@colbymchenry/codegraph-darwin-x64 1.1.1 → 1.1.3

package/lib/dist/mcp/query-pool.js

@@ -0,0 +1,297 @@
+"use strict";
+/**
+ * Query pool — runs CPU-heavy read-tool calls on a pool of worker threads so
+ * the shared daemon's main event loop stays free for the MCP transport.
+ *
+ * Why this exists: see {@link ./query-worker}. One daemon, one event loop, one
+ * synchronous SQLite connection serializes every concurrent `codegraph_explore`
+ * AND starves the transport (a 10-way wave delivered 0 transport heartbeats in
+ * 25s — responses can't flush until the whole batch drains, so clients time
+ * out). Spreading the dispatch across worker threads (each its own WAL read
+ * connection) restores true multi-core parallelism and an idle main loop.
+ *
+ * Properties:
+ *   - lazy growth: one warm worker on construct, grows to `size` on demand, so a
+ *     single-agent session pays for one connection and a 10-subagent burst grows
+ *     to the core budget.
+ *   - crash recovery: a dead worker is respawned and its in-flight call retried
+ *     once; a poison call that keeps crashing fails gracefully (never wedges the
+ *     pool). A crash budget trips a circuit breaker (`healthy` → false) so the
+ *     caller falls back to in-process dispatch instead of thrashing respawns.
+ *   - graceful backstop: a call that can't be served within `softTimeoutMs`
+ *     resolves with SUCCESS-shaped "busy, retry" guidance — never `isError`, so
+ *     a momentary overload can't teach the agent to abandon codegraph — instead
+ *     of hanging past the client's hard timeout.
+ */
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.QueryPool = void 0;
+exports.resolvePoolSize = resolvePoolSize;
+const worker_threads_1 = require("worker_threads");
+const path = __importStar(require("path"));
+const os = __importStar(require("os"));
+/** Compiled sibling — `query-worker.js` lives next to this file in `dist/mcp/`. */
+const WORKER_FILE = path.join(__dirname, 'query-worker.js');
+/** Default linger before a queued call is answered with busy-guidance. */
+const DEFAULT_BUSY_TIMEOUT_MS = 45_000; // < the ~60s MCP client request timeout
+/** Hard ceiling on pool size regardless of core count / env. */
+const MAX_POOL_SIZE = 16;
+/**
+ * Total worker deaths before the pool declares itself unhealthy and the caller
+ * reverts to in-process dispatch. High enough to ride out a few transient
+ * crashes, low enough that a systematically-broken worker (e.g. a platform that
+ * can't spawn threads) degrades quickly instead of respawning forever.
+ */
+const CRASH_BUDGET = 12;
+/**
+ * Max workers cold-starting at once. A worker's cold start is heavy — full
+ * module load (tree-sitter etc.) + opening a large WAL DB — and starting the
+ * whole pool simultaneously thrashes CPU/I-O so badly it can stall the daemon's
+ * main loop for tens of seconds. Warming a couple at a time keeps each start
+ * fast; as one reports ready the next begins, so the pool still reaches full
+ * size within a few calls of a burst, just without the thundering herd.
+ */
+const MAX_CONCURRENT_SPAWN = 2;
+/**
+ * Resolve the pool size from the `CODEGRAPH_QUERY_POOL_SIZE` override and the
+ * machine's core count. `0` (or a negative) explicitly disables the pool (the
+ * caller serves in-process — today's behavior). Unset → `clamp(cores-1, 1, 16)`:
+ * leave a core for the main loop + OS, but never zero, since even one worker
+ * frees the transport and lets responses flush incrementally.
+ */
+function resolvePoolSize(envVal, cpuCount) {
+    if (envVal !== undefined && envVal !== '') {
+        const n = Number(envVal);
+        if (Number.isFinite(n) && n >= 0)
+            return Math.min(Math.floor(n), MAX_POOL_SIZE);
+        // non-numeric / negative → fall through to the default
+    }
+    return Math.max(1, Math.min(cpuCount - 1, MAX_POOL_SIZE));
+}
+function resolveBusyTimeoutMs() {
+    const raw = process.env.CODEGRAPH_QUERY_BUSY_TIMEOUT_MS;
+    if (raw === undefined || raw === '')
+        return DEFAULT_BUSY_TIMEOUT_MS;
+    const n = Number(raw);
+    if (!Number.isFinite(n) || n < 1000)
+        return DEFAULT_BUSY_TIMEOUT_MS;
+    return Math.floor(n);
+}
+/** Success-shaped overload guidance (NEVER isError — see the abandonment rule). */
+function busyGuidance(waitedMs) {
+    const secs = Math.max(1, Math.round(waitedMs / 1000));
+    return {
+        content: [{
+                type: 'text',
+                text: `CodeGraph is busy serving other concurrent requests right now (this call waited ${secs}s in the queue). ` +
+                    `This is NOT an error and the index is fine — wait a few seconds and retry this exact call; it will return normally. ` +
+                    `If you can't wait, use your built-in tools for just this one step.`,
+            }],
+    };
+}
+class QueryPool {
+    idle = [];
+    queue = [];
+    inflight = new Map();
+    workers = new Set();
+    // Workers spawned but not yet 'ready'. Growth must count these so a single
+    // first call (with the eager worker still starting) doesn't spawn the WHOLE
+    // pool at once — N simultaneous cold worker starts (each a full module load +
+    // a large DB open) saturate the box and starve the main loop. Grow only when
+    // the queue outstrips idle + pending.
+    pendingWorkers = new Set();
+    nextId = 1;
+    totalCrashes = 0;
+    destroyed = false;
+    root;
+    maxSize;
+    softTimeoutMs;
+    maxRetries;
+    createWorker;
+    constructor(opts) {
+        this.root = opts.root;
+        this.maxSize = Math.max(1, Math.min(opts.size ?? Math.max(1, os.cpus().length - 1), MAX_POOL_SIZE));
+        this.softTimeoutMs = opts.softTimeoutMs ?? resolveBusyTimeoutMs();
+        this.maxRetries = opts.maxRetries ?? 1;
+        this.createWorker = opts.createWorker ?? (() => new worker_threads_1.Worker(WORKER_FILE, { workerData: { root: this.root } }));
+        this.spawnOne(); // one eager warm worker, ready for the first call
+    }
+    /** Pool size cap (for logging/status). */
+    get size() { return this.maxSize; }
+    /** Live worker count (for tests/status). */
+    get liveWorkers() { return this.workers.size; }
+    /**
+     * False once the crash budget is exhausted (or after destroy). The ToolHandler
+     * checks this and falls back to in-process dispatch — a broken worker platform
+     * degrades to today's behavior instead of failing tool calls.
+     */
+    get healthy() {
+        return !this.destroyed && this.totalCrashes < CRASH_BUDGET;
+    }
+    spawnOne() {
+        if (this.destroyed || this.workers.size >= this.maxSize)
+            return;
+        let w;
+        try {
+            w = this.createWorker();
+        }
+        catch {
+            this.totalCrashes++; // counts toward the circuit breaker
+            return;
+        }
+        this.workers.add(w);
+        this.pendingWorkers.add(w);
+        w.on('message', (m) => this.onMessage(w, (m ?? {})));
+        w.on('error', () => this.onWorkerGone(w));
+        w.on('exit', (code) => { if (code !== 0)
+            this.onWorkerGone(w); });
+    }
+    onMessage(w, m) {
+        if (!m)
+            return;
+        if (m.type === 'ready') {
+            this.pendingWorkers.delete(w);
+            if (m.ok === false)
+                this.totalCrashes++; // hard open failure
+            this.idle.push(w);
+            this.drain();
+            return;
+        }
+        if (m.type === 'result') {
+            const job = this.inflight.get(w);
+            this.inflight.delete(w);
+            this.idle.push(w);
+            if (job)
+                this.settle(job, m.result ?? busyGuidance(0));
+            this.drain();
+        }
+    }
+    // A worker died (crash hook, OOM, segfault, exit≠0). Respawn a replacement and
+    // retry its in-flight job once; a job that keeps crashing workers fails
+    // gracefully so it can't loop the pool forever.
+    onWorkerGone(w) {
+        if (!this.workers.has(w))
+            return; // already handled (error+exit both fire)
+        this.workers.delete(w);
+        this.pendingWorkers.delete(w);
+        this.idle = this.idle.filter((x) => x !== w);
+        this.totalCrashes++;
+        const job = this.inflight.get(w);
+        this.inflight.delete(w);
+        try {
+            void w.terminate();
+        }
+        catch { /* already gone */ }
+        if (this.healthy)
+            this.spawnOne(); // keep capacity
+        if (job) {
+            if (job.retries < this.maxRetries && this.healthy) {
+                job.retries++;
+                this.queue.unshift(job); // head of line — retry promptly
+            }
+            else {
+                this.settle(job, { isError: true, content: [{ type: 'text', text: 'codegraph worker crashed; please retry the call.' }] });
+            }
+        }
+        this.drain();
+    }
+    drain() {
+        // Grow toward maxSize while queued work outstrips workers that are idle OR
+        // already on their way up (pending) — so we never spawn the whole pool for a
+        // single call whose eager worker just hasn't reported ready yet.
+        while (this.queue.length > this.idle.length + this.pendingWorkers.size &&
+            this.workers.size < this.maxSize &&
+            this.pendingWorkers.size < MAX_CONCURRENT_SPAWN &&
+            this.healthy) {
+            this.spawnOne();
+        }
+        while (this.idle.length && this.queue.length) {
+            // Skip jobs the backstop already answered.
+            let job;
+            while (this.queue.length && (job = this.queue.shift()) && job.settled)
+                job = undefined;
+            if (!job || job.settled)
+                break;
+            const w = this.idle.pop();
+            this.inflight.set(w, job);
+            w.postMessage({ type: 'call', id: job.id, toolName: job.toolName, args: job.args });
+        }
+    }
+    settle(job, result) {
+        if (job.settled)
+            return; // already answered (by backstop or worker)
+        job.settled = true;
+        if (job.softTimer)
+            clearTimeout(job.softTimer);
+        job.resolve(result);
+    }
+    /** Run a read tool on the pool. Always resolves (never rejects). */
+    run(toolName, args) {
+        return new Promise((resolve) => {
+            const job = {
+                id: this.nextId++, toolName, args, resolve,
+                retries: 0, settled: false, enqueuedAt: Date.now(),
+            };
+            // Don't let the caller wait past softTimeoutMs. The worker may still be
+            // busy (we can't cancel synchronous CPU), but the CLIENT gets a prompt,
+            // success-shaped "retry" instead of a hard timeout.
+            job.softTimer = setTimeout(() => {
+                if (!job.settled)
+                    this.settle(job, busyGuidance(Date.now() - job.enqueuedAt));
+            }, this.softTimeoutMs);
+            job.softTimer.unref?.();
+            this.queue.push(job);
+            this.drain();
+        });
+    }
+    /** Terminate all workers and answer any outstanding calls gracefully. */
+    async destroy() {
+        if (this.destroyed)
+            return;
+        this.destroyed = true;
+        const ws = [...this.workers];
+        this.workers.clear();
+        this.pendingWorkers.clear();
+        this.idle = [];
+        for (const job of [...this.inflight.values(), ...this.queue]) {
+            this.settle(job, { isError: true, content: [{ type: 'text', text: 'codegraph is shutting down; retry shortly.' }] });
+        }
+        this.inflight.clear();
+        this.queue = [];
+        await Promise.all(ws.map((w) => Promise.resolve(w.terminate()).catch(() => { })));
+    }
+}
+exports.QueryPool = QueryPool;
+//# sourceMappingURL=query-pool.js.map

package/lib/dist/mcp/query-pool.js.map

@@ -0,0 +1 @@
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package/lib/dist/mcp/query-worker.d.ts

@@ -0,0 +1,24 @@
+/**
+ * Query worker thread — issue: concurrent MCP tool calls starve the daemon.
+ *
+ * The shared daemon serves every session on ONE event loop with synchronous
+ * `node:sqlite`. `codegraph_explore` is CPU-heavy (FTS + RWR/personalized-
+ * PageRank + impact + output building) stitched together by microtask `await`s,
+ * so N concurrent explores keep the microtask queue continuously full and
+ * starve the macrotask phases — timers AND socket I/O. The transport freezes:
+ * no response flushes, no request is read, until the whole batch drains. With
+ * ~10 subagents that routinely exceeds the MCP client's request timeout.
+ *
+ * This worker moves the heavy read-tool dispatch OFF the daemon's main loop.
+ * Each worker owns its OWN read connection (node:sqlite WAL allows N concurrent
+ * readers across connections — verified: a worker reader sees the main writer's
+ * committed catch-up/watcher writes), so {@link QueryPool} runs N tool calls in
+ * true parallel up to core count while the main loop stays free for the MCP
+ * transport. The worker runs {@link ToolHandler.executeReadTool} — validation +
+ * dispatch + error classification — and returns the raw {@link ToolResult}; the
+ * MAIN thread keeps the catch-up gate, the watcher-state notices (staleness /
+ * worktree), `codegraph_status`, and telemetry, none of which a watcher-less
+ * read connection can answer.
+ */
+export {};
+//# sourceMappingURL=query-worker.d.ts.map

package/lib/dist/mcp/query-worker.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"query-worker.d.ts","sourceRoot":"","sources":["../../src/mcp/query-worker.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;GAqBG"}

package/lib/dist/mcp/query-worker.js

@@ -0,0 +1,87 @@
+"use strict";
+/**
+ * Query worker thread — issue: concurrent MCP tool calls starve the daemon.
+ *
+ * The shared daemon serves every session on ONE event loop with synchronous
+ * `node:sqlite`. `codegraph_explore` is CPU-heavy (FTS + RWR/personalized-
+ * PageRank + impact + output building) stitched together by microtask `await`s,
+ * so N concurrent explores keep the microtask queue continuously full and
+ * starve the macrotask phases — timers AND socket I/O. The transport freezes:
+ * no response flushes, no request is read, until the whole batch drains. With
+ * ~10 subagents that routinely exceeds the MCP client's request timeout.
+ *
+ * This worker moves the heavy read-tool dispatch OFF the daemon's main loop.
+ * Each worker owns its OWN read connection (node:sqlite WAL allows N concurrent
+ * readers across connections — verified: a worker reader sees the main writer's
+ * committed catch-up/watcher writes), so {@link QueryPool} runs N tool calls in
+ * true parallel up to core count while the main loop stays free for the MCP
+ * transport. The worker runs {@link ToolHandler.executeReadTool} — validation +
+ * dispatch + error classification — and returns the raw {@link ToolResult}; the
+ * MAIN thread keeps the catch-up gate, the watcher-state notices (staleness /
+ * worktree), `codegraph_status`, and telemetry, none of which a watcher-less
+ * read connection can answer.
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+const worker_threads_1 = require("worker_threads");
+// Mirror the engine's lazy-require of the heavy CodeGraph + tools chain. This
+// module is only ever loaded as a Worker, so the require runs once on spawn.
+const loadCodeGraph = () => require('../index').default;
+const loadToolHandler = () => require('./tools').ToolHandler;
+if (worker_threads_1.parentPort) {
+    const port = worker_threads_1.parentPort;
+    const { root } = worker_threads_1.workerData;
+    // Open the default project's READ connection once, at spawn. Other repos are
+    // opened lazily on first cross-project (projectPath) call by the ToolHandler's
+    // own per-handler cache. openSync does not start a watcher — workers are pure
+    // readers; the single watcher/writer stays on the daemon's main thread.
+    let handler = null;
+    let initError = null;
+    try {
+        const cg = loadCodeGraph().openSync(root);
+        handler = new (loadToolHandler())(cg);
+    }
+    catch (err) {
+        initError = err instanceof Error ? err.message : String(err);
+    }
+    // Tell the pool we're up. `ok:false` lets the pool count a hard open failure
+    // against its crash budget (→ fall back to in-process) without hanging.
+    port.postMessage({ type: 'ready', ok: initError === null, error: initError });
+    port.on('message', (msg) => {
+        if (!msg || msg.type !== 'call')
+            return;
+        void serve(msg);
+    });
+    const serve = async (msg) => {
+        // Test-only crash hook so the pool's worker-recovery path is exercisable
+        // deterministically. Gated behind an env flag only the suite sets — inert in
+        // normal operation (and `__test_crash__` isn't a real tool name anyway).
+        if (msg.toolName === '__test_crash__' && process.env.CODEGRAPH_QUERY_WORKER_ALLOW_TEST_CRASH === '1') {
+            process.exit(13);
+        }
+        if (!handler) {
+            port.postMessage({
+                type: 'result',
+                id: msg.id,
+                result: errorResult(`codegraph worker could not open the project: ${initError}`),
+            });
+            return;
+        }
+        try {
+            // executeReadTool already classifies NotIndexed/PathRefusal/internal errors
+            // into a ToolResult and never throws — the catch is belt-and-suspenders.
+            const result = await handler.executeReadTool(msg.toolName, msg.args);
+            port.postMessage({ type: 'result', id: msg.id, result });
+        }
+        catch (err) {
+            port.postMessage({
+                type: 'result',
+                id: msg.id,
+                result: errorResult(err instanceof Error ? err.message : String(err)),
+            });
+        }
+    };
+}
+function errorResult(text) {
+    return { isError: true, content: [{ type: 'text', text }] };
+}
+//# sourceMappingURL=query-worker.js.map

package/lib/dist/mcp/query-worker.js.map

@@ -0,0 +1 @@
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package/lib/dist/mcp/tools.d.ts

@@ -4,6 +4,7 @@
  * Defines the tools exposed by the CodeGraph MCP server.
  */
 import type CodeGraph from '../index';
+import type { QueryPool } from './query-pool';
 import type { PendingFile } from '../sync';
 /**
  * An expected, recoverable "codegraph can't serve this" condition — most
@@ -113,6 +114,33 @@ export interface ToolDefinition {
         properties: Record<string, PropertySchema>;
         required?: string[];
     };
+    /** Behavioral hints for clients (see {@link ToolAnnotations}). */
+    annotations?: ToolAnnotations;
+}
+/**
+ * MCP ToolAnnotations — behavioral hints a client MAY use to decide how, or
+ * whether, to run a tool (introduced in the 2025-03-26 spec, carried in
+ * 2025-06-18). They are advisory and never to be trusted for security, but
+ * clients gate on them: Cursor's Ask mode, for one, refuses any MCP tool that
+ * doesn't advertise `readOnlyHint: true` (issue #1018).
+ *
+ * The field is purely additive — a client that predates annotations ignores it
+ * — so codegraph advertises these even though `initialize` still negotiates the
+ * 2024-11-05 protocol version.
+ *
+ * https://modelcontextprotocol.io/specification/2025-06-18/schema#toolannotations
+ */
+export interface ToolAnnotations {
+    /** Human-readable title for the tool. */
+    title?: string;
+    /** If true, the tool does not modify its environment. Default (unset): false. */
+    readOnlyHint?: boolean;
+    /** Meaningful only when NOT read-only: may the tool perform destructive updates? */
+    destructiveHint?: boolean;
+    /** If true, repeat calls with the same arguments have no additional effect. */
+    idempotentHint?: boolean;
+    /** If true, the tool interacts with an open world of external entities. */
+    openWorldHint?: boolean;
 }
 interface PropertySchema {
     type: string;
@@ -159,7 +187,15 @@ export declare class ToolHandler {
     private defaultProjectHint;
     private worktreeMismatchCache;
     private catchUpGate;
+    private queryPool;
     constructor(cg: CodeGraph | null);
+    /**
+     * Engine-only: attach (or detach with null) the worker-thread query pool. The
+     * shared daemon sets this once its default project is open; the workers each
+     * hold their own WAL read connection and run {@link executeReadTool}. A
+     * worker's own ToolHandler never has a pool, so there is no nested off-loading.
+     */
+    setQueryPool(pool: QueryPool | null): void;
     /**
      * Update the default CodeGraph instance (e.g. after lazy initialization)
      */
@@ -286,6 +322,27 @@ export declare class ToolHandler {
      * Execute a tool by name
      */
     execute(toolName: string, args: Record<string, unknown>): Promise<ToolResult>;
+    /**
+     * Run a single read tool to completion and return its raw {@link ToolResult},
+     * classifying expected failures the same way {@link execute}'s catch does so
+     * the SHAPE is identical whether dispatch runs in-process or on a worker:
+     * NotIndexed → success-shaped guidance, PathRefusal → clean error, anything
+     * else → internal-error-with-retry. Never throws.
+     *
+     * This is the worker thread's entry point (see {@link ./query-worker}) and the
+     * in-process fallback for {@link execute}. It deliberately does NOT run the
+     * catch-up gate or the staleness/worktree notices — those need the daemon's
+     * watched main instance and stay on the main thread. Cross-cutting allowlist +
+     * path validation already ran in {@link execute} before routing here.
+     */
+    executeReadTool(toolName: string, args: Record<string, unknown>): Promise<ToolResult>;
+    /**
+     * Pure dispatch over the read tools — the switch, with no gate, no notices, no
+     * allowlist/validation (the caller owns those). `codegraph_status` is handled
+     * on the main thread in {@link execute} and never reaches here. May throw
+     * NotIndexed/PathRefusal, which {@link executeReadTool} classifies.
+     */
+    private dispatchTool;
     /**
      * Handle codegraph_search
      */

package/lib/dist/mcp/tools.d.ts.map

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