homegraph 1.2.0 → 1.5.0

package/dist/mcp/query-cache.d.ts

@@ -1,9 +1,16 @@
 /**
- * MCP query cache — stores serialized tool responses in homegraph.db.
+ * MCP query cache — memory key index + serialized tool responses in homegraph.db.
+ *
+ * A per-project in-memory Set of cache keys gives O(1) negative lookup so misses
+ * skip the SQLite SELECT. Payloads stay in homegraph.db; the Set is warmed from
+ * DB on first use after daemon restart when the index stamp is still valid.
  *
  * Invalidated wholesale when the index stamp or cache format version changes.
  * Per-call staleness/worktree notices are applied AFTER cache lookup so hits
  * stay fresh.
+ *
+ * The key Set lives on the daemon main thread only (cache read/write runs there
+ * before/after worker-pool explore dispatch), so no cross-thread locking is needed.
  */
 import type { QueryBuilder } from '../db/queries';
 import type { ToolResult } from './tools';
@@ -11,6 +18,33 @@ import type { ToolResult } from './tools';
 export declare const QUERY_CACHE_FORMAT_VERSION = 1;
 export declare function isMcpQueryCacheEnabled(): boolean;
 export declare function isCacheableMcpTool(toolName: string): boolean;
+/**
+ * In-memory index of cache keys for one project. Negative lookup (key absent)
+ * returns immediately without touching SQLite; positive lookup fetches the
+ * JSON payload from mcp_query_cache.
+ */
+export declare class McpQueryCacheIndex {
+    private keys;
+    /** Stamp/format this Set was last synchronized against (null = cold). */
+    private syncedStamp;
+    private syncedFormat;
+    /** Whether `cacheKey` is known to exist — O(1), no DB I/O. */
+    has(cacheKey: string): boolean;
+    /**
+     * Align the in-memory key Set with DB metadata. Clears both layers when the
+     * index stamp or format version changed; otherwise warms keys from DB on first
+     * use after process restart.
+     */
+    ensureValid(queries: QueryBuilder, getIndexStamp: () => number | null): void;
+    /** Drop in-memory keys (e.g. after the DB file was replaced on disk). */
+    reset(): void;
+    getEntry(queries: QueryBuilder, cacheKey: string): ToolResult | null;
+    setEntry(queries: QueryBuilder, cacheKey: string, toolName: string, result: ToolResult): void;
+    private loadKeysFromDb;
+}
+export declare function getMcpQueryCacheIndex(projectRoot: string): McpQueryCacheIndex;
+/** Test helper — drop all per-project indices between cases. */
+export declare function resetMcpQueryCacheIndices(): void;
 /**
  * Tokenize a natural-language explore query into a stable, order-independent
  * symbol bag for cache keys — different phrasing, same symbols → same key.
@@ -19,7 +53,4 @@ export declare function normalizeExploreQueryTerms(query: string): string[];
 /** Build the pre-hash fingerprint string for a tool + args pair. */
 export declare function buildMcpQueryCacheFingerprint(toolName: string, args: Record<string, unknown>, fileCount?: number): string;
 export declare function buildMcpQueryCacheKey(toolName: string, args: Record<string, unknown>, fileCount?: number): string;
-export declare function ensureMcpQueryCacheValid(queries: QueryBuilder, getIndexStamp: () => number | null): void;
-export declare function getMcpQueryCacheEntry(queries: QueryBuilder, cacheKey: string): ToolResult | null;
-export declare function setMcpQueryCacheEntry(queries: QueryBuilder, cacheKey: string, toolName: string, result: ToolResult): void;
 //# sourceMappingURL=query-cache.d.ts.map

package/dist/mcp/query-cache.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"query-cache.d.ts","sourceRoot":"","sources":["../../src/mcp/query-cache.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AAGH,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,eAAe,CAAC;AAClD,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,SAAS,CAAC;AAS1C,yEAAyE;AACzE,eAAO,MAAM,0BAA0B,IAAI,CAAC;AAW5C,wBAAgB,sBAAsB,IAAI,OAAO,CAGhD;AAED,wBAAgB,kBAAkB,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAE5D;AAED;;;;GAIG;AACH,qBAAa,kBAAkB;IAC7B,OAAO,CAAC,IAAI,CAAqB;IACjC,yEAAyE;IACzE,OAAO,CAAC,WAAW,CAAuB;IAC1C,OAAO,CAAC,YAAY,CAAuB;IAE3C,8DAA8D;IAC9D,GAAG,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO;IAI9B;;;;OAIG;IACH,WAAW,CAAC,OAAO,EAAE,YAAY,EAAE,aAAa,EAAE,MAAM,MAAM,GAAG,IAAI,GAAG,IAAI;IAuB5E,yEAAyE;IACzE,KAAK,IAAI,IAAI;IAMb,QAAQ,CAAC,OAAO,EAAE,YAAY,EAAE,QAAQ,EAAE,MAAM,GAAG,UAAU,GAAG,IAAI;IAKpE,QAAQ,CACN,OAAO,EAAE,YAAY,EACrB,QAAQ,EAAE,MAAM,EAChB,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,UAAU,GACjB,IAAI;IAKP,OAAO,CAAC,cAAc;CAMvB;AAED,wBAAgB,qBAAqB,CAAC,WAAW,EAAE,MAAM,GAAG,kBAAkB,CAO7E;AAED,gEAAgE;AAChE,wBAAgB,yBAAyB,IAAI,IAAI,CAEhD;AAED;;;GAGG;AACH,wBAAgB,0BAA0B,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,EAAE,CAQlE;AAwBD,oEAAoE;AACpE,wBAAgB,6BAA6B,CAC3C,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,SAAS,CAAC,EAAE,MAAM,GACjB,MAAM,CAqER;AAUD,wBAAgB,qBAAqB,CACnC,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,SAAS,CAAC,EAAE,MAAM,GACjB,MAAM,CAGR"}

package/dist/mcp/query-cache.js

@@ -1,21 +1,27 @@
 "use strict";
 /**
- * MCP query cache — stores serialized tool responses in homegraph.db.
+ * MCP query cache — memory key index + serialized tool responses in homegraph.db.
+ *
+ * A per-project in-memory Set of cache keys gives O(1) negative lookup so misses
+ * skip the SQLite SELECT. Payloads stay in homegraph.db; the Set is warmed from
+ * DB on first use after daemon restart when the index stamp is still valid.
  *
  * Invalidated wholesale when the index stamp or cache format version changes.
  * Per-call staleness/worktree notices are applied AFTER cache lookup so hits
  * stay fresh.
+ *
+ * The key Set lives on the daemon main thread only (cache read/write runs there
+ * before/after worker-pool explore dispatch), so no cross-thread locking is needed.
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.QUERY_CACHE_FORMAT_VERSION = void 0;
+exports.McpQueryCacheIndex = exports.QUERY_CACHE_FORMAT_VERSION = void 0;
 exports.isMcpQueryCacheEnabled = isMcpQueryCacheEnabled;
 exports.isCacheableMcpTool = isCacheableMcpTool;
+exports.getMcpQueryCacheIndex = getMcpQueryCacheIndex;
+exports.resetMcpQueryCacheIndices = resetMcpQueryCacheIndices;
 exports.normalizeExploreQueryTerms = normalizeExploreQueryTerms;
 exports.buildMcpQueryCacheFingerprint = buildMcpQueryCacheFingerprint;
 exports.buildMcpQueryCacheKey = buildMcpQueryCacheKey;
-exports.ensureMcpQueryCacheValid = ensureMcpQueryCacheValid;
-exports.getMcpQueryCacheEntry = getMcpQueryCacheEntry;
-exports.setMcpQueryCacheEntry = setMcpQueryCacheEntry;
 const node_crypto_1 = require("node:crypto");
 /** Mirrors `getExploreOutputBudget` tier breakpoints — cache-key only. */
 function defaultExploreMaxFiles(fileCount) {
@@ -31,6 +37,8 @@ const METADATA_INDEX_STAMP = 'query_cache_index_stamp';
 const METADATA_FORMAT_VERSION = 'query_cache_format_version';
 /** Tools that must stay live — never cached. */
 const NON_CACHEABLE_TOOLS = new Set(['homegraph_status', 'homegraph_spec_match']);
+/** Per resolved project root — one index per homegraph.db. */
+const cacheIndices = new Map();
 function isMcpQueryCacheEnabled() {
     const raw = process.env.HOMEGRAPH_MCP_CACHE;
     return raw === '1' || raw === 'true';
@@ -38,6 +46,80 @@ function isMcpQueryCacheEnabled() {
 function isCacheableMcpTool(toolName) {
     return !NON_CACHEABLE_TOOLS.has(toolName);
 }
+/**
+ * In-memory index of cache keys for one project. Negative lookup (key absent)
+ * returns immediately without touching SQLite; positive lookup fetches the
+ * JSON payload from mcp_query_cache.
+ */
+class McpQueryCacheIndex {
+    keys = new Set();
+    /** Stamp/format this Set was last synchronized against (null = cold). */
+    syncedStamp = null;
+    syncedFormat = null;
+    /** Whether `cacheKey` is known to exist — O(1), no DB I/O. */
+    has(cacheKey) {
+        return this.keys.has(cacheKey);
+    }
+    /**
+     * Align the in-memory key Set with DB metadata. Clears both layers when the
+     * index stamp or format version changed; otherwise warms keys from DB on first
+     * use after process restart.
+     */
+    ensureValid(queries, getIndexStamp) {
+        const currentStamp = String(getIndexStamp() ?? 0);
+        const currentFormat = String(exports.QUERY_CACHE_FORMAT_VERSION);
+        const storedStamp = queries.getMetadata(METADATA_INDEX_STAMP);
+        const storedFormat = queries.getMetadata(METADATA_FORMAT_VERSION);
+        if (storedStamp === currentStamp && storedFormat === currentFormat) {
+            if (this.syncedStamp !== currentStamp || this.syncedFormat !== currentFormat) {
+                this.loadKeysFromDb(queries);
+                this.syncedStamp = currentStamp;
+                this.syncedFormat = currentFormat;
+            }
+            return;
+        }
+        queries.clearMcpQueryCache();
+        queries.setMetadata(METADATA_INDEX_STAMP, currentStamp);
+        queries.setMetadata(METADATA_FORMAT_VERSION, currentFormat);
+        this.keys.clear();
+        this.syncedStamp = currentStamp;
+        this.syncedFormat = currentFormat;
+    }
+    /** Drop in-memory keys (e.g. after the DB file was replaced on disk). */
+    reset() {
+        this.keys.clear();
+        this.syncedStamp = null;
+        this.syncedFormat = null;
+    }
+    getEntry(queries, cacheKey) {
+        if (!this.keys.has(cacheKey))
+            return null;
+        return readMcpQueryCachePayload(queries, cacheKey);
+    }
+    setEntry(queries, cacheKey, toolName, result) {
+        writeMcpQueryCachePayload(queries, cacheKey, toolName, result);
+        this.keys.add(cacheKey);
+    }
+    loadKeysFromDb(queries) {
+        this.keys.clear();
+        for (const key of queries.listMcpQueryCacheKeys()) {
+            this.keys.add(key);
+        }
+    }
+}
+exports.McpQueryCacheIndex = McpQueryCacheIndex;
+function getMcpQueryCacheIndex(projectRoot) {
+    let index = cacheIndices.get(projectRoot);
+    if (!index) {
+        index = new McpQueryCacheIndex();
+        cacheIndices.set(projectRoot, index);
+    }
+    return index;
+}
+/** Test helper — drop all per-project indices between cases. */
+function resetMcpQueryCacheIndices() {
+    cacheIndices.clear();
+}
 /**
  * Tokenize a natural-language explore query into a stable, order-independent
  * symbol bag for cache keys — different phrasing, same symbols → same key.
@@ -158,19 +240,7 @@ function buildMcpQueryCacheKey(toolName, args, fileCount) {
     const fingerprint = buildMcpQueryCacheFingerprint(toolName, args, fileCount);
     return (0, node_crypto_1.createHash)('sha256').update(fingerprint, 'utf8').digest('hex');
 }
-function ensureMcpQueryCacheValid(queries, getIndexStamp) {
-    const currentStamp = String(getIndexStamp() ?? 0);
-    const storedStamp = queries.getMetadata(METADATA_INDEX_STAMP);
-    const storedFormat = queries.getMetadata(METADATA_FORMAT_VERSION);
-    const currentFormat = String(exports.QUERY_CACHE_FORMAT_VERSION);
-    if (storedStamp === currentStamp && storedFormat === currentFormat) {
-        return;
-    }
-    queries.clearMcpQueryCache();
-    queries.setMetadata(METADATA_INDEX_STAMP, currentStamp);
-    queries.setMetadata(METADATA_FORMAT_VERSION, currentFormat);
-}
-function getMcpQueryCacheEntry(queries, cacheKey) {
+function readMcpQueryCachePayload(queries, cacheKey) {
     const row = queries.getMcpQueryCache(cacheKey);
     if (!row)
         return null;
@@ -184,7 +254,7 @@ function getMcpQueryCacheEntry(queries, cacheKey) {
         return null;
     }
 }
-function setMcpQueryCacheEntry(queries, cacheKey, toolName, result) {
+function writeMcpQueryCachePayload(queries, cacheKey, toolName, result) {
     const shortTool = toolName.replace(/^homegraph_/, '');
     queries.setMcpQueryCache(cacheKey, shortTool, JSON.stringify(result), Date.now());
 }

package/dist/mcp/query-cache.js.map

@@ -1 +1 @@
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package/dist/mcp/query-pool.d.ts

@@ -10,17 +10,25 @@
  * 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.
+ *   - lazy growth: **no worker until the first heavy call**, then grows to
+ *     `size` on demand. Eager warm-start used to open a second full DB on every
+ *     MCP session and balloon RSS (~5GB on ~800MB indexes).
+ *   - **default concurrency is 1** — each worker is another V8 + WAL open; on
+ *     large indexes two workers routinely doubled working-set into multi-GB.
+ *     Override with `CODEGRAPH_QUERY_POOL_SIZE` when you truly need more.
+ *   - **admission**: when outstanding work already fills `size` in-flight plus
+ *     another `size` waiting, further calls resolve immediately with
+ *     success-shaped busy/partial guidance instead of queuing up to die at the
+ *     client hard timeout.
  *   - 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.
+ *     (default 20s, clamped ≤30s — well under typical ~60s MCP client timeouts)
+ *     resolves with SUCCESS-shaped static "Partial / busy, retry" guidance —
+ *     never `isError`, and never DB/FTS work on the timeout callback (that
+ *     can freeze the transport so the client still sees empty `-32001`).
  */
 import type { ToolResult } from './tools';
 /**
@@ -39,9 +47,9 @@ export interface PoolWorker {
 export interface QueryPoolOptions {
     /** Default project root each worker opens at spawn. */
     root: string;
-    /** Max worker threads. Defaults to `clamp(cores-1, 1, 16)`. */
+    /** Max worker threads. Defaults to `clamp(cores-1, 1, DEFAULT_POOL_CAP)`. */
     size?: number;
-    /** Linger before a queued call gets busy-guidance. Default 45s. */
+    /** Linger before a queued/in-flight call gets busy-guidance. Default 20s (≤30s clamp). */
     softTimeoutMs?: number;
     /** Retries for an in-flight call whose worker crashed. Default 1. */
     maxRetries?: number;
@@ -51,11 +59,19 @@ export interface QueryPoolOptions {
 /**
  * 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.
+ * caller serves in-process — today's behavior). Unset → `clamp(cores-1, 1, 1)`:
+ * one parallel explore without a second full-DB RSS hit. Explicit overrides still
+ * honor up to {@link MAX_POOL_SIZE}.
  */
 export declare function resolvePoolSize(envVal: string | undefined, cpuCount: number): number;
+/**
+ * Soft / tool deadline. Env `CODEGRAPH_QUERY_BUSY_TIMEOUT_MS` may raise or
+ * lower it, but is always clamped into `[1000, MAX_BUSY_TIMEOUT_MS]` so a
+ * mistaken `60000` cannot race DevEco/Cursor's ~60s MCP hard timeout.
+ */
+export declare function resolveBusyTimeoutMs(): number;
+/** Same as {@link resolveBusyTimeoutMs} — used by ToolHandler for all tools. */
+export declare function resolveToolDeadlineMs(): number;
 export declare class QueryPool {
     private idle;
     private queue;
@@ -70,7 +86,14 @@ export declare class QueryPool {
     private readonly softTimeoutMs;
     private readonly maxRetries;
     private readonly createWorker;
+    private everReady;
     constructor(opts: QueryPoolOptions);
+    /**
+     * True once at least one worker has completed a successful cold-start handshake.
+     * False during the cold-start window (and after destroy) so ToolHandler can
+     * fall back to in-process dispatch instead of queuing behind a busy backstop.
+     */
+    get ready(): boolean;
     /** Pool size cap (for logging/status). */
     get size(): number;
     /** Live worker count (for tests/status). */
@@ -81,13 +104,24 @@ export declare class QueryPool {
      * degrades to today's behavior instead of failing tool calls.
      */
     get healthy(): boolean;
+    /** In-flight + unsettled queued jobs (for admission / tests). */
+    outstandingCount(): number;
+    /**
+     * How many unsettled jobs we tolerate before refusing new ones immediately.
+     * One full wave running + one full wave waiting — further fan-out gets
+     * busy/partial guidance instead of stacking up to the soft timeout.
+     */
+    private admissionLimit;
     private spawnOne;
     private onMessage;
     private onWorkerGone;
     private drain;
     private settle;
+    private settleBusyOrPartial;
     /** Run a read tool on the pool. Always resolves (never rejects). */
-    run(toolName: string, args: Record<string, unknown>): Promise<ToolResult>;
+    run(toolName: string, args: Record<string, unknown>, opts?: {
+        onSoftTimeout?: () => ToolResult | null | undefined;
+    }): Promise<ToolResult>;
     /** Terminate all workers and answer any outstanding calls gracefully. */
     destroy(): Promise<void>;
 }

package/dist/mcp/query-pool.d.ts.map

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package/dist/mcp/query-pool.js

@@ -11,17 +11,25 @@
  * 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.
+ *   - lazy growth: **no worker until the first heavy call**, then grows to
+ *     `size` on demand. Eager warm-start used to open a second full DB on every
+ *     MCP session and balloon RSS (~5GB on ~800MB indexes).
+ *   - **default concurrency is 1** — each worker is another V8 + WAL open; on
+ *     large indexes two workers routinely doubled working-set into multi-GB.
+ *     Override with `CODEGRAPH_QUERY_POOL_SIZE` when you truly need more.
+ *   - **admission**: when outstanding work already fills `size` in-flight plus
+ *     another `size` waiting, further calls resolve immediately with
+ *     success-shaped busy/partial guidance instead of queuing up to die at the
+ *     client hard timeout.
  *   - 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.
+ *     (default 20s, clamped ≤30s — well under typical ~60s MCP client timeouts)
+ *     resolves with SUCCESS-shaped static "Partial / busy, retry" guidance —
+ *     never `isError`, and never DB/FTS work on the timeout callback (that
+ *     can freeze the transport so the client still sees empty `-32001`).
  */
 var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
     if (k2 === undefined) k2 = k;
@@ -59,13 +67,29 @@ var __importStar = (this && this.__importStar) || (function () {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.QueryPool = void 0;
 exports.resolvePoolSize = resolvePoolSize;
+exports.resolveBusyTimeoutMs = resolveBusyTimeoutMs;
+exports.resolveToolDeadlineMs = resolveToolDeadlineMs;
 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
+/**
+ * Default soft backstop — must stay **well below** typical MCP client hard
+ * timeouts (~60s). Eval / agent configs sometimes set the env to 60000, which
+ * races the client and yields empty `-32001`; we clamp to
+ * {@link MAX_BUSY_TIMEOUT_MS} regardless. Prefer returning busy/partial early
+ * so the agent can retry once instead of waiting out the client hard cut.
+ */
+const DEFAULT_BUSY_TIMEOUT_MS = 15_000;
+/** Hard ceiling — leave headroom under ~30–60s client timeouts (flush / scheduling). */
+const MAX_BUSY_TIMEOUT_MS = 20_000;
+/**
+ * Default concurrent workers when env is unset. Keep at 1: a second connection
+ * on a large index is a multi-GB RSS hit. Explicit env overrides still go up to
+ * {@link MAX_POOL_SIZE}.
+ */
+const DEFAULT_POOL_CAP = 1;
 /** Hard ceiling on pool size regardless of core count / env. */
 const MAX_POOL_SIZE = 16;
 /**
@@ -87,9 +111,9 @@ 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.
+ * caller serves in-process — today's behavior). Unset → `clamp(cores-1, 1, 1)`:
+ * one parallel explore without a second full-DB RSS hit. Explicit overrides still
+ * honor up to {@link MAX_POOL_SIZE}.
  */
 function resolvePoolSize(envVal, cpuCount) {
     if (envVal !== undefined && envVal !== '') {
@@ -98,8 +122,13 @@ function resolvePoolSize(envVal, cpuCount) {
             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));
+    return Math.max(1, Math.min(cpuCount - 1, DEFAULT_POOL_CAP));
 }
+/**
+ * Soft / tool deadline. Env `CODEGRAPH_QUERY_BUSY_TIMEOUT_MS` may raise or
+ * lower it, but is always clamped into `[1000, MAX_BUSY_TIMEOUT_MS]` so a
+ * mistaken `60000` cannot race DevEco/Cursor's ~60s MCP hard timeout.
+ */
 function resolveBusyTimeoutMs() {
     const raw = process.env.CODEGRAPH_QUERY_BUSY_TIMEOUT_MS;
     if (raw === undefined || raw === '')
@@ -107,17 +136,25 @@ function resolveBusyTimeoutMs() {
     const n = Number(raw);
     if (!Number.isFinite(n) || n < 1000)
         return DEFAULT_BUSY_TIMEOUT_MS;
-    return Math.floor(n);
+    return Math.min(Math.floor(n), MAX_BUSY_TIMEOUT_MS);
+}
+/** Same as {@link resolveBusyTimeoutMs} — used by ToolHandler for all tools. */
+function resolveToolDeadlineMs() {
+    return resolveBusyTimeoutMs();
 }
 /** Success-shaped overload guidance (NEVER isError — see the abandonment rule). */
-function busyGuidance(waitedMs) {
+function busyGuidance(waitedMs, reason = 'timeout') {
     const secs = Math.max(1, Math.round(waitedMs / 1000));
+    const why = reason === 'admission'
+        ? 'too many concurrent HomeGraph queries are already in flight'
+        : `this call waited ${secs}s in the queue / on a worker`;
     return {
         content: [{
                 type: 'text',
-                text: `CodeGraph is busy serving other concurrent requests right now (this call waited ${secs}s in the queue). ` +
-                    `This is NOT an error and the index is fine — wait a few seconds and retry this exact call; it will return normally. ` +
-                    `If you can't wait, use your built-in tools for just this one step.`,
+                text: `⚠️ **Partial result** — HomeGraph is busy (${why}). This is NOT an error. ` +
+                    `Retry ONE \`homegraph_explore\` with the concrete symbol/file names from the question — ` +
+                    `do not fire search+explore or node+callers+callees in parallel, and do not fall back to grep/read ` +
+                    `for symbols you already named (that duplicates tokens). A single retry usually returns full source.`,
             }],
     };
 }
@@ -140,13 +177,23 @@ class QueryPool {
     softTimeoutMs;
     maxRetries;
     createWorker;
+    everReady = false;
     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.maxSize = Math.max(1, Math.min(opts.size ?? Math.min(DEFAULT_POOL_CAP, 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
+        // One eager warm worker so the first tool call isn't queued behind a cold start (#662).
+        this.spawnOne();
+    }
+    /**
+     * True once at least one worker has completed a successful cold-start handshake.
+     * False during the cold-start window (and after destroy) so ToolHandler can
+     * fall back to in-process dispatch instead of queuing behind a busy backstop.
+     */
+    get ready() {
+        return this.everReady && !this.destroyed;
     }
     /** Pool size cap (for logging/status). */
     get size() { return this.maxSize; }
@@ -160,6 +207,18 @@ class QueryPool {
     get healthy() {
         return !this.destroyed && this.totalCrashes < CRASH_BUDGET;
     }
+    /** In-flight + unsettled queued jobs (for admission / tests). */
+    outstandingCount() {
+        return this.inflight.size + this.queue.filter((j) => !j.settled).length;
+    }
+    /**
+     * How many unsettled jobs we tolerate before refusing new ones immediately.
+     * One full wave running + one full wave waiting — further fan-out gets
+     * busy/partial guidance instead of stacking up to the soft timeout.
+     */
+    admissionLimit() {
+        return this.maxSize * 2;
+    }
     spawnOne() {
         if (this.destroyed || this.workers.size >= this.maxSize)
             return;
@@ -185,6 +244,8 @@ class QueryPool {
             this.pendingWorkers.delete(w);
             if (m.ok === false)
                 this.totalCrashes++; // hard open failure
+            else
+                this.everReady = true;
             this.idle.push(w);
             this.drain();
             return;
@@ -257,19 +318,35 @@ class QueryPool {
             clearTimeout(job.softTimer);
         job.resolve(result);
     }
+    settleBusyOrPartial(job, reason) {
+        if (job.settled)
+            return;
+        const partial = job.onSoftTimeout?.();
+        if (partial) {
+            this.settle(job, partial);
+            return;
+        }
+        this.settle(job, busyGuidance(Date.now() - job.enqueuedAt, reason));
+    }
     /** Run a read tool on the pool. Always resolves (never rejects). */
-    run(toolName, args) {
+    run(toolName, args, opts) {
         return new Promise((resolve) => {
             const job = {
                 id: this.nextId++, toolName, args, resolve,
                 retries: 0, settled: false, enqueuedAt: Date.now(),
+                onSoftTimeout: opts?.onSoftTimeout,
             };
+            // Hard admission: refuse to stack another wave that would sit until soft
+            // timeout / client hard timeout. Caller gets partial/busy NOW.
+            if (this.outstandingCount() >= this.admissionLimit()) {
+                this.settleBusyOrPartial(job, 'admission');
+                return;
+            }
             // 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.
+            // success-shaped "retry"/partial instead of a hard timeout.
             job.softTimer = setTimeout(() => {
-                if (!job.settled)
-                    this.settle(job, busyGuidance(Date.now() - job.enqueuedAt));
+                this.settleBusyOrPartial(job, 'timeout');
             }, this.softTimeoutMs);
             job.softTimer.unref?.();
             this.queue.push(job);