (v${version})` : ''}`,
+        };
+    }
+    // #2599: Self-heal on plain `doctor` (not just --fix). The project-side resolver
+    // fails when the sidecar is stale or missing (e.g. npx cache generation rotated),
+    // but the CLI process itself can resolve @claude-flow/memory from its own module
+    // context. Write the sidecar automatically instead of hard-failing the check.
+    const record = recordMemoryPackagePath(cwd, 'doctor-auto');
+    if (record) {
+        const version = readMemoryPackageVersion(record.distPath);
+        return {
+            name: 'Learning Bridge',
+            status: 'pass',
+            message: `@claude-flow/memory resolvable via auto-recorded sidecar${version ? ` (v${version})` : ''}`,
+        };
+    }
+    return {
+        name: 'Learning Bridge',
+        status: 'fail',
+        message: '@claude-flow/memory NOT resolvable — SessionStart self-learning imports are a silent no-op',
+        fix: 'npm i -D @claude-flow/memory   (optional dep appears absent — likely --omit=optional install)',
+    };
+}
+// 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';
+    // Canonical MCP-server key is `claude-flow` — matches the `mcp__claude-flow__*`
+    // prefix that ~166 plugin tool references depend on (#2206). A `ruflo`-keyed
+    // entry pointing at the same binary is the legacy duplicate created by
+    // pre-rename setup docs that #2612 tracks; doctor treats it as removable.
+    const isCurrentRufloKey = (k) => k === 'claude-flow' || k === 'claude-flow_alpha';
+    const isLegacyRufloKey = (k) => k === 'ruflo' || k === 'ruflo_alpha';
+    const isRufloServer = (server) => {
+        if (!server || typeof server !== 'object')
+            return false;
+        const entry = server;
+        const command = typeof entry.command === 'string' ? entry.command : '';
+        const args = Array.isArray(entry.args)
+            ? entry.args.filter((arg) => typeof arg === 'string')
+            : [];
+        const haystack = [command, ...args].join(' ');
+        return /\b(?:ruflo|claude-flow|@claude-flow\/cli)(?:@[\w.-]+)?\b/.test(haystack);
+    };
+    let totalServersSeen = 0;
+    const rufloLocations = [];
+    const duplicateLocations = [];
+    const legacyLocations = [];
+    const currentLocations = [];
+    const inspectServers = (servers, location) => {
+        if (!servers || typeof servers !== 'object')
+            return { total: 0, hasRuflo: false };
+        const entries = Object.entries(servers);
+        const activeRufloEntries = entries.filter(([key, server]) => isRufloKey(key) && isRufloServer(server));
+        const hasLegacy = activeRufloEntries.some(([key]) => isLegacyRufloKey(key));
+        const hasCurrent = activeRufloEntries.some(([key]) => isCurrentRufloKey(key));
+        if (activeRufloEntries.length > 0) {
+            rufloLocations.push(`${location}: ${activeRufloEntries.map(([key]) => key).join(', ')}`);
+        }
+        if (hasLegacy && hasCurrent) {
+            duplicateLocations.push(`${location}: ${activeRufloEntries.map(([key]) => key).join(' + ')}`);
+        }
+        for (const [key] of activeRufloEntries) {
+            if (isLegacyRufloKey(key))
+                legacyLocations.push(`${location}: ${key}`);
+            if (isCurrentRufloKey(key))
+                currentLocations.push(`${location}: ${key}`);
+        }
+        return { total: entries.length, hasRuflo: activeRufloEntries.length > 0 };
+    };
+    for (const configPath of mcpConfigPaths) {
+        if (!existsSync(configPath))
+            continue;
+        try {
+            const content = JSON.parse(readFileSync(configPath, 'utf8'));
+            // Top-level mcpServers (legacy / desktop form)
+            const topResult = inspectServers(content.mcpServers || content.servers || {}, `${configPath} top-level`);
+            totalServersSeen += topResult.total;
+            // Project-scoped (Claude Code shape): projects[*].mcpServers.ruflo
+            if (content.projects && typeof content.projects === 'object') {
+                for (const [projectKey, projectVal] of Object.entries(content.projects)) {
+                    const pm = projectVal?.mcpServers;
+                    if (pm && typeof pm === 'object') {
+                        const projectResult = inspectServers(pm, `${configPath} projects[${projectKey}]`);
+                        totalServersSeen += projectResult.total;
+                    }
+                }
+            }
+        }
+        catch {
+            // continue to next path
+        }
+    }
+    if (duplicateLocations.length > 0 || (legacyLocations.length > 0 && currentLocations.length > 0)) {
+        const locations = duplicateLocations.length > 0
+            ? duplicateLocations.join('; ')
+            : `legacy ${legacyLocations.join('; ')} + current ${currentLocations.join('; ')}`;
+        return {
+            name: 'MCP Servers',
+            status: 'warn',
+            message: `Duplicate Ruflo MCP registrations found (${locations}) — Claude Code will start both tool schemas`,
+            fix: 'Remove the legacy `ruflo`-keyed MCP registration (pre-rename duplicate) and keep the canonical `claude-flow` entry: `claude mcp add claude-flow -- npx -y ruflo@latest mcp start`. The canonical key stays `claude-flow` so the ~166 `mcp__claude-flow__*` plugin tool references keep resolving (#2206).',
+        };
+    }
+    if (rufloLocations.length > 0) {
+        return {
+            name: 'MCP Servers',
+            status: 'pass',
+            message: `${totalServersSeen} servers (ruflo configured: ${rufloLocations.join('; ')})`,
+        };
+    }
+    if (totalServersSeen > 0) {
+        return {
+            name: 'MCP Servers',
+            status: 'warn',
+            message: `${totalServersSeen} servers (ruflo not found)`,
+            fix: 'claude mcp add claude-flow -- npx -y ruflo@latest mcp start',
+        };
+    }
+    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)
+// ADR-150 — surface MetaHarness availability + harnessFit score in
+// the standard ruflo doctor flow. Graceful degradation: when metaharness
+// is not installed (no network, optionalDep skipped), the check returns
+// `warn` with a hint instead of `fail` — ruflo continues to function.
+/**
+ * iter 45 — verify the ruflo-side MetaHarness integration is intact.
+ *
+ * The existing `checkMetaharness` verifies the UPSTREAM `metaharness`
+ * package is reachable (warn if missing — it's optional per ADR-150).
+ * This check verifies the INTEGRATION LAYER (plugin scripts, production
+ * module, subprocess bridge) is intact. Unlike upstream, the integration
+ * layer is shipped with ruflo — missing files mean ruflo's install is
+ * corrupted, not that an optional dep is absent.
+ *
+ * Status mapping:
+ *   pass — all required files present + module loads + similarity() smoke OK
+ *   fail — any required file missing OR module fails to import
+ *   warn — files present but module import errored at runtime
+ *
+ * Verified files (iter 36-53 surfaces — full ADR-150 deep-integration set):
+ *   - plugins/ruflo-metaharness/scripts/_harness.mjs                (subprocess bridge)
+ *   - plugins/ruflo-metaharness/scripts/_similarity.mjs             (ADR-152 §3.1 module, iter 36)
+ *   - plugins/ruflo-metaharness/scripts/similarity.mjs              (CLI skill, iter 36)
+ *   - plugins/ruflo-metaharness/scripts/_spike-similarity.mjs       (regression anchor, iter 35)
+ *   - plugins/ruflo-metaharness/scripts/drift-from-history.mjs      (1-command primitive, iter 53)
+ *   - plugins/ruflo-metaharness/skills/harness-similarity/SKILL.md
+ *   - plugins/ruflo-metaharness/skills/harness-drift-from-history/SKILL.md  (iter 53)
+ */
+/**
+ * ADR-305 — funnel state audit. Reports the effective enabled/disabled
+ * state and, critically for enterprise audit verification, WHICH
+ * precedence source decided it (env > enterprise > user > default).
+ * Informational: both states are `pass`; only a resolver failure warns.
+ */
+async function checkFunnel() {
+    try {
+        const { resolveFunnelEnabled, getDisclosure } = await import('../funnel/index.js');
+        const decision = resolveFunnelEnabled();
+        const disclosure = getDisclosure();
+        return {
+            name: 'Funnel (ADR-305)',
+            status: 'pass',
+            message: `${decision.enabled ? 'enabled' : 'disabled'} (decided by: ${decision.decidedBy}; disclosure: ${disclosure.state})`,
+        };
+    }
+    catch (err) {
+        return {
+            name: 'Funnel (ADR-305)',
+            status: 'warn',
+            message: `state unreadable: ${err instanceof Error ? err.message : String(err)}`,
+            fix: 'ruflo funnel status',
+        };
+    }
+}
+/** Meta LLM Proxy — sponsored-downtime health (ADR-313). */
+async function checkProxySponsoredConsent() {
+    try {
+        const { funnelStateDir, hasConsent, readRateLimitStatus, lastRecordedEvent } = await import('../funnel/index.js');
+        const dir = funnelStateDir();
+        const installed = existsSync(join(dir, 'proxy-token'));
+        const consented = hasConsent('sponsored-downtime');
+        const rateLimited = readRateLimitStatus();
+        const lastExhausted = lastRecordedEvent('sponsor_capacity_exhausted');
+        if (!installed) {
+            return {
+                name: 'Meta LLM Proxy (ADR-313)',
+                status: 'warn',
+                message: 'not installed — no proxy-token found; sponsored-downtime capacity is unavailable',
+                fix: 'See cognitum-one/meta-proxy (private) for install instructions',
+            };
+        }
+        const parts = [
+            `sponsored consent: ${consented ? 'granted' : 'not granted'}`,
+            `rate-limit flag: ${rateLimited.limited ? `set (since ${rateLimited.since})` : 'not set'}`,
+        ];
+        if (lastExhausted)
+            parts.push(`last capacity-exhausted: ${lastExhausted}`);
+        if (rateLimited.limited && !consented) {
+            return {
+                name: 'Meta LLM Proxy (ADR-313)',
+                status: 'warn',
+                message: `${parts.join('; ')} — flagged rate-limited but sponsored capacity isn't enabled`,
+                fix: 'ruflo proxy sponsor-enable --yes',
+            };
+        }
+        return { name: 'Meta LLM Proxy (ADR-313)', status: 'pass', message: parts.join('; ') };
+    }
+    catch (err) {
+        return {
+            name: 'Meta LLM Proxy (ADR-313)',
+            status: 'warn',
+            message: `state unreadable: ${err instanceof Error ? err.message : String(err)}`,
+            fix: 'ruflo proxy sponsor-status',
+        };
+    }
+}
+/**
+ * Binary presence + tamper check (ADR-307). Deliberately NEVER spawns the
+ * binary to probe a version — confirmed empirically (2026-07-16) that
+ * `meta-proxy` has no `--version`/`--help` flag and starts the live server
+ * as a side effect of ANY invocation, which a doctor health check must never
+ * do. Version info instead comes from install-manifest.json (written at
+ * install time) and, once running, the proxy's own `/status` endpoint via
+ * checkProxyProcess below.
+ */
+async function checkProxyBinary() {
+    const NAME = 'Meta LLM Proxy binary (ADR-307)';
+    try {
+        const { proxyBinaryPath, proxyInstallManifestPath } = await import('../proxy/paths.js');
+        const binPath = proxyBinaryPath();
+        if (!existsSync(binPath)) {
+            return { name: NAME, status: 'warn', message: 'not installed', fix: 'ruflo proxy install' };
+        }
+        const manifestPath = proxyInstallManifestPath();
+        if (!existsSync(manifestPath)) {
+            return {
+                name: NAME,
+                status: 'warn',
+                message: 'binary present but no install-manifest.json — provenance unknown (installed outside `ruflo proxy install`?)',
+                fix: 'ruflo proxy update --release <x.y.z>',
+            };
+        }
+        const manifest = JSON.parse(readFileSync(manifestPath, 'utf-8'));
+        const liveSha = createHash('sha256').update(readFileSync(binPath)).digest('hex');
+        if (liveSha !== manifest.sha256) {
+            return {
+                name: NAME,
+                status: 'fail',
+                message: `binary sha256 does not match the recorded install manifest — possible tampering or a manual overwrite (expected ${manifest.sha256.slice(0, 12)}…, got ${liveSha.slice(0, 12)}…)`,
+                fix: 'ruflo proxy update --release <x.y.z>',
+            };
+        }
+        return { name: NAME, status: 'pass', message: `v${manifest.version}, signature-verified at install (${manifest.verifiedAt})` };
+    }
+    catch (err) {
+        return { name: NAME, status: 'warn', message: `check failed: ${err instanceof Error ? err.message : String(err)}` };
+    }
+}
+/** PID-file liveness (ADR-307) — mirrors daemon.ts's signal-0 probe pattern. */
+async function checkProxyProcess() {
+    const NAME = 'Meta LLM Proxy process (ADR-307)';
+    try {
+        const { proxyPidFilePath } = await import('../proxy/paths.js');
+        const pidPath = proxyPidFilePath();
+        if (!existsSync(pidPath)) {
+            return { name: NAME, status: 'warn', message: 'not running (no PID file)', fix: 'ruflo proxy start' };
+        }
+        const pidRaw = readFileSync(pidPath, 'utf-8').trim();
+        const pid = parseInt(pidRaw, 10);
+        if (!Number.isFinite(pid)) {
+            return { name: NAME, status: 'warn', message: `PID file is malformed: ${JSON.stringify(pidRaw)}`, fix: 'ruflo proxy stop && ruflo proxy start' };
+        }
+        try {
+            process.kill(pid, 0); // signal-0 liveness probe — throws if the process is dead
+        }
+        catch {
+            return { name: NAME, status: 'warn', message: `PID file points at ${pid}, which is not running — stale PID file`, fix: 'ruflo proxy start' };
+        }
+        // Live version-compat + data-plane info, ONLY once PID liveness already
+        // confirmed a process is running (never spawns anything — see
+        // checkProxyBinary's comment on why probing via process launch is unsafe).
+        // GET /status shape confirmed against the real v0.1.0 binary:
+        // {"version","data_plane","bind","sponsored_available","proxy_token_valid"}.
+        const { proxyConfigPath, proxyTokenPath, proxyInstallManifestPath } = await import('../proxy/paths.js');
+        const bindMatch = existsSync(proxyConfigPath())
+            ? readFileSync(proxyConfigPath(), 'utf-8').match(/^bind\s*=\s*"([^"]*)"/m)
+            : null;
+        const bind = bindMatch ? bindMatch[1] : '127.0.0.1:11435';
+        let token;
+        try {
+            token = readFileSync(proxyTokenPath(), 'utf-8').trim();
+        }
+        catch {
+            return { name: NAME, status: 'pass', message: `running (pid ${pid}); no proxy-token to query /status` };
+        }
+        try {
+            const controller = new AbortController();
+            const timer = setTimeout(() => controller.abort(), 2000);
+            const resp = await fetch(`http://${bind}/status`, {
+                headers: { authorization: `Bearer ${token}` },
+                signal: controller.signal,
+            });
+            clearTimeout(timer);
+            if (!resp.ok) {
+                return { name: NAME, status: 'warn', message: `running (pid ${pid}); /status returned HTTP ${resp.status}` };
+            }
+            const body = (await resp.json());
+            let versionNote = '';
+            if (existsSync(proxyInstallManifestPath())) {
+                const manifest = JSON.parse(readFileSync(proxyInstallManifestPath(), 'utf-8'));
+                if (manifest.version && body.version && manifest.version !== body.version) {
+                    return {
+                        name: NAME,
+                        status: 'warn',
+                        message: `running (pid ${pid}) reports v${body.version}, but the installed binary is v${manifest.version} — a stale process from a previous version?`,
+                        fix: 'ruflo proxy stop && ruflo proxy start',
+                    };
+                }
+                versionNote = body.version ? ` v${body.version}` : '';
+            }
+            return {
+                name: NAME,
+                status: 'pass',
+                message: `running (pid ${pid})${versionNote}; data plane: ${body.data_plane ?? 'unknown'}`,
+            };
+        }
+        catch (err) {
+            // Live process but /status unreachable (still starting up, or a
+            // network hiccup) — not a failure, PID liveness already passed.
+            return {
+                name: NAME,
+                status: 'pass',
+                message: `running (pid ${pid}); /status unreachable (${err instanceof Error ? err.message : String(err)})`,
+            };
+        }
+    }
+    catch (err) {
+        return { name: NAME, status: 'warn', message: `check failed: ${err instanceof Error ? err.message : String(err)}` };
+    }
+}
+/** Non-loopback bind exposure warning (ADR-307's mandated startup warning, surfaced in doctor too). */
+async function checkProxyBindAddress() {
+    const NAME = 'Meta LLM Proxy bind address (ADR-307)';
+    try {
+        const { proxyConfigPath, isLoopbackBind } = await import('../proxy/paths.js');
+        const cfgPath = proxyConfigPath();
+        if (!existsSync(cfgPath)) {
+            return { name: NAME, status: 'pass', message: 'no config file yet — defaults to loopback-only (127.0.0.1:11435)' };
+        }
+        const raw = readFileSync(cfgPath, 'utf-8');
+        const match = raw.match(/^bind\s*=\s*"([^"]*)"/m);
+        const bind = match ? match[1] : '127.0.0.1:11435';
+        if (!isLoopbackBind(bind)) {
+            return {
+                name: NAME,
+                status: 'warn',
+                message: `bound to non-loopback address ${bind} — this exposes the proxy to your network`,
+                fix: 'Set bind back to 127.0.0.1:<port> in proxy-config.toml unless external exposure is intended',
+            };
+        }
+        return { name: NAME, status: 'pass', message: `loopback-only (${bind})` };
+    }
+    catch (err) {
+        return { name: NAME, status: 'warn', message: `check failed: ${err instanceof Error ? err.message : String(err)}` };
+    }
+}
+/** `ruflo auth` health (ADR-306). Warn (never fail) on absence — auth is never required for core functionality. */
+async function checkAuth() {
+    const NAME = 'Cognitum identity (ADR-306)';
+    try {
+        const { listProfiles } = await import('../auth/state.js');
+        const { domainForScope } = await import('../auth/scopes.js');
+        const { hasConsent } = await import('../funnel/index.js');
+        const { profiles } = listProfiles();
+        if (profiles.length === 0) {
+            return { name: NAME, status: 'warn', message: 'not logged in', fix: 'ruflo auth login' };
+        }
+        let keychainAvailable = 'unknown';
+        try {
+            const sec = await import('@claude-flow/security');
+            keychainAvailable = await (await sec.createKeychainAdapter()).isAvailable();
+        }
+        catch {
+            keychainAvailable = 'unknown'; // security package unavailable — surfaced by checkProxyBinary's sibling concerns, not duplicated here
+        }
+        // Scope-vs-receipt consistency check (ADR-306: "fail-closed... reports").
+        // Unlike every other check in this file, a violation here is a FAIL, not
+        // a warn — a scope present without a matching consent receipt is exactly
+        // the condition ADR-306 says must never silently pass.
+        const violations = [];
+        for (const p of profiles) {
+            for (const scope of p.scopes) {
+                const domain = domainForScope(scope);
+                if (domain && !hasConsent(domain))
+                    violations.push(`${p.profile}: ${scope}`);
+            }
+        }
+        if (violations.length > 0) {
+            return {
+                name: NAME,
+                status: 'fail',
+                message: `scope granted without a matching consent receipt: ${violations.join(', ')}`,
+                fix: 'ruflo auth logout && ruflo auth login',
+            };
+        }
+        const names = profiles.map((p) => p.profile).join(', ');
+        const sessionOnly = profiles.filter((p) => !p.keychainRef).map((p) => p.profile);
+        const parts = [`profiles: ${names}`];
+        if (keychainAvailable === false)
+            parts.push('keychain backend unreachable — falling back to session-only tokens');
+        if (sessionOnly.length > 0)
+            parts.push(`session-only (no persisted refresh token): ${sessionOnly.join(', ')}`);
+        return { name: NAME, status: 'pass', message: parts.join('; ') };
+    }
+    catch (err) {
+        return { name: NAME, status: 'warn', message: `check failed: ${err instanceof Error ? err.message : String(err)}` };
+    }
+}
+async function checkMetaharnessIntegration() {
+    // Locate plugins dir.
+    //
+    // Pre-#2437 fix this only walked up from `process.cwd()` + checked one
+    // hard-coded `<cwd>/node_modules/@claude-flow/cli/...` candidate. That
+    // missed the two cases users actually run from:
+    //   (a) `npx @claude-flow/cli@<tag>` → resolves to a per-version cache
+    //       under `~/.npm/_npx/<hash>/node_modules/@claude-flow/cli/...`
+    //   (b) `npm install -g @claude-flow/cli` → lives at
+    //       `$(npm prefix -g)/lib/node_modules/@claude-flow/cli/...`
+    //
+    // The bulletproof fix: resolve relative to THIS file's own location via
+    // `import.meta.url`. The plugins dir is always a sibling of the package
+    // root regardless of where the package was installed. Walk up from
+    // `dist/src/commands/doctor.js` (built) or `src/commands/doctor.ts`
+    // (dev) until we find a directory containing `plugins/ruflo-metaharness/`.
+    const candidates = [];
+    // Strategy 1: walk up from this module's own URL — covers npx + global install.
+    try {
+        const selfDir = dirname(fileURLToPath(import.meta.url));
+        let q = selfDir;
+        for (let i = 0; i < 8; i++) {
+            candidates.push(join(q, 'plugins', 'ruflo-metaharness'));
+            q = dirname(q);
+        }
+    }
+    catch {
+        // import.meta.url unavailable under some bundlers — fall through to cwd walk.
+    }
+    // Strategy 2: walk up from cwd — covers monorepo dev (running from a sub-package).
+    let p = process.cwd();
+    for (let i = 0; i < 8; i++) {
+        candidates.push(join(p, 'plugins', 'ruflo-metaharness'));
+        p = dirname(p);
+    }
+    // Strategy 3: explicit node_modules path relative to cwd — covers project-local install.
+    candidates.push(join(process.cwd(), 'node_modules', '@claude-flow', 'cli', 'plugins', 'ruflo-metaharness'));
+    let pluginDir = null;
+    for (const c of candidates) {
+        if (existsSync(join(c, 'scripts', '_harness.mjs'))) {
+            pluginDir = c;
+            break;
+        }
+    }
+    if (!pluginDir) {
+        // #2437: MetaHarness is documented as an optional dependency in
+        // optionalDependencies (per ADR-150 architectural constraint #2 —
+        // "Optional in package.json"). A genuinely-absent plugin therefore
+        // warrants WARN, not FAIL — same posture as the runtime path which
+        // returns {degraded: true, exit 0}. FAIL is reserved for misconfigured
+        // installs where the plugin SHOULD be present but is broken.
+        return {
+            name: 'MetaHarness integration (ADR-150)',
+            status: 'warn',
+            message: 'plugins/ruflo-metaharness/ not found — MetaHarness skills will degrade gracefully',
+            fix: 'Optional: install via `npm i -D @metaharness/darwin metaharness` or run `ruflo plugins install ruflo-metaharness`',
+        };
+    }
+    // Required files (iter 36+44 surfaces, +ADR-153 darwin surfaces in v3.13.0)
+    const required = [
+        'scripts/_harness.mjs',
+        'scripts/_similarity.mjs',
+        'scripts/similarity.mjs',
+        'scripts/_spike-similarity.mjs',
+        // iter 53 surfaces — gated against silent deletion
+        'scripts/drift-from-history.mjs',
+        'skills/harness-similarity/SKILL.md',
+        'skills/harness-drift-from-history/SKILL.md',
+        // ADR-153 Darwin Mode surfaces (v3.13.0) — added to gate against silent deletion
+        'scripts/_darwin.mjs',
+        'scripts/evolve.mjs',
+        'scripts/security-bench.mjs',
+        'scripts/bench.mjs',
+        'skills/harness-evolve/SKILL.md',
+        'skills/harness-security-bench/SKILL.md',
+        'skills/harness-bench/SKILL.md',
+    ];
+    const missing = required.filter((f) => !existsSync(join(pluginDir, f)));
+    if (missing.length > 0) {
+        return {
+            name: 'MetaHarness integration (ADR-150)',
+            status: 'fail',
+            message: `Missing files: ${missing.join(', ')}`,
+            fix: 'Reinstall ruflo or restore from git: `git checkout HEAD -- plugins/ruflo-metaharness/`',
+        };
+    }
+    // Runtime smoke: import the similarity module and exercise it
+    try {
+        const modPath = join(pluginDir, 'scripts', '_similarity.mjs');
+        const mod = await import(modPath);
+        if (typeof mod.similarity !== 'function') {
+            return {
+                name: 'MetaHarness integration (ADR-150)',
+                status: 'fail',
+                message: '_similarity.mjs does not export similarity()',
+                fix: 'Reinstall ruflo or restore the file from git',
+            };
+        }
+        const result = mod.similarity({}, {});
+        if (typeof result?.overall !== 'number') {
+            return {
+                name: 'MetaHarness integration (ADR-150)',
+                status: 'warn',
+                message: 'similarity() returned unexpected shape; module may be stale',
+            };
+        }
+        // iter 52 — also verify the iter-50 mcp-scan text parser exports
+        // correctly. parseMcpScanText is the shared util both mcp-scan.mjs
+        // and oia-audit.mjs depend on; if it's missing the audit-trend
+        // introduced/cleared diff silently degrades to dead code.
+        //
+        // iter 61 — additionally verify iter-56's async exports
+        // (runHarnessAsync / runMetaharnessAsync). These are the
+        // parallelization primitives oia-audit depends on; if they're
+        // missing, oia-audit's import fails and the whole pipeline breaks.
+        const harnessPath = join(pluginDir, 'scripts', '_harness.mjs');
+        const harnessMod = await import(harnessPath);
+        if (typeof harnessMod.parseMcpScanText !== 'function') {
+            return {
+                name: 'MetaHarness integration (ADR-150)',
+                status: 'fail',
+                message: '_harness.mjs does not export parseMcpScanText (iter 50 — needed by mcp-scan + oia-audit)',
+                fix: 'Reinstall ruflo or restore _harness.mjs from git',
+            };
+        }
+        if (typeof harnessMod.runHarnessAsync !== 'function' || typeof harnessMod.runMetaharnessAsync !== 'function') {
+            return {
+                name: 'MetaHarness integration (ADR-150)',
+                status: 'fail',
+                message: '_harness.mjs missing iter-56 async exports (runHarnessAsync / runMetaharnessAsync) — oia-audit parallelization will fail',
+                fix: 'Reinstall ruflo or restore _harness.mjs from git',
+            };
+        }
+        // Smoke: parser handles empty input gracefully
+        const parsed = harnessMod.parseMcpScanText('');
+        if (!Array.isArray(parsed?.findings)) {
+            return {
+                name: 'MetaHarness integration (ADR-150)',
+                status: 'warn',
+                message: 'parseMcpScanText returned unexpected shape on empty input',
+            };
+        }
+        return {
+            name: 'MetaHarness integration (ADR-150)',
+            status: 'pass',
+            message: 'plugin scripts intact, _similarity.mjs + parseMcpScanText load, smoke OK',
+        };
+    }
+    catch (e) {
+        return {
+            name: 'MetaHarness integration (ADR-150)',
+            status: 'warn',
+            message: `Module import errored: ${e.message.slice(0, 60)}`,
+        };
+    }
+}
+async function checkMetaharness() {
+    try {
+        const version = await runCommand('npx -y metaharness@latest --version 2>&1', 15000);
+        // metaharness emits multi-line stdout; parse a version-shaped line.
+        const versionMatch = version.match(/(\d+\.\d+\.\d+)/);
+        if (!versionMatch) {
+            return {
+                name: 'MetaHarness (ADR-150)',
+                status: 'warn',
+                message: 'Installed but version-string not parseable; integration may still work',
+            };
+        }
+        return {
+            name: 'MetaHarness (ADR-150)',
+            status: 'pass',
+            message: `v${versionMatch[1]} — run \`npx ruflo metaharness score\` for the full scorecard`,
+        };
+    }
+    catch {
+        return {
+            name: 'MetaHarness (ADR-150)',
+            status: 'warn',
+            message: 'Not installed — `npx ruflo metaharness *` commands will degrade gracefully',
+            fix: 'npm install --include=optional  # to enable the metaharness optional dep',
+        };
+    }
+}
+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, agentic-flow, encryption, federation, funnel, proxy, auth, metaharness)',
+            type: 'string'
+        },
+        {
+            name: 'verbose',
+            short: 'v',
+            description: 'Verbose output',
+            type: 'boolean',
+            default: false
+        },
+        {
+            name: 'fix-handles',
+            // Windows-only mitigation for anthropics/claude-code#67888 — Claude Code's
+            // Bash tool spawns cmd.exe/bash.exe without cleaning up child conhost.exe
+            // handles, so a long session accumulates dozens (observed live: 26+
+            // orphaned conhost.exe after a ~4h session). Each holds a kernel object
+            // + ~1MB, and combined with memory pressure this measurably slows the
+            // machine. This flag kills orphan conhost.exe (safe — Windows respawns
+            // on demand). Deliberately does NOT touch cmd.exe/bash.exe — those can
+            // be the invoking shell, and killing them 255's the caller.
+            description: 'Windows only: kill orphaned conhost.exe processes leaked by Claude Code (mitigation for anthropics/claude-code#67888)',
+            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' },
+        { command: 'claude-flow doctor --fix-handles', description: 'Windows: kill leaked conhost.exe from Claude Code sessions' }
+    ],
+    action: async (ctx) => {
+        const showFix = ctx.flags.fix;
+        const autoInstall = ctx.flags.install;
+        const component = ctx.flags.component;
+        const verbose = ctx.flags.verbose;
+        // Parser camelCases kebab-case flag names — read via `fixHandles`, not `['fix-handles']`.
+        const fixHandles = ctx.flags.fixHandles;
+        // Early-return short-circuit: `--fix-handles` is a targeted mitigation, not
+        // part of the health-check flow. Runs, reports, exits.
+        if (fixHandles) {
+            output.writeln();
+            output.writeln(output.bold('RuFlo Doctor — fix-handles'));
+            output.writeln(output.dim('─'.repeat(50)));
+            output.writeln();
+            if (process.platform !== 'win32') {
+                output.printInfo('--fix-handles is a Windows-only mitigation. On this platform (' + process.platform + '), no action taken.');
+                return { success: true };
+            }
+            const { spawnSync } = await import('child_process');
+            // PowerShell one-liner: read before-count, kill conhost, read after-count, report delta.
+            const psScript = [
+                "$before = (Get-Process conhost -EA SilentlyContinue).Count",
+                "$mem_before = [math]::Round((Get-CimInstance Win32_OperatingSystem).FreePhysicalMemory / 1MB, 2)",
+                "$killed = 0",
+                "Get-Process conhost -EA SilentlyContinue | ForEach-Object {",
+                "  try { Stop-Process -Id $_.Id -Force -EA Stop; $killed++ } catch {}",
+                "}",
+                "Start-Sleep -Seconds 1",
+                "$after = (Get-Process conhost -EA SilentlyContinue).Count",
+                "$mem_after = [math]::Round((Get-CimInstance Win32_OperatingSystem).FreePhysicalMemory / 1MB, 2)",
+                "Write-Output ('BEFORE_COUNT=' + $before)",
+                "Write-Output ('KILLED=' + $killed)",
+                "Write-Output ('AFTER_COUNT=' + $after)",
+                "Write-Output ('MEM_BEFORE_GB=' + $mem_before)",
+                "Write-Output ('MEM_AFTER_GB=' + $mem_after)",
+            ].join('; ');
+            const res = spawnSync('powershell', ['-NoProfile', '-Command', psScript], {
+                encoding: 'utf-8', timeout: 30000, windowsHide: true,
+            });
+            if (res.status !== 0) {
+                output.printError('PowerShell exited with code ' + res.status);
+                if (res.stderr)
+                    output.writeln(output.dim(res.stderr));
+                return { success: false, exitCode: 1 };
+            }
+            const parse = (key) => {
+                const line = (res.stdout || '').split('\n').find((l) => l.startsWith(key + '='));
+                return line ? line.slice(key.length + 1).trim() : '?';
+            };
+            const before = parse('BEFORE_COUNT');
+            const killed = parse('KILLED');
+            const after = parse('AFTER_COUNT');
+            const memBefore = parse('MEM_BEFORE_GB');
+            const memAfter = parse('MEM_AFTER_GB');
+            output.writeln('conhost.exe processes:');
+            output.writeln('  before:  ' + before);
+            output.writeln('  killed:  ' + output.success(killed));
+            output.writeln('  after:   ' + after);
+            output.writeln('');
+            output.writeln('Free RAM:');
+            output.writeln('  before:  ' + memBefore + ' GB');
+            output.writeln('  after:   ' + memAfter + ' GB');
+            output.writeln('');
+            output.writeln(output.dim('Note: does NOT touch cmd.exe/bash.exe/node.exe — those may be the invoking shell'));
+            output.writeln(output.dim('      or an active MCP server. Kill them manually if you need to.'));
+            output.writeln('');
+            output.writeln(output.dim('Upstream tracking: https://github.com/anthropics/claude-code/issues/67888'));
+            return { success: true };
+        }
+        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,
+            checkStaleSettingsNpx, // #2448 — runaway `npx @latest` in statusLine/hooks
+            checkDaemonStatus,
+            checkMemoryDatabase,
+            checkLearningBridge, // #2545 — can the auto-memory hook actually load @claude-flow/memory?
+            checkApiKeys,
+            checkMcpServers,
+            checkAIDefence, // #1807
+            checkDiskSpace,
+            checkBuildTools,
+            checkAgenticFlow,
+            checkEncryptionAtRest, // ADR-096 Phase 5
+            checkFederationBreaker, // ADR-097 Phase 4
+            checkMetaharness, // ADR-150 — MetaHarness upstream package
+            checkMetaharnessIntegration, // iter 45 — ruflo-side integration layer
+            checkFunnel, // ADR-305 — effective funnel state + deciding precedence source
+            checkProxySponsoredConsent, // ADR-313 — Meta LLM Proxy sponsored-downtime health
+            checkAuth, // ADR-306 — Cognitum identity (warn-only; never fails bare `ruflo doctor`)
+        ];
+        // #2677: `--component memory` now runs the whole memory-health suite,
+        // not just the existence check. Values can be a single check or an
+        // array — expanded at execution time. Stuinfla's report showed the
+        // existence-only check reporting PASS on a 99.97%-empty and even a
+        // SQLite-malformed DB; the array here layers integrity → content →
+        // embedding coverage over the existing existence probe, ordered so
+        // the earliest chain-break is always the first red the user sees.
+        const componentMap = {
+            'version': checkVersionFreshness,
+            'freshness': checkVersionFreshness,
+            'node': checkNodeVersion,
+            'npm': checkNpmVersion,
+            'claude': checkClaudeCode,
+            'config': checkConfigFile,
+            'stale-settings': checkStaleSettingsNpx, // #2448
+            'daemon': checkDaemonStatus,
+            'memory': [
+                checkMemoryDatabase, // existing: exists + statable (unchanged)
+                checkMemoryIntegrity, // #2677 check 1: sql.js open + PRAGMA integrity_check
+                checkMemoryContent, // #2677 check 2: memory_entries content coverage
+                checkMemoryEmbeddingCoverage, // #2677 check 3: vector coverage on populated rows
+            ],
+            'learning': checkLearningBridge, // #2545
+            'learning-bridge': checkLearningBridge, // #2545
+            '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
+            'metaharness': checkMetaharness, // ADR-150 — upstream package
+            'metaharness-integration': checkMetaharnessIntegration, // iter 45 — ruflo-side
+            'funnel': checkFunnel, // ADR-305
+            // ADR-307 — deep-dive array, same pattern as 'memory' above: the cheap
+            // sponsored-consent check first, then binary/process/bind in the order
+            // a user would actually debug them (is it installed? running? exposed?).
+            'proxy': [checkProxySponsoredConsent, checkProxyBinary, checkProxyProcess, checkProxyBindAddress],
+            'auth': checkAuth, // ADR-306
+        };
+        let checksToRun = allChecks;
+        if (component && componentMap[component]) {
+            const entry = componentMap[component];
+            checksToRun = Array.isArray(entry) ? entry : [entry];
+        }
+        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'));
+        }
+        // #2545: --fix / --install can actually repair the Learning Bridge by
+        // recording the resolver sidecar. When doctor runs via `npx ruflo`, the CLI
+        // CAN resolve its optional @claude-flow/memory dep (it is in the same npx
+        // cache), so writing the sidecar makes the SessionStart hook find it.
+        if ((showFix || autoInstall)) {
+            const lbResult = results.find(r => r.name === 'Learning Bridge');
+            if (lbResult && lbResult.status === 'fail') {
+                const record = recordMemoryPackagePath(process.cwd(), 'doctor');
+                if (record) {
+                    const newCheck = await checkLearningBridge();
+                    const idx = results.findIndex(r => r.name === 'Learning Bridge');
+                    if (idx !== -1)
+                        results[idx] = newCheck;
+                    const fixIdx = fixes.findIndex(f => f.startsWith('Learning Bridge:'));
+                    if (fixIdx !== -1 && newCheck.status === 'pass')
+                        fixes.splice(fixIdx, 1);
+                    output.writeln(output.success(`Repaired Learning Bridge — wrote .claude-flow/memory-package.json → ${record.distPath}`));
+                    output.writeln(formatCheck(newCheck));
+                }
+            }
+        }
+        // Auto-install missing dependencies if requested
+        if (autoInstall) {
+            const claudeCodeResult = results.find(r => r.name === 'Claude Code CLI');
+            if (claudeCodeResult && claudeCodeResult.status !== 'pass') {
+                const installed = await installClaudeCode();
+                if (installed) {
+                    // Re-check Claude Code after installation
+                    const newCheck = await checkClaudeCode();
+                    const idx = results.findIndex(r => r.name === 'Claude Code CLI');
+                    if (idx !== -1) {
+                        results[idx] = newCheck;
+                        // Update fixes list
+                        const fixIdx = fixes.findIndex(f => f.startsWith('Claude Code CLI:'));
+                        if (fixIdx !== -1 && newCheck.status === 'pass') {
+                            fixes.splice(fixIdx, 1);
+                        }
+                    }
+                    output.writeln(formatCheck(newCheck));
+                }
+            }
+        }
+        // Summary
+        const passed = results.filter(r => r.status === 'pass').length;
+        const warnings = results.filter(r => r.status === 'warn').length;
+        const failed = results.filter(r => r.status === 'fail').length;
+        output.writeln();
+        output.writeln(output.dim('─'.repeat(50)));
+        output.writeln();
+        const summaryParts = [
+            output.success(`${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