@monoes/monomindcli 2.16.2 → 2.16.3

package/dist/src/commands/doctor-mode.js

@@ -0,0 +1,109 @@
+/**
+ * `doctor --read-only` and `doctor --offline` (issue #335): a health check a
+ * caller can run without it changing anything or touching the network.
+ * doc/agent-exec-protocol.md §10.
+ *
+ * Read-only is the default under `--json` (mono-agent's checks never change
+ * anything) unless `--fix`/`--install` asks for writes. It is about files, not
+ * the network: the version check still asks the npm registry, through a
+ * throwaway npm cache. `--offline` skips every check that needs the network.
+ */
+import { output } from '../output.js';
+export const DOCTOR_MODE_OPTIONS = [
+    {
+        name: 'read-only',
+        description: 'Change no file: no fixes, no registry refresh, no update check (default with --json unless --fix/--install)',
+        type: 'boolean',
+    },
+    {
+        name: 'offline',
+        description: 'Skip the checks that use the network; they are reported as skipped',
+        type: 'boolean',
+        default: false,
+    },
+];
+export function resolveDoctorMode(flags) {
+    const json = Boolean(flags.json) || flags.format === 'json';
+    const writes = Boolean(flags.fix) || Boolean(flags.install);
+    const explicit = flags.readOnly ?? flags['read-only'];
+    const mode = {
+        readOnly: typeof explicit === 'boolean' ? explicit : json && !writes,
+        offline: Boolean(flags.offline),
+    };
+    if (explicit === true && writes)
+        return { ...mode, error: '--read-only cannot be combined with --fix or --install' };
+    if (mode.offline && flags.install)
+        return {
+            ...mode,
+            error: '--offline cannot be combined with --install (it downloads software)',
+        };
+    return mode;
+}
+/** `Mode: read-only, offline` for the human header, or '' for a plain run. */
+export function modeLabel(mode) {
+    const on = [mode.readOnly && 'read-only', mode.offline && 'offline'].filter(Boolean);
+    return on.length ? `Mode: ${on.join(', ')}` : '';
+}
+/** A run refused before any check (e.g. `--read-only --fix`). */
+export function doctorError(error) {
+    output.writeln(output.error(error));
+    return {
+        success: false,
+        exitCode: 1,
+        data: { passed: 0, warnings: 0, failed: 1, results: [], error },
+    };
+}
+/**
+ * Checks a mode skips, with the name their result would carry. `probe`
+ * entries only apply to `-c <component>`: the full run already uses their
+ * config-only variant, which needs neither the network nor any writes.
+ */
+const SKIPS = {
+    version: { name: 'Version Freshness', when: ['offline'], why: 'asks the npm registry' },
+    freshness: { name: 'Version Freshness', when: ['offline'], why: 'asks the npm registry' },
+    'monoes-tools': { name: 'monoes Tools', when: ['offline'], why: 'queries GitHub releases' },
+    jev: {
+        name: 'Decision Model (Jev)',
+        when: ['offline'],
+        why: 'probes the decision-model providers over HTTP',
+        probe: true,
+    },
+    decision: {
+        name: 'Decision Model (Jev)',
+        when: ['offline'],
+        why: 'probes the decision-model providers over HTTP',
+        probe: true,
+    },
+    mcp: {
+        name: 'MCP Servers',
+        when: ['offline', 'read-only'],
+        why: 'starts the configured MCP server, which may download it and runs its own startup',
+        probe: true,
+    },
+    kg: {
+        name: 'Memory Knowledge Graph',
+        when: ['read-only'],
+        why: 'counting it opens the memory database, which writes to it',
+    },
+    pick: {
+        name: 'Agent/Skill Picking',
+        when: ['read-only'],
+        why: 'rebuilds stale agent and skill indexes',
+    },
+};
+/** The result for a check this mode skips, or null when it runs. */
+export function skippedCheck(component, mode, single) {
+    const s = SKIPS[component];
+    if (!s || (s.probe && !single))
+        return null;
+    const reason = s.when.find((r) => (r === 'offline' ? mode.offline : mode.readOnly));
+    if (!reason)
+        return null;
+    return {
+        name: s.name,
+        status: 'skipped',
+        skippedReason: reason,
+        message: `Skipped (${reason === 'offline' ? '--offline' : 'read-only'}): ${s.why}`,
+    };
+}
+//# sourceMappingURL=doctor-mode.js.map

package/dist/src/commands/doctor-mode.js.map

@@ -0,0 +1 @@
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package/dist/src/commands/doctor-monoes-checks.d.ts.map

@@ -1 +1 @@
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package/dist/src/commands/doctor-monoes-checks.js

@@ -356,9 +356,11 @@ export async function fixMonoesTools() {
             // 2min timeout: generous enough for an interactive sudo password prompt
             // (mono-agent's fix uses sudo mv), but still bounded — avoids hanging the
             // whole `doctor --install` run on a stalled brew/curl network call.
+            // stdin stays inherited for that prompt; output goes to stderr, since
+            // under `doctor --json` stdout is the JSON.
             execSync(issue.fixCommand, {
                 encoding: 'utf8',
-                stdio: 'inherit',
+                stdio: ['inherit', process.stderr, process.stderr],
                 shell: '/bin/bash',
                 timeout: 120_000,
             });

package/dist/src/commands/doctor-monoes-checks.js.map

@@ -1 +1 @@
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package/dist/src/commands/doctor-pick-checks.d.ts

@@ -0,0 +1,19 @@
+import type { HealthCheck } from './doctor-env-checks.js';
+export interface PickAdherence {
+    /** Picks the prompt hook recorded (route-outcomes.jsonl). */
+    routes: number;
+    /** Of those, how many were shown as a [PICK] line. */
+    shown: number;
+    /** Task/Agent spawns made while a pick was on record (pick-adherence.jsonl). */
+    spawns: number;
+    /** Of those, how many used the picked agent. */
+    followed: number;
+}
+/**
+ * Route and adherence counts straight from the hook logs, so doctor reports
+ * them even where the pick-stats helper is not installed. Outcome rates come
+ * from readPickStats.
+ */
+export declare function readPickAdherence(root: string): PickAdherence;
+export declare function checkPick(cwd?: string, env?: NodeJS.ProcessEnv): Promise<HealthCheck>;
+//# sourceMappingURL=doctor-pick-checks.d.ts.map

package/dist/src/commands/doctor-pick-checks.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"doctor-pick-checks.d.ts","sourceRoot":"","sources":["../../../src/commands/doctor-pick-checks.ts"],"names":[],"mappings":"AA2BA,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAC;AAM1D,MAAM,WAAW,aAAa;IAC5B,6DAA6D;IAC7D,MAAM,EAAE,MAAM,CAAC;IACf,sDAAsD;IACtD,KAAK,EAAE,MAAM,CAAC;IACd,gFAAgF;IAChF,MAAM,EAAE,MAAM,CAAC;IACf,gDAAgD;IAChD,QAAQ,EAAE,MAAM,CAAC;CAClB;AAiCD;;;;GAIG;AACH,wBAAgB,iBAAiB,CAAC,IAAI,EAAE,MAAM,GAAG,aAAa,CAY7D;AAmBD,wBAAsB,SAAS,CAC7B,GAAG,GAAE,MAAsB,EAC3B,GAAG,GAAE,MAAM,CAAC,UAAwB,GACnC,OAAO,CAAC,WAAW,CAAC,CA2FtB"}

package/dist/src/commands/doctor-pick-checks.js

@@ -0,0 +1,164 @@
+/**
+ * Doctor — agent/skill picking (`doctor -c pick`). One row covering what
+ * `monomind pick`, the MCP `pick` tool and the [PICK] hook line rank over:
+ * the agent registry, the skill index, the decision model (configuration
+ * only, no network), the keyword eval on the frozen tests/pick-eval set when
+ * the project carries one, and adherence from the hook logs.
+ *
+ * Not part of the default doctor run: it rebuilds stale indexes and scores
+ * the eval set, which a plain `doctor` should not spend time on.
+ */
+import { closeSync, openSync, readFileSync, readSync, statSync } from 'node:fs';
+import { join } from 'node:path';
+import { findProjectRoot, registryIsStale, registryPath } from '../agents/registry-freshness.js';
+import { agentCatalog, skillIndex, skillIndexIsStale, taskSkillCatalog, } from '../decision/catalogs.js';
+import { jevModule } from '../decision/jev.js';
+import { formatScore, keywordEval, readEvalSnapshot, readEvalTasks, } from '../decision/pick-eval.js';
+import { readPickStats } from '../decision/pick-stats.js';
+const NAME = 'Agent/Skill Picking';
+/** Only the newest part of a large log is read. */
+const MAX_LOG_BYTES = 4 * 1024 * 1024;
+function tailLines(file) {
+    let fd;
+    try {
+        const size = statSync(file).size;
+        const length = Math.min(size, MAX_LOG_BYTES);
+        const buf = Buffer.alloc(length);
+        fd = openSync(file, 'r');
+        readSync(fd, buf, 0, length, size - length);
+        const lines = buf.toString('utf-8').split('\n');
+        if (length < size)
+            lines.shift(); // a partial first line
+        return lines.filter(Boolean);
+    }
+    catch {
+        return [];
+    }
+    finally {
+        if (fd !== undefined)
+            closeSync(fd);
+    }
+}
+function records(file) {
+    const out = [];
+    for (const line of tailLines(file)) {
+        try {
+            const rec = JSON.parse(line);
+            if (rec && typeof rec === 'object')
+                out.push(rec);
+        }
+        catch {
+            /* a torn line */
+        }
+    }
+    return out;
+}
+/**
+ * Route and adherence counts straight from the hook logs, so doctor reports
+ * them even where the pick-stats helper is not installed. Outcome rates come
+ * from readPickStats.
+ */
+export function readPickAdherence(root) {
+    const dir = join(root, '.monomind');
+    const routes = records(join(dir, 'route-outcomes.jsonl'));
+    const spawns = records(join(dir, 'pick-adherence.jsonl')).filter((r) => typeof r.followed === 'boolean');
+    return {
+        routes: routes.length,
+        shown: routes.filter((r) => r.shown === true).length,
+        spawns: spawns.length,
+        followed: spawns.filter((r) => r.followed === true).length,
+    };
+}
+/** What the registry file holds: every agent (deprecated included) and slug clashes. */
+function registryCounts(root) {
+    try {
+        const reg = JSON.parse(readFileSync(registryPath(root), 'utf-8'));
+        const agents = Array.isArray(reg.agents) ? reg.agents : [];
+        return {
+            total: agents.length,
+            deprecated: agents.filter((a) => a?.deprecated === true).length,
+            duplicates: Array.isArray(reg.duplicates) ? reg.duplicates.length : 0,
+        };
+    }
+    catch {
+        return { total: 0, deprecated: 0, duplicates: 0 };
+    }
+}
+const plural = (n, word) => `${n} ${word}${n === 1 ? '' : 's'}`;
+export async function checkPick(cwd = process.cwd(), env = process.env) {
+    const root = findProjectRoot(cwd) ?? cwd;
+    const lines = [];
+    const problems = [];
+    const fixes = [];
+    const registryWasStale = registryIsStale(root);
+    const agents = agentCatalog(root); // rebuilds a stale registry
+    // Picks rank the non-deprecated agents; the registry file holds them all.
+    const reg = registryCounts(root);
+    const dupes = reg.duplicates;
+    const hidden = Math.max(0, reg.total - agents.length);
+    const hiddenNote = hidden
+        ? ` (${hidden} hidden: ${hidden === reg.deprecated ? 'deprecated' : `${reg.deprecated} deprecated, ${hidden - reg.deprecated} other`})`
+        : '';
+    lines.push(`registry: ${plural(agents.length, 'pickable agent')} of ${reg.total} registered${hiddenNote}, ${plural(dupes, 'duplicate')}, ${registryWasStale ? 'was stale (rebuilt)' : 'fresh'}`);
+    if (agents.length === 0) {
+        problems.push('no agents to pick from');
+        fixes.push('monomind init  (installs agent definitions)');
+    }
+    if (dupes > 0) {
+        problems.push('duplicate agent slugs');
+        fixes.push('Give each duplicated agent a unique `slug:` (see `doctor -c registry`)');
+    }
+    const indexWasStale = skillIndexIsStale(root);
+    const index = skillIndex(root);
+    const skills = taskSkillCatalog(root);
+    const user = (index?.skills ?? []).filter((s) => s.origin === 'user').length;
+    const org = skills.filter((s) => s.source === 'org').length;
+    // User skills (~/.claude/skills) sit in the platform pool.
+    const platform = Math.max(0, skills.length - org - user);
+    const freshness = indexWasStale === undefined
+        ? 'builder missing'
+        : indexWasStale
+            ? 'was stale (rebuilt)'
+            : 'fresh';
+    // The index lists commands and skills separately; picks count a
+    // command/skill pair once, so the two numbers differ.
+    const indexed = index?.skills?.length ?? 0;
+    lines.push(`skills: ${skills.length} pickable (${platform} platform, ${org} org, ${user} user); skill index holds ${indexed} ${indexed === 1 ? 'entry' : 'entries'}, ${freshness}`);
+    if (skills.length === 0) {
+        problems.push('no skills to pick from');
+        fixes.push('monomind init  (installs skills)');
+    }
+    const providers = jevModule()?.resolveProviders(env) ?? [];
+    lines.push(providers.length
+        ? `decision model: configured (${providers.map((p) => p.name).join(' → ')}); probe with \`doctor -c jev\``
+        : 'decision model: not configured (keyword ranking)');
+    const tasks = readEvalTasks(root);
+    const snapshot = readEvalSnapshot(root);
+    if (tasks && snapshot) {
+        const r = keywordEval(tasks, snapshot);
+        lines.push(`eval (frozen catalog, keyword): agents ${formatScore(r.agents)} · skills ${formatScore(r.skills)}`);
+    }
+    else
+        lines.push('eval: no tests/pick-eval set in this project (monomind source checkout only)');
+    const a = readPickAdherence(root);
+    if (a.routes === 0 && a.spawns === 0)
+        lines.push('adherence: no picks logged yet');
+    else {
+        const rate = a.spawns ? ` (${Math.round((100 * a.followed) / a.spawns)}%)` : '';
+        lines.push(`adherence: ${a.routes} routes, ${a.shown} shown; spawns followed the pick ${a.followed}/${a.spawns}${rate}`);
+    }
+    const s = readPickStats(root);
+    const pct = (v) => (v === null ? 'n/a' : `${Math.round(100 * v)}%`);
+    if (s.followedSuccessRate !== null || s.notFollowedSuccessRate !== null)
+        lines.push(`outcomes: subagent success ${pct(s.followedSuccessRate)} when the pick was followed, ${pct(s.notFollowedSuccessRate)} when overridden`);
+    const message = lines.join('\n  ');
+    return problems.length
+        ? {
+            name: NAME,
+            status: 'warn',
+            message: `${problems.join('; ')}\n  ${message}`,
+            fix: fixes.join('; '),
+        }
+        : { name: NAME, status: 'pass', message };
+}
+//# sourceMappingURL=doctor-pick-checks.js.map

package/dist/src/commands/doctor-pick-checks.js.map

@@ -0,0 +1 @@
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package/dist/src/commands/doctor-project-checks.d.ts

@@ -57,7 +57,9 @@ export declare function checkGitignoreCoverage(): Promise<HealthCheck>;
 /** Creates or appends the missing gitignore entries. Returns true if it wrote.
  *  Append-only and idempotent: never rewrites lines the user already has. */
 export declare function fixGitignoreCoverage(): Promise<boolean>;
-export declare function checkAgentRegistry(): Promise<HealthCheck>;
+export declare function checkAgentRegistry(opts?: {
+    readOnly?: boolean;
+}): Promise<HealthCheck>;
 export declare function checkGuidanceGates(): Promise<HealthCheck>;
 /**
  * Worker metrics freshness — reports the age of the @monoes/hooks worker

package/dist/src/commands/doctor-project-checks.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"doctor-project-checks.d.ts","sourceRoot":"","sources":["../../../src/commands/doctor-project-checks.ts"],"names":[],"mappings":"AAAA;;;GAGG;AA8BH,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAC;AAS1D,YAAY,EAAE,WAAW,EAAE,CAAC;AAE5B,wBAAsB,eAAe,IAAI,OAAO,CAAC,WAAW,CAAC,CA4B5D;AAED;;;;;;;;;;;;;;;;;iDAiBiD;AACjD,wBAAsB,gBAAgB,IAAI,OAAO,CAAC,WAAW,CAAC,CA2B7D;AAED,wBAAsB,mBAAmB,IAAI,OAAO,CAAC,WAAW,CAAC,CAkBhE;AAED;;2CAE2C;AAC3C,wBAAsB,yBAAyB,IAAI,OAAO,CAAC,WAAW,CAAC,CAqDtE;AAeD;;;wEAGwE;AACxE,wBAAsB,qBAAqB,IAAI,OAAO,CAAC,WAAW,CAAC,CAuElE;AAED,wBAAsB,YAAY,IAAI,OAAO,CAAC,WAAW,CAAC,CAiDzD;AAED,MAAM,WAAW,eAAe;IAC9B;;;;;OAKG;IACH,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,sDAAsD;IACtD,SAAS,CAAC,EAAE,MAAM,CAAC;CACpB;AAED,wBAAsB,eAAe,CAAC,OAAO,GAAE,eAAoB,GAAG,OAAO,CAAC,WAAW,CAAC,CA+CzF;AAkGD,wBAAsB,cAAc,IAAI,OAAO,CAAC,WAAW,CAAC,CAe3D;AAmDD,wBAAsB,uBAAuB,IAAI,OAAO,CAAC,WAAW,CAAC,CA4LpE;AAED,wBAAsB,iBAAiB,IAAI,OAAO,CAAC,WAAW,CAAC,CAkB9D;AAsID,wBAAsB,eAAe,IAAI,OAAO,CAAC,OAAO,CAAC,CAuBxD;AAED,wBAAsB,iBAAiB,IAAI,OAAO,CAAC,WAAW,CAAC,CA4C9D;AAiFD,wBAAsB,sBAAsB,IAAI,OAAO,CAAC,WAAW,CAAC,CAoBnE;AAkDD,wBAAsB,sBAAsB,IAAI,OAAO,CAAC,WAAW,CAAC,CAqCnE;AA2BD;6EAC6E;AAC7E,wBAAsB,oBAAoB,IAAI,OAAO,CAAC,OAAO,CAAC,CA2B7D;AAED,wBAAsB,kBAAkB,CAAC,IAAI,GAAE;IAAE,QAAQ,CAAC,EAAE,OAAO,CAAA;CAAO,GAAG,OAAO,CAAC,WAAW,CAAC,CAkFhG;AAED,wBAAsB,kBAAkB,IAAI,OAAO,CAAC,WAAW,CAAC,CAoF/D;AAmBD;;;;;GAKG;AACH,wBAAsB,qBAAqB,IAAI,OAAO,CAAC,WAAW,CAAC,CAoDlE;AAED;;GAEG;AACH,wBAAsB,0BAA0B,IAAI,OAAO,CAAC,WAAW,CAAC,CAwCvE;AAED;;GAEG;AACH,wBAAsB,sBAAsB,IAAI,OAAO,CAAC,WAAW,CAAC,CA6BnE;AAED;;;;;;;;;;;;;GAaG;AACH,wBAAsB,wBAAwB,IAAI,OAAO,CAAC,WAAW,CAAC,CAcrE;AAED;;sBAEsB;AACtB,wBAAgB,uBAAuB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,EAAE,CAyB7D;AAED,6EAA6E;AAC7E,wBAAgB,sBAAsB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAW1D;AAiBD;;;;;yDAKyD;AACzD,wBAAsB,uBAAuB,IAAI,OAAO,CAAC,WAAW,EAAE,CAAC,CAoBtE"}

package/dist/src/commands/doctor-project-checks.js

@@ -6,7 +6,7 @@ import { execSync } from 'node:child_process';
 import { appendFileSync, copyFileSync, existsSync, mkdirSync, readdirSync, readFileSync, rmSync, statSync, writeFileSync, } from 'node:fs';
 import { createRequire } from 'node:module';
 import { homedir } from 'node:os';
-import { dirname, join } from 'node:path';
+import { dirname, join, sep } from 'node:path';
 import { fileURLToPath } from 'node:url';
 import { DOCTOR_TRACKED_HELPERS, OBSOLETE_HELPER_NAMES } from '../init/helpers-generator.js';
 import { MONOMIND_NEVER_COMMIT } from '../init/never-commit.js';
@@ -794,7 +794,12 @@ function _bundledTopLevelHelperNames() {
         return [];
     }
 }
-async function _detectStaleHelpers() {
+// The installed helper copies doctor compares against the bundle: the Claude
+// Code tree, plus the copy init writes to .gemini/helpers (Antigravity's status
+// bar runs .gemini/helpers/statusline.cjs), which is only checked when present.
+const CLAUDE_HELPERS = join('.claude', 'helpers');
+const GEMINI_HELPERS = join('.gemini', 'helpers');
+async function _detectStaleHelpers(helpersDir = CLAUDE_HELPERS) {
     const stale = [];
     const missing = [];
     // Helpers this product shipped under a name it has since renamed away from
@@ -816,7 +821,7 @@ async function _detectStaleHelpers() {
             missing.push(name);
             continue;
         }
-        const local = join(process.cwd(), '.claude', 'helpers', name);
+        const local = join(process.cwd(), helpersDir, name);
         if (!existsSync(local)) {
             stale.push(name);
             continue;
@@ -837,11 +842,23 @@ async function _detectStaleHelpers() {
     }
     return { stale, missing, orphaned };
 }
+/** Stale helpers in the Gemini copy, as `.gemini/helpers/<name>`; none if not installed. */
+async function _detectStaleGeminiHelpers() {
+    if (!existsSync(join(process.cwd(), GEMINI_HELPERS)))
+        return [];
+    const { stale } = await _detectStaleHelpers(GEMINI_HELPERS);
+    return stale.map((name) => `.gemini/helpers/${name.split(sep).join('/')}`);
+}
 export async function fixStaleHelpers() {
     const { stale } = await _detectStaleHelpers();
+    const targets = stale.map((name) => ({ name, local: join(process.cwd(), CLAUDE_HELPERS, name) }));
+    if (existsSync(join(process.cwd(), GEMINI_HELPERS))) {
+        for (const name of (await _detectStaleHelpers(GEMINI_HELPERS)).stale) {
+            targets.push({ name, local: join(process.cwd(), GEMINI_HELPERS, name) });
+        }
+    }
     let fixed = 0;
-    for (const name of stale) {
-        const local = join(process.cwd(), '.claude', 'helpers', name);
+    for (const { name, local } of targets) {
         const bundled = _resolveBundledHelper(join('.claude', 'helpers', name));
         if (bundled) {
             try {
@@ -859,13 +876,16 @@ export async function fixStaleHelpers() {
 }
 export async function checkHelpersFresh() {
     try {
-        const { stale, missing, orphaned } = await _detectStaleHelpers();
+        const { stale: claudeStale, missing, orphaned } = await _detectStaleHelpers();
+        const stale = [...claudeStale, ...(await _detectStaleGeminiHelpers())];
         if (orphaned.length > 0) {
             return {
                 name: 'Helper Files',
                 status: 'warn',
                 message: `Found ${orphaned.length} hook(s) from before a rename, still on disk: ${orphaned.join(', ')}. Run \`monomind init --force\` to update your hooks and rebuild the Monograph graph.`,
                 fix: 'monomind init --force',
+                // `--fix` only copies stale helpers; it never removes these.
+                fixSafety: 'manual',
             };
         }
         if (stale.length === 0 && missing.length === 0) {
@@ -881,6 +901,7 @@ export async function checkHelpersFresh() {
                 status: 'warn',
                 message: `${stale.length} stale helper(s): ${stale.join(', ')}`,
                 fix: 'monomind init upgrade',
+                fixSafety: 'auto',
             };
         }
         return {
@@ -888,6 +909,7 @@ export async function checkHelpersFresh() {
             status: 'warn',
             message: `Could not locate bundled copies of: ${missing.join(', ')}`,
             fix: 'Reinstall monomind or run `monomind init upgrade`',
+            fixSafety: 'manual',
         };
     }
     catch (e) {
@@ -1133,27 +1155,40 @@ export async function fixGitignoreCoverage() {
         return false;
     }
 }
-export async function checkAgentRegistry() {
+export async function checkAgentRegistry(opts = {}) {
     try {
         const { buildUnifiedRegistry, computeAgentRoots } = await import('../agents/registry-builder.js');
-        const cwd = process.cwd();
+        const { findProjectRoot, registryPath } = await import('../agents/registry-freshness.js');
+        const project = findProjectRoot(process.cwd());
+        const cwd = project ?? process.cwd();
         const roots = computeAgentRoots(cwd);
-        const outDir = join(cwd, '.monomind');
-        mkdirSync(outDir, { recursive: true });
-        // Rebuilds fresh in-memory (and refreshes .monomind/registry.json on disk)
-        // rather than reading a file that a separate, unawaited startup task also
-        // writes — avoids reporting stale results from a race between the two.
-        const registry = buildUnifiedRegistry(roots, join(outDir, 'registry.json'));
+        const write = project !== null && !opts.readOnly;
+        if (write)
+            mkdirSync(join(cwd, '.monomind'), { recursive: true });
+        // Rebuilds fresh in-memory (and, inside a project, refreshes
+        // .monomind/registry.json on disk, never replacing a non-empty registry
+        // with an empty one) rather than reading a file a separate startup task
+        // may also be writing. Outside a project, and in read-only mode (issue
+        // #335), nothing is written.
+        const registry = buildUnifiedRegistry(roots, write ? registryPath(cwd) : undefined, {
+            base: cwd,
+        });
         const entries = registry.agents;
+        // An extra root (MONOMIND_EXTRA_AGENT_PATHS or a sibling agency-agents dir)
+        // wins slug conflicts over .claude/agents — say so instead of hiding it.
+        const extras = roots.slice(0, -1);
+        const extraNote = extras.length
+            ? `; extra agent roots (win on conflict): ${extras.join(', ')}`
+            : '';
         if (entries.length === 0) {
             return {
                 name: 'Agent Registry',
                 status: 'warn',
-                message: 'No agents found under .claude/agents',
+                message: `No agents found under .claude/agents${extraNote}`,
                 fix: 'monomind init  (installs agent definitions)',
             };
         }
-        let missingSlug = 0, missingName = 0, missingDescription = 0;
+        let missingSlug = 0, missingName = 0, missingDescription = 0, missingWhenToUse = 0;
         for (const agent of entries) {
             if (!agent.slug)
                 missingSlug++;
@@ -1161,27 +1196,39 @@ export async function checkAgentRegistry() {
                 missingName++;
             if (!agent.description)
                 missingDescription++;
+            // The pick index leads with when_to_use; older installs lack it.
+            if (!agent.whenToUse)
+                missingWhenToUse++;
         }
-        const total = missingSlug + missingName + missingDescription;
+        const dupes = registry.duplicates;
+        const total = missingSlug + missingName + missingDescription + missingWhenToUse + dupes.length;
         if (total === 0) {
             return {
                 name: 'Agent Registry',
                 status: 'pass',
-                message: `${entries.length} agent(s), all metadata complete`,
+                message: `${entries.length} agent(s), all metadata complete${extraNote}`,
             };
         }
         const parts = [
             missingSlug > 0 ? `${missingSlug} missing slug` : null,
             missingName > 0 ? `${missingName} missing name` : null,
             missingDescription > 0 ? `${missingDescription} missing description` : null,
+            missingWhenToUse > 0 ? `${missingWhenToUse} missing when_to_use` : null,
+            dupes.length > 0
+                ? `duplicate slug ${dupes.map((d) => `"${d.slug}" (kept ${d.kept}, dropped ${d.dropped.join(', ')})`).join('; ')}`
+                : null,
         ]
             .filter(Boolean)
             .join(', ');
         return {
             name: 'Agent Registry',
             status: 'warn',
-            message: `${total} metadata issue(s) across ${entries.length} agent(s): ${parts}`,
-            fix: 'Add the missing field(s) to frontmatter in .claude/agents/*.md',
+            message: `${total} metadata issue(s) across ${entries.length} agent(s): ${parts}${extraNote}`,
+            fix: dupes.length
+                ? 'Give each duplicated agent a unique `slug:` in its frontmatter'
+                : missingWhenToUse > 0
+                    ? 'monomind init upgrade  (refreshes unedited bundled agents; add `when_to_use:` to your own agents in .claude/agents/*.md)'
+                    : 'Add the missing field(s) to frontmatter in .claude/agents/*.md',
         };
     }
     catch {