@monoes/monomindcli 2.16.4 → 2.16.6

package/README.md

@@ -36,7 +36,7 @@ Monomind is an **open-source CLI and MCP server** that plugs into Claude Code, [
 - **Codebase knowledge graph** — tree-sitter parses your code into a SQLite-backed graph of files, functions, classes, and their relationships. Query imports, callers, and blast radius before making changes.
 - **Persistent memory** — a JSON pattern store with episodic recall that survives across sessions. Agents and orgs share context without re-prompting.
 - **Multi-agent coordination** — in-session, spawn ad-hoc agent teams via Claude Code's Task tool; for persistent background work, `monomind org run` starts a real SDK-backed daemon with policy-gated role agents and a live dashboard.
-- **Agents, skills and picking** — ships <!-- doc-count:pickable-agents -->84<!-- /doc-count:pickable-agents --> pickable agents, <!-- doc-count:pickable-skills -->84<!-- /doc-count:pickable-skills --> skills and <!-- doc-count:org-skills -->376<!-- /doc-count:org-skills --> Org skills, and you add your own as Markdown files. One index of all of them ranks the best fit for each task; the prompt hook puts it in Claude's context as a `[PICK]` line, and `monomind pick` or the `pick` MCP tool return it on request. See [Agents & Skills](doc/concepts/agents-and-skills.md) and [Routing](doc/concepts/routing.md).
+- **Agents, skills and picking** — ships <!-- doc-count:pickable-agents -->84<!-- /doc-count:pickable-agents --> pickable agents, <!-- doc-count:pickable-skills -->83<!-- /doc-count:pickable-skills --> skills and <!-- doc-count:org-skills -->376<!-- /doc-count:org-skills --> Org skills, and you add your own as Markdown files. One index of all of them ranks the best fit for each task; the prompt hook puts it in Claude's context as a `[PICK]` line, and `monomind pick` or the `pick` MCP tool return it on request. See [Agents & Skills](doc/concepts/agents-and-skills.md) and [Routing](doc/concepts/routing.md).
 - **Reusable slash commands** — <!-- doc-count:mastermind-commands -->42<!-- /doc-count:mastermind-commands --> workflows (plan, execute, review, debug, release, research, worktree) available as `/mastermind:*` commands inside Claude Code.
 
 ```bash

package/dist/src/agents/registry-builder.d.ts

@@ -15,7 +15,7 @@ type AgentRegistryEntry = {
     /** One-line `when_to_use:` frontmatter — the picker's lead description. */
     whenToUse?: string;
     tags: string[];
-    /** Optional `vibe:` frontmatter (personality line), ranked as extra text. */
+    /** Optional `vibe:` frontmatter (personality line); stored, never ranked. */
     vibe?: string;
     capabilities: string[];
     taskTypes: string[];

package/dist/src/commands/cleanup-plan.d.ts

@@ -15,8 +15,9 @@
  *     other databases, org configs, backups) is kept unless `--purge-data`.
  *  3. Whole-path removal needs proof of ownership: a monomind-only namespace
  *     (.monomind/, monomind.config.json, legacy .swarm/.hive-mind), an entry
- *     listed in init's manifest, a file named `monomind*` inside a provider
- *     dir, or a file whose content is nothing but monomind marker blocks.
+ *     listed in init's manifest, a file whose content still matches the hash
+ *     init recorded for it, a file named `monomind*` inside a provider dir, or
+ *     a file whose content is nothing but monomind marker blocks.
  *  4. A file that mixes monomind marker blocks (or a `monomind` JSON entry)
  *     with other content only loses the monomind part.
  *  5. Anything else is kept and reported with the reason.

package/dist/src/commands/cleanup-plan.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"cleanup-plan.d.ts","sourceRoot":"","sources":["../../../src/commands/cleanup-plan.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;GAsBG;AAQH,MAAM,MAAM,aAAa,GAAG,QAAQ,GAAG,OAAO,GAAG,MAAM,CAAC;AAExD,MAAM,WAAW,gBAAgB;IAC/B,wDAAwD;IACxD,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,KAAK,GAAG,MAAM,CAAC;IACrB,MAAM,EAAE,aAAa,CAAC;IACtB,MAAM,EAAE,MAAM,CAAC;IACf,IAAI,EAAE,MAAM,CAAC;IACb,2DAA2D;IAC3D,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,oCAAoC;IACpC,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB;AAED,MAAM,WAAW,kBAAkB;IACjC,UAAU,EAAE,OAAO,CAAC;IACpB,SAAS,EAAE,OAAO,CAAC;IACnB,oCAAoC;IACpC,UAAU,CAAC,EAAE,MAAM,CAAC;CACrB;AAED,MAAM,MAAM,iBAAiB,GACzB;IAAE,EAAE,EAAE,IAAI,CAAC;IAAC,OAAO,EAAE,gBAAgB,EAAE,CAAA;CAAE,GACzC;IAAE,EAAE,EAAE,KAAK,CAAC;IAAC,KAAK,EAAE,MAAM,CAAA;CAAE,CAAC;AA6CjC,4EAA4E;AAC5E,wBAAgB,mBAAmB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAY/D;AAED,2EAA2E;AAC3E,wBAAgB,oBAAoB,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAOzD;AAmRD,wBAAgB,gBAAgB,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE,kBAAkB,GAAG,iBAAiB,CAWzF;AAED,8EAA8E;AAC9E,wBAAgB,iBAAiB,CAAC,GAAG,EAAE,MAAM,EAAE,CAAC,EAAE,gBAAgB,GAAG,IAAI,CAIxE"}
+{"version":3,"file":"cleanup-plan.d.ts","sourceRoot":"","sources":["../../../src/commands/cleanup-plan.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;GAuBG;AASH,MAAM,MAAM,aAAa,GAAG,QAAQ,GAAG,OAAO,GAAG,MAAM,CAAC;AAExD,MAAM,WAAW,gBAAgB;IAC/B,wDAAwD;IACxD,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,KAAK,GAAG,MAAM,CAAC;IACrB,MAAM,EAAE,aAAa,CAAC;IACtB,MAAM,EAAE,MAAM,CAAC;IACf,IAAI,EAAE,MAAM,CAAC;IACb,2DAA2D;IAC3D,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,oCAAoC;IACpC,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB;AAED,MAAM,WAAW,kBAAkB;IACjC,UAAU,EAAE,OAAO,CAAC;IACpB,SAAS,EAAE,OAAO,CAAC;IACnB,oCAAoC;IACpC,UAAU,CAAC,EAAE,MAAM,CAAC;CACrB;AAED,MAAM,MAAM,iBAAiB,GACzB;IAAE,EAAE,EAAE,IAAI,CAAC;IAAC,OAAO,EAAE,gBAAgB,EAAE,CAAA;CAAE,GACzC;IAAE,EAAE,EAAE,KAAK,CAAC;IAAC,KAAK,EAAE,MAAM,CAAA;CAAE,CAAC;AA6CjC,4EAA4E;AAC5E,wBAAgB,mBAAmB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAY/D;AAED,2EAA2E;AAC3E,wBAAgB,oBAAoB,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAOzD;AAiSD,wBAAgB,gBAAgB,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE,kBAAkB,GAAG,iBAAiB,CAWzF;AAED,8EAA8E;AAC9E,wBAAgB,iBAAiB,CAAC,GAAG,EAAE,MAAM,EAAE,CAAC,EAAE,gBAAgB,GAAG,IAAI,CAIxE"}

package/dist/src/commands/cleanup-plan.js

@@ -15,13 +15,15 @@
  *     other databases, org configs, backups) is kept unless `--purge-data`.
  *  3. Whole-path removal needs proof of ownership: a monomind-only namespace
  *     (.monomind/, monomind.config.json, legacy .swarm/.hive-mind), an entry
- *     listed in init's manifest, a file named `monomind*` inside a provider
- *     dir, or a file whose content is nothing but monomind marker blocks.
+ *     listed in init's manifest, a file whose content still matches the hash
+ *     init recorded for it, a file named `monomind*` inside a provider dir, or
+ *     a file whose content is nothing but monomind marker blocks.
  *  4. A file that mixes monomind marker blocks (or a `monomind` JSON entry)
  *     with other content only loses the monomind part.
  *  5. Anything else is kept and reported with the reason.
  */
 import { execFileSync } from 'node:child_process';
+import { createHash } from 'node:crypto';
 import { existsSync, lstatSync, readdirSync, readFileSync, rmSync, writeFileSync } from 'node:fs';
 import { dirname, isAbsolute, join, relative, resolve, sep } from 'node:path';
 import { readInitManifest } from '../init/shared.js';
@@ -154,6 +156,8 @@ class Planner {
     entries = [];
     dataPaths;
     owned;
+    /** sha256 of each file init installed, keyed by project-relative path. */
+    installed;
     constructor(cwd, tracked, opts) {
         this.cwd = cwd;
         this.tracked = tracked;
@@ -174,6 +178,21 @@ class Planner {
             ...(m?.kimiPluginCommands ?? []).map((n) => `.kimi-code/plugin/commands/${n}`),
             ...(m?.opencodeSkills ?? []).map((n) => `.opencode/skills/${n}`),
         ]);
+        this.installed = m?.files ?? {};
+    }
+    /** A regular file init installed and nobody edited since. */
+    isUneditedInstall(rel) {
+        const recorded = this.installed[rel];
+        try {
+            if (!recorded || !lstatSync(this.abs(rel)).isFile())
+                return false;
+            return (createHash('sha256')
+                .update(readFileSync(this.abs(rel)))
+                .digest('hex') === recorded);
+        }
+        catch {
+            return false;
+        }
     }
     abs(rel) {
         return join(this.cwd, ...rel.split('/'));
@@ -233,10 +252,11 @@ class Planner {
             this.add(rel, kind, 'skip', 'tracked by git');
             return false;
         }
-        const owned = this.owned.has(rel) || (ownsUnmarked && kind === 'file');
+        const listed = this.owned.has(rel) || (kind === 'file' && this.isUneditedInstall(rel));
+        const owned = listed || (ownsUnmarked && kind === 'file');
         if (kind === 'file' || lstatSync(this.abs(rel)).isSymbolicLink()) {
             if (owned || /^monomind/i.test(rel.slice(rel.lastIndexOf('/') + 1))) {
-                this.add(rel, kind, 'remove', this.owned.has(rel) ? 'listed in init manifest' : 'monomind-owned');
+                this.add(rel, kind, 'remove', listed ? 'listed in init manifest' : 'monomind-owned');
                 return true;
             }
             return this.planMarkedFile(rel);

package/dist/src/commands/cleanup-plan.js.map

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

@@ -1,12 +1,13 @@
 import type { HealthCheck } from './doctor-env-checks.js';
 export interface PickAdherence {
-    /** Picks the prompt hook recorded (route-outcomes.jsonl). */
+    /** Picks the prompt hook recorded (route-outcomes.jsonl), slash commands left out. */
     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). */
+    /** Picks on record when a Task/Agent spawn was made (pick-adherence.jsonl),
+     *  each route once however many spawns it had. */
     spawns: number;
-    /** Of those, how many used the picked agent. */
+    /** Of those, how many had a spawn of the picked agent. */
     followed: number;
 }
 /**
@@ -16,4 +17,20 @@ export interface PickAdherence {
  */
 export declare function readPickAdherence(root: string): PickAdherence;
 export declare function checkPick(cwd?: string, env?: NodeJS.ProcessEnv): Promise<HealthCheck>;
+export interface McpServerProcess {
+    pid: number;
+    /** Epoch ms the process started. */
+    startedAt: number;
+    /** The script node runs (resolved through symlinks when possible). */
+    script: string;
+    /** The process's working directory, when the platform exposes it. */
+    cwd?: string;
+}
+/** Running `… monomind … mcp start` node processes (POSIX `ps`). */
+export declare function listMcpServerProcesses(now?: number): McpServerProcess[];
+export declare function checkRunningMcpServer(cwd?: string, deps?: {
+    processes?: () => McpServerProcess[];
+    now?: number;
+    version?: string;
+}): Promise<HealthCheck>;
 //# sourceMappingURL=doctor-pick-checks.d.ts.map

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

@@ -1 +1 @@
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+{"version":3,"file":"doctor-pick-checks.d.ts","sourceRoot":"","sources":["../../../src/commands/doctor-pick-checks.ts"],"names":[],"mappings":"AAgCA,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAC;AAI1D,MAAM,WAAW,aAAa;IAC5B,sFAAsF;IACtF,MAAM,EAAE,MAAM,CAAC;IACf,sDAAsD;IACtD,KAAK,EAAE,MAAM,CAAC;IACd;sDACkD;IAClD,MAAM,EAAE,MAAM,CAAC;IACf,0DAA0D;IAC1D,QAAQ,EAAE,MAAM,CAAC;CAClB;AAKD;;;;GAIG;AACH,wBAAgB,iBAAiB,CAAC,IAAI,EAAE,MAAM,GAAG,aAAa,CAuB7D;AAmBD,wBAAsB,SAAS,CAC7B,GAAG,GAAE,MAAsB,EAC3B,GAAG,GAAE,MAAM,CAAC,UAAwB,GACnC,OAAO,CAAC,WAAW,CAAC,CA6FtB;AAeD,MAAM,WAAW,gBAAgB;IAC/B,GAAG,EAAE,MAAM,CAAC;IACZ,oCAAoC;IACpC,SAAS,EAAE,MAAM,CAAC;IAClB,sEAAsE;IACtE,MAAM,EAAE,MAAM,CAAC;IACf,qEAAqE;IACrE,GAAG,CAAC,EAAE,MAAM,CAAC;CACd;AAWD,oEAAoE;AACpE,wBAAgB,sBAAsB,CAAC,GAAG,GAAE,MAAmB,GAAG,gBAAgB,EAAE,CAuCnF;AAqBD,wBAAsB,qBAAqB,CACzC,GAAG,GAAE,MAAsB,EAC3B,IAAI,GAAE;IAAE,SAAS,CAAC,EAAE,MAAM,gBAAgB,EAAE,CAAC;IAAC,GAAG,CAAC,EAAE,MAAM,CAAC;IAAC,OAAO,CAAC,EAAE,MAAM,CAAA;CAAO,GAClF,OAAO,CAAC,WAAW,CAAC,CA8BtB"}

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

@@ -10,15 +10,19 @@
  * The real-use line re-ranks logged prompts that led to a spawn
  * (decision/pick-real.ts; `pick-eval.mjs --logs` has the full report).
  */
-import { readFileSync } from 'node:fs';
-import { join } from 'node:path';
+import { execFileSync } from 'node:child_process';
+import { existsSync, readFileSync, readlinkSync, realpathSync, statSync } from 'node:fs';
+import { dirname, join, resolve, sep } 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 { readHookLog, realUseLine } from '../decision/pick-real.js';
 import { readPickStats } from '../decision/pick-stats.js';
+import { VERSION } from '../index.js';
 const NAME = 'Agent/Skill Picking';
+/** A prompt that is a slash command (the route hook's rule): not a pick. */
+const COMMAND_PROMPT = /^\/[a-z0-9_-]+(:[a-z0-9_-]+)*(\s|$)/i;
 /**
  * Route and adherence counts straight from the hook logs, so doctor reports
  * them even where the pick-stats helper is not installed. Outcome rates come
@@ -26,13 +30,27 @@ const NAME = 'Agent/Skill Picking';
  */
 export function readPickAdherence(root) {
     const dir = join(root, '.monomind');
-    const routes = readHookLog(join(dir, 'route-outcomes.jsonl'));
-    const spawns = readHookLog(join(dir, 'pick-adherence.jsonl')).filter((r) => typeof r.followed === 'boolean');
+    const logged = readHookLog(join(dir, 'route-outcomes.jsonl'));
+    const commands = new Set(logged
+        .filter((r) => COMMAND_PROMPT.test(String(r.promptPreview ?? r.task ?? '').trim()))
+        .map((r) => r.routeId));
+    const routes = logged.filter((r) => !commands.has(r.routeId));
+    // One outcome per route: followed when any of its spawns used the pick.
+    const byRoute = new Map();
+    let unkeyed = 0;
+    for (const r of readHookLog(join(dir, 'pick-adherence.jsonl'))) {
+        if (typeof r.followed !== 'boolean' || commands.has(r.routeId))
+            continue;
+        if (!r.routeId)
+            byRoute.set(unkeyed++, r.followed);
+        else
+            byRoute.set(r.routeId, byRoute.get(r.routeId) === true || r.followed);
+    }
     return {
         routes: routes.length,
         shown: routes.filter((r) => r.shown === true).length,
-        spawns: spawns.length,
-        followed: spawns.filter((r) => r.followed === true).length,
+        spawns: byRoute.size,
+        followed: [...byRoute.values()].filter(Boolean).length,
     };
 }
 /** What the registry file holds: every agent (deprecated included) and slug clashes. */
@@ -112,7 +130,7 @@ export async function checkPick(cwd = process.cwd(), env = process.env) {
         lines.push('adherence: no picks logged yet');
     else {
         const rate = a.spawns ? ` (${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}`);
+        lines.push(`adherence: ${a.routes} routes, ${a.shown} shown; picks followed by a spawn of the picked agent ${a.followed}/${a.spawns}${rate}`);
     }
     lines.push(realUseLine(root, agents));
     const s = readPickStats(root);
@@ -129,4 +147,111 @@ export async function checkPick(cwd = process.cwd(), env = process.env) {
         }
         : { name: NAME, status: 'pass', message };
 }
+const CLI_PACKAGES = new Set(['@monoes/monomindcli', 'monomind']);
+/** `[[dd-]hh:]mm:ss` (ps etime) as seconds; NaN when it does not parse. */
+function etimeSeconds(etime) {
+    const m = /^(?:(\d+)-)?(?:(\d+):)?(\d+):(\d+)$/.exec(etime.trim());
+    if (!m)
+        return Number.NaN;
+    return ((Number(m[1] ?? 0) * 24 + Number(m[2] ?? 0)) * 60 + Number(m[3])) * 60 + Number(m[4]);
+}
+/** Running `… monomind … mcp start` node processes (POSIX `ps`). */
+export function listMcpServerProcesses(now = Date.now()) {
+    if (process.platform === 'win32')
+        return [];
+    let out = '';
+    try {
+        out = execFileSync('ps', ['-axo', 'pid=,etime=,args='], { encoding: 'utf-8', timeout: 3000 });
+    }
+    catch {
+        return [];
+    }
+    const found = [];
+    for (const line of out.split('\n')) {
+        const m = /^\s*(\d+)\s+(\S+)\s+(.*)$/.exec(line);
+        if (!m || !/\bmcp\s+start\b/.test(m[3]))
+            continue;
+        // The script is the first argument that is a file of this CLI.
+        const script = m[3]
+            .split(/\s+/)
+            .slice(1)
+            .find((a) => /monomind/.test(a) && existsSync(a));
+        if (!script)
+            continue;
+        const pid = Number(m[1]);
+        let cwd;
+        try {
+            cwd = readlinkSync(`/proc/${pid}/cwd`);
+        }
+        catch {
+            /* no /proc */
+        }
+        let real = script;
+        try {
+            real = realpathSync(script);
+        }
+        catch {
+            /* keep the path as given */
+        }
+        found.push({
+            pid,
+            startedAt: now - etimeSeconds(m[2]) * 1000,
+            script: real,
+            ...(cwd ? { cwd } : {}),
+        });
+    }
+    return found.filter((p) => Number.isFinite(p.startedAt));
+}
+/** The CLI package a server script belongs to: version and install time. */
+function serverPackage(script) {
+    let dir = dirname(script);
+    for (let i = 0; i < 6; i++) {
+        const file = join(dir, 'package.json');
+        try {
+            const pkg = JSON.parse(readFileSync(file, 'utf-8'));
+            if (pkg.name && CLI_PACKAGES.has(pkg.name) && typeof pkg.version === 'string')
+                return { version: pkg.version, installedAt: statSync(file).mtimeMs };
+        }
+        catch {
+            /* not here */
+        }
+        const up = dirname(dir);
+        if (up === dir)
+            break;
+        dir = up;
+    }
+    return null;
+}
+export async function checkRunningMcpServer(cwd = process.cwd(), deps = {}) {
+    const name = 'MCP Server Version';
+    const now = deps.now ?? Date.now();
+    const version = deps.version ?? VERSION;
+    if (!deps.processes && process.platform === 'win32')
+        return { name, status: 'pass', message: 'not checked on Windows' };
+    const root = resolve(findProjectRoot(cwd) ?? cwd);
+    const mine = (deps.processes ?? (() => listMcpServerProcesses(now)))().filter((p) => !p.cwd || p.cwd === root || p.cwd.startsWith(root + sep));
+    if (mine.length === 0)
+        return { name, status: 'pass', message: `no running monomind MCP server found for ${root}` };
+    const stale = [];
+    const current = [];
+    for (const p of mine) {
+        const pkg = serverPackage(p.script);
+        if (!pkg)
+            current.push(`pid ${p.pid} (version unknown)`);
+        else if (pkg.version !== version)
+            stale.push(`pid ${p.pid} runs v${pkg.version}, this CLI is v${version}`);
+        else if (pkg.installedAt > p.startedAt)
+            stale.push(`pid ${p.pid}: v${pkg.version} was updated after it started`);
+        else
+            current.push(`pid ${p.pid} v${pkg.version}`);
+    }
+    if (stale.length === 0)
+        return { name, status: 'pass', message: current.join('; ') };
+    return {
+        name,
+        status: 'warn',
+        message: `a running MCP server predates this install (${stale.join('; ')}): tools the hooks suggest, such as org_skill_show, may be missing`,
+        fix: 'Restart Claude Code (or reconnect monomind in /mcp) to load the current server; until then read an Org skill with `npx -y monomind org skills show <name>`',
+    };
+}
 //# sourceMappingURL=doctor-pick-checks.js.map

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

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

@@ -53,10 +53,10 @@ export declare function checkMonoesMemory(): Promise<HealthCheck>;
 export declare function fixStaleHelpers(): Promise<boolean>;
 export declare function checkHelpersFresh(): Promise<HealthCheck>;
 export declare function checkMonoesIntegration(): Promise<HealthCheck>;
-export declare function checkGitignoreCoverage(): Promise<HealthCheck>;
+export declare function checkGitignoreCoverage(root?: string): 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 fixGitignoreCoverage(root?: string): Promise<boolean>;
 export declare function checkAgentRegistry(opts?: {
     readOnly?: boolean;
 }): Promise<HealthCheck>;

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;AA+BH,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,CAyBxD;AAED,wBAAsB,iBAAiB,IAAI,OAAO,CAAC,WAAW,CAAC,CA4C9D;AAiFD,wBAAsB,sBAAsB,IAAI,OAAO,CAAC,WAAW,CAAC,CAoBnE;AAkDD,wBAAsB,sBAAsB,CAAC,IAAI,SAAgB,GAAG,OAAO,CAAC,WAAW,CAAC,CAqCvF;AAyBD;6EAC6E;AAC7E,wBAAsB,oBAAoB,CAAC,IAAI,SAAgB,GAAG,OAAO,CAAC,OAAO,CAAC,CA2BjF;AAED,wBAAsB,kBAAkB,CAAC,IAAI,GAAE;IAAE,QAAQ,CAAC,EAAE,OAAO,CAAA;CAAO,GAAG,OAAO,CAAC,WAAW,CAAC,CAqFhG;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

@@ -8,6 +8,7 @@ import { createRequire } from 'node:module';
 import { homedir } from 'node:os';
 import { dirname, join, sep } from 'node:path';
 import { fileURLToPath } from 'node:url';
+import { isKeptUserEdit } from '../init/file-guard.js';
 import { DOCTOR_TRACKED_HELPERS, OBSOLETE_HELPER_NAMES } from '../init/helpers-generator.js';
 import { MONOMIND_NEVER_COMMIT } from '../init/never-commit.js';
 import { mcpAddHint } from '../platform-adapters/renderers/mcp.js';
@@ -859,6 +860,9 @@ export async function fixStaleHelpers() {
     }
     let fixed = 0;
     for (const { name, local } of targets) {
+        // A helper `monomind init` kept because the user edited it is theirs.
+        if (isKeptUserEdit(process.cwd(), local))
+            continue;
         const bundled = _resolveBundledHelper(join('.claude', 'helpers', name));
         if (bundled) {
             try {
@@ -1068,8 +1072,8 @@ function gitignoreLineCovers(line, required) {
     // ancestor of `.monomind/sessions`.
     return !l.includes('*') && r.startsWith(`${l}/`);
 }
-export async function checkGitignoreCoverage() {
-    const gitignorePath = join(process.cwd(), '.gitignore');
+export async function checkGitignoreCoverage(root = process.cwd()) {
+    const gitignorePath = join(root, '.gitignore');
     if (!existsSync(gitignorePath)) {
         // The old hint was `echo ".monomind/\n**/.monomind/" >> .gitignore`, which
         // writes a literal backslash-n (sh/bash echo does not interpret escapes
@@ -1106,16 +1110,14 @@ export async function checkGitignoreCoverage() {
 }
 /** Patterns written by `doctor --fix` when there is no .gitignore at all.
  *  Covers monomind runtime state plus the standard secrets files, since a repo
- *  with no .gitignore has nothing protecting those either. */
+ *  with no .gitignore has nothing protecting those either. The runtime paths
+ *  are the specific ones the check requires, never a blanket `.monomind/`:
+ *  git cannot re-include a file below an ignored directory, so a blanket line
+ *  disables init's own `.monomind/.gitignore` allow-list (config.yaml,
+ *  CAPABILITIES.md, org definitions). */
 const GITIGNORE_FIX_PATTERNS = [
     '# monomind runtime state',
-    '.monomind/',
-    '**/.monomind/',
-    '.monomind/monoswarm/',
-    '**/.claude-flow/',
-    'data/sessions/',
-    'data/mastermind-*.json',
-    'data/mastermind-*.jsonl',
+    ...REQUIRED_GITIGNORE_PATTERNS.map(({ pattern }) => pattern),
     '',
     '# secrets / local env',
     '.env',
@@ -1130,8 +1132,8 @@ const GITIGNORE_FIX_PATTERNS = [
 ];
 /** Creates or appends the missing gitignore entries. Returns true if it wrote.
  *  Append-only and idempotent: never rewrites lines the user already has. */
-export async function fixGitignoreCoverage() {
-    const gitignorePath = join(process.cwd(), '.gitignore');
+export async function fixGitignoreCoverage(root = process.cwd()) {
+    const gitignorePath = join(root, '.gitignore');
     try {
         if (!existsSync(gitignorePath)) {
             writeFileSync(gitignorePath, `${GITIGNORE_FIX_PATTERNS.join('\n')}\n`, 'utf-8');