@cleocode/nexus 2026.9.12 → 2026.9.14

package/dist/src/pipeline/filesystem-walker.d.ts

@@ -40,6 +40,14 @@ export interface ScannedFile {
      */
     language: string | null;
 }
+/** Floor for one ignore-assessment batch, before the per-path allowance. */
+export declare const GIT_IGNORE_BASE_TIMEOUT_MS = 10000;
+/** Added per path in the batch, so the budget scales with the work asked of git. */
+export declare const GIT_IGNORE_PER_PATH_TIMEOUT_MS = 40;
+/** Budget for the one-shot `rev-parse` ownership probe. */
+export declare const GIT_PROBE_TIMEOUT_MS = 10000;
+/** Operator override for the ignore-assessment budget, in milliseconds. */
+export declare const GIT_IGNORE_TIMEOUT_ENV = "CLEO_NEXUS_GIT_TIMEOUT_MS";
 /**
  * Walk the repository directory tree and return a list of scanned files.
  *

package/dist/src/pipeline/filesystem-walker.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"filesystem-walker.d.ts","sourceRoot":"","sources":["../../../src/pipeline/filesystem-walker.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;GAoBG;AAOH,OAAO,KAAK,EAAE,oBAAoB,EAAE,MAAM,qBAAqB,CAAC;AAuDhE;;;;GAIG;AACH,MAAM,WAAW,WAAW;IAC1B,wEAAwE;IACxE,IAAI,EAAE,MAAM,CAAC;IACb,0BAA0B;IAC1B,IAAI,EAAE,MAAM,CAAC;IACb,4DAA4D;IAC5D,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,kDAAkD;IAClD,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB;;;OAGG;IACH,QAAQ,EAAE,MAAM,GAAG,IAAI,CAAC;CACzB;AA0BD,4EAA4E;AAC5E,eAAO,MAAM,0BAA0B,QAAS,CAAC;AAEjD,oFAAoF;AACpF,eAAO,MAAM,8BAA8B,KAAK,CAAC;AAEjD,2DAA2D;AAC3D,eAAO,MAAM,oBAAoB,QAAS,CAAC;AAK3C,2EAA2E;AAC3E,eAAO,MAAM,sBAAsB,8BAA8B,CAAC;AAoHlE;;;;;;;;;;GAUG;AACH,wBAAsB,mBAAmB,CACvC,QAAQ,EAAE,MAAM,EAChB,UAAU,CAAC,EAAE,CAAC,OAAO,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,KAAK,IAAI,EACvE,YAAY,CAAC,EAAE,CAAC,MAAM,EAAE,oBAAoB,KAAK,IAAI,EACrD,oBAAoB,GAAE,SAAS,MAAM,EAAO,GAC3C,OAAO,CAAC,WAAW,EAAE,CAAC,CAuKxB"}

package/dist/src/pipeline/filesystem-walker.js

@@ -90,31 +90,100 @@ async function readIgnorePatterns(ignorePath) {
         throw error;
     }
 }
-/** Ask Git itself to apply repository, info/exclude and configured global excludes. */
+/** Paths handed to one `git check-ignore` invocation. */
+const GIT_IGNORE_BATCH_SIZE = 256;
+/** Floor for one ignore-assessment batch, before the per-path allowance. */
+export const GIT_IGNORE_BASE_TIMEOUT_MS = 10_000;
+/** Added per path in the batch, so the budget scales with the work asked of git. */
+export const GIT_IGNORE_PER_PATH_TIMEOUT_MS = 40;
+/** Budget for the one-shot `rev-parse` ownership probe. */
+export const GIT_PROBE_TIMEOUT_MS = 10_000;
+/** Multiplier applied to a batch's budget on its single retry. */
+const GIT_IGNORE_RETRY_FACTOR = 4;
+/** Operator override for the ignore-assessment budget, in milliseconds. */
+export const GIT_IGNORE_TIMEOUT_ENV = 'CLEO_NEXUS_GIT_TIMEOUT_MS';
+/**
+ * Milliseconds allowed for one ignore-assessment batch.
+ *
+ * Scales with batch size rather than standing at a constant, because the work
+ * git is asked to do scales with it and the filesystem underneath may be far
+ * slower than the one the constant was written on.
+ *
+ * @param batchSize - Paths in this invocation.
+ * @param env - Environment to read the operator override from.
+ * @returns The budget in milliseconds.
+ */
+function gitIgnoreTimeoutMs(batchSize, env = process.env) {
+    const override = Number.parseInt(env[GIT_IGNORE_TIMEOUT_ENV] ?? '', 10);
+    if (Number.isFinite(override) && override > 0)
+        return override;
+    return GIT_IGNORE_BASE_TIMEOUT_MS + batchSize * GIT_IGNORE_PER_PATH_TIMEOUT_MS;
+}
+/**
+ * Ask Git itself to apply repository, info/exclude and configured global excludes.
+ *
+ * ## Why the budget is not a constant (T12312)
+ *
+ * This used to allow `git rev-parse` 1 s and each `git check-ignore` batch 2 s,
+ * and to `throw result.error` verbatim on an overrun. Measured 2026-09-23 on a
+ * fuseblk mount 23–49× slower than local disk, warm cache, idle machine:
+ * rev-parse 152/152/188 ms, and check-ignore over 256 paths 797/974/**1701** ms
+ * — one run at 85 % of its budget, a 2.1× spread between runs. A repository of
+ * 9 141 tracked files is 36 batches, so that budget was rolled 36 times per
+ * `nexus analyze` and one slow roll killed the entire index rebuild with the
+ * bare Node string `spawnSync git ETIMEDOUT`: no invocation named, no budget
+ * quoted, no remedy. Intermittent by construction, which is why it reproduced
+ * for one agent and not the next.
+ *
+ * The budget now scales with the batch, a transient overrun is retried once
+ * with a larger one, and a genuine timeout says what it was doing and how to
+ * raise the ceiling. Being ignored is not something git can be asked about
+ * approximately, so an exhausted retry still fails the scan — loudly, rather
+ * than by silently indexing a vendored tree.
+ *
+ * @param repoPath - Repository to assess; never inferred from cwd.
+ * @param paths - Repo-relative paths to classify.
+ * @returns The subset git considers ignored.
+ */
 function gitExcludedPaths(repoPath, paths) {
     const probe = spawnSync('git', ['rev-parse', '--is-inside-work-tree'], {
         cwd: repoPath,
         encoding: 'utf8',
-        timeout: 1000,
+        timeout: GIT_PROBE_TIMEOUT_MS,
     });
-    if (probe.error)
-        throw probe.error;
+    if (probe.error) {
+        throw new Error(`Git ownership probe (git rev-parse --is-inside-work-tree) in ${repoPath} did not complete ` +
+            `within ${GIT_PROBE_TIMEOUT_MS}ms: ${probe.error.message}. ` +
+            `Raise the ignore-assessment budget with ${GIT_IGNORE_TIMEOUT_ENV}=<ms>, or run the scan ` +
+            `from a faster filesystem — a network or FUSE mount can exceed this on a loaded machine.`, { cause: probe.error });
+    }
     if (probe.status === 128 && !existsSync(path.join(repoPath, '.git')))
         return new Set();
     if (probe.status !== 0)
         throw new Error(`Git source ownership check failed: ${probe.stderr.trim()}`);
     const excluded = new Set();
-    for (let offset = 0; offset < paths.length; offset += 256) {
-        const batch = paths.slice(offset, offset + 256);
-        const result = spawnSync('git', ['check-ignore', '--no-index', '-z', '--stdin'], {
-            cwd: repoPath,
-            encoding: 'utf8',
-            input: `${batch.join('\0')}\0`,
-            timeout: 2000,
-            maxBuffer: 4 * 1024 * 1024,
-        });
-        if (result.error)
-            throw result.error;
+    for (let offset = 0; offset < paths.length; offset += GIT_IGNORE_BATCH_SIZE) {
+        const batch = paths.slice(offset, offset + GIT_IGNORE_BATCH_SIZE);
+        const budget = gitIgnoreTimeoutMs(batch.length);
+        const batchNumber = Math.floor(offset / GIT_IGNORE_BATCH_SIZE) + 1;
+        const batchCount = Math.ceil(paths.length / GIT_IGNORE_BATCH_SIZE);
+        // One retry with a larger budget: an overrun under momentary load is not
+        // evidence that the budget is wrong, and abandoning a whole index rebuild
+        // on a single slow roll is the failure this replaces.
+        let result = runGitCheckIgnore(repoPath, batch, budget);
+        let elapsedBudget = budget;
+        if (result.error) {
+            elapsedBudget = budget * GIT_IGNORE_RETRY_FACTOR;
+            result = runGitCheckIgnore(repoPath, batch, elapsedBudget);
+        }
+        if (result.error) {
+            throw new Error(`Git ignore assessment (git check-ignore) timed out on batch ${batchNumber} of ` +
+                `${batchCount} (${batch.length} paths) in ${repoPath}: allowed ${budget}ms, then ` +
+                `${elapsedBudget}ms on retry, and neither completed (${result.error.message}). ` +
+                `Raise the per-batch budget with ${GIT_IGNORE_TIMEOUT_ENV}=<ms>. The scan is abandoned ` +
+                `rather than continued, because a batch git could not classify would otherwise be ` +
+                `indexed as if nothing in it were ignored.`, { cause: result.error });
+        }
         // Git documents exit 1 for no ignored paths; other failures invalidate the scan.
         if (result.status !== 0 && result.status !== 1)
             throw new Error(`Git ignore assessment failed: ${result.stderr.trim()}`);
@@ -124,6 +193,16 @@ function gitExcludedPaths(repoPath, paths) {
     }
     return excluded;
 }
+/** One `git check-ignore` invocation over a batch, under an explicit budget. */
+function runGitCheckIgnore(repoPath, batch, timeout) {
+    return spawnSync('git', ['check-ignore', '--no-index', '-z', '--stdin'], {
+        cwd: repoPath,
+        encoding: 'utf8',
+        input: `${batch.join('\0')}\0`,
+        timeout,
+        maxBuffer: 4 * 1024 * 1024,
+    });
+}
 // ---------------------------------------------------------------------------
 // Core walker
 // ---------------------------------------------------------------------------

package/dist/src/pipeline/filesystem-walker.js.map

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package/dist/src/pipeline/workers/worker-pool.d.ts

@@ -37,6 +37,10 @@ export interface WorkerPool {
     /** Number of workers in the pool. */
     readonly size: number;
 }
+/** Operator override for the per-file parse budget, in milliseconds. */
+export declare const PARSE_TIMEOUT_ENV = "CLEO_NEXUS_PARSE_TIMEOUT_MS";
+/** Operator override for each parse worker's V8 old-space cap, in MiB. */
+export declare const WORKER_HEAP_ENV = "CLEO_NEXUS_WORKER_HEAP_MB";
 /**
  * Create a pool of worker threads for parallel file parsing.
  *

package/dist/src/pipeline/workers/worker-pool.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"worker-pool.d.ts","sourceRoot":"","sources":["../../../../src/pipeline/workers/worker-pool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;GAiBG;AAMH,OAAO,KAAK,EACV,qBAAqB,EACrB,mBAAmB,EAEpB,MAAM,qBAAqB,CAAC;AAW7B;;GAEG;AACH,MAAM,WAAW,UAAU;IACzB;;;;;;;;;OASG;IACH,QAAQ,CAAC,MAAM,EAAE,OAAO,EACtB,KAAK,EAAE,MAAM,EAAE,EACf,UAAU,CAAC,EAAE,CAAC,cAAc,EAAE,MAAM,KAAK,IAAI,GAC5C,OAAO,CAAC,OAAO,EAAE,CAAC,CAAC;IAEtB,sEAAsE;IACtE,SAAS,IAAI,OAAO,CAAC,IAAI,CAAC,CAAC;IAE3B,qCAAqC;IACrC,QAAQ,CAAC,IAAI,EAAE,MAAM,CAAC;CACvB;AA0CD,wEAAwE;AACxE,eAAO,MAAM,iBAAiB,gCAAgC,CAAC;AAE/D,0EAA0E;AAC1E,eAAO,MAAM,eAAe,8BAA8B,CAAC;AAsD3D;;;;;;;;;;GAUG;AACH,wBAAgB,gBAAgB,CAC9B,SAAS,EAAE,GAAG,EACd,QAAQ,CAAC,EAAE,MAAM,EACjB,MAAM,GAAE,qBAA0B,EAClC,SAAS,CAAC,EAAE,mBAAmB,GAC9B,UAAU,CAsRZ"}

package/dist/src/pipeline/workers/worker-pool.js

@@ -20,6 +20,7 @@ import fs from 'node:fs';
 import os from 'node:os';
 import { fileURLToPath } from 'node:url';
 import { Worker } from 'node:worker_threads';
+import { PARSER_WORKER_HEAP_DEFAULT_MB, PARSER_WORKER_HEAP_MAX_MB, PARSER_WORKER_HEAP_MIN_MB, } from '@cleocode/contracts';
 // ---------------------------------------------------------------------------
 // Constants
 // ---------------------------------------------------------------------------
@@ -29,10 +30,68 @@ import { Worker } from 'node:worker_threads';
  */
 const SUB_BATCH_SIZE = 1;
 /**
- * Per sub-batch timeout in milliseconds.
- * If a sub-batch takes longer than this, likely a pathological file.
+ * Per-file wall budget for a parse worker, in milliseconds.
+ *
+ * `SUB_BATCH_SIZE` is 1, so this is the time allowed for ONE file — and an
+ * overrun rejects the whole dispatch, discarding every file already parsed
+ * ("generation not published"). Measured 2026-09-23 on a fuseblk mount under
+ * concurrent load from other builds: `cleo nexus analyze` over 4 498 files died
+ * with `E_PARSE_WORKER_TIMEOUT: Worker 0 file timed out after 5000ms`, naming
+ * no file and no remedy, after 212 s of work.
+ *
+ * A normal parse is milliseconds; this budget exists to bound a pathological
+ * file, not to race a loaded machine. It is generous for that reason, and
+ * overridable per {@link PARSE_TIMEOUT_ENV}.
+ *
+ * @task T12312
  */
-const SUB_BATCH_TIMEOUT_MS = 5_000;
+const SUB_BATCH_TIMEOUT_MS = 30_000;
+/** Operator override for the per-file parse budget, in milliseconds. */
+export const PARSE_TIMEOUT_ENV = 'CLEO_NEXUS_PARSE_TIMEOUT_MS';
+/** Operator override for each parse worker's V8 old-space cap, in MiB. */
+export const WORKER_HEAP_ENV = 'CLEO_NEXUS_WORKER_HEAP_MB';
+/** Default V8 old-space cap per parse worker, in MiB. */
+const DEFAULT_WORKER_HEAP_MB = PARSER_WORKER_HEAP_DEFAULT_MB;
+/** Highest cap an operator may request; the default stays conservative. */
+const MAX_WORKER_HEAP_MB = PARSER_WORKER_HEAP_MAX_MB;
+/**
+ * V8 old-space cap for one parse worker, honouring the operator override.
+ *
+ * A worker that exceeds its cap exits with a null code and the dispatch
+ * rejects, discarding every file parsed in the run. Measured 2026-09-23 over
+ * 4 498 files: workers died both inside CLEO's `cleo-tool-*.scope` (a memcg
+ * kill at 251 MB RSS, confirmed in the kernel log) and outside it with no
+ * kernel OOM at all — the second being the V8 cap itself. The default is
+ * unchanged; what was missing was any way to raise it without editing source.
+ *
+ * @task T12312
+ */
+function resolveWorkerHeapMb(explicit, env = process.env) {
+    if (explicit !== undefined)
+        return explicit;
+    const override = Number.parseInt(env[WORKER_HEAP_ENV] ?? '', 10);
+    if (Number.isFinite(override) && override > 0)
+        return override;
+    return DEFAULT_WORKER_HEAP_MB;
+}
+/** Per-file parse budget, honouring the operator override. */
+function resolveParseTimeoutMs(explicit, env = process.env) {
+    if (explicit !== undefined)
+        return explicit;
+    const override = Number.parseInt(env[PARSE_TIMEOUT_ENV] ?? '', 10);
+    if (Number.isFinite(override) && override > 0)
+        return override;
+    return SUB_BATCH_TIMEOUT_MS;
+}
+/** Best-effort path of a dispatched work item, for diagnostics only. */
+function describeWorkItem(item) {
+    if (typeof item === 'object' && item !== null && 'path' in item) {
+        const { path } = item;
+        if (typeof path === 'string' && path.length > 0)
+            return path;
+    }
+    return '<unknown file>';
+}
 // ---------------------------------------------------------------------------
 // Factory
 // ---------------------------------------------------------------------------
@@ -55,16 +114,18 @@ export function createWorkerPool(workerUrl, poolSize, limits = {}, execution) {
         throw new Error(`Worker script not found: ${workerPath}`);
     }
     const size = poolSize ?? Math.min(8, Math.max(1, os.cpus().length - 1));
-    const timeoutMs = limits.timeoutMs ?? SUB_BATCH_TIMEOUT_MS;
-    const workerHeapMb = limits.workerHeapMb ?? 128;
+    const timeoutMs = resolveParseTimeoutMs(limits.timeoutMs);
+    const workerHeapMb = resolveWorkerHeapMb(limits.workerHeapMb);
     if (!Number.isSafeInteger(size) || size < 1 || size > 8) {
         throw new RangeError('Parser pool size must be an integer from 1 to 8');
     }
     if (!Number.isFinite(timeoutMs) || timeoutMs <= 0) {
         throw new RangeError('Parser worker timeout must be positive and finite');
     }
-    if (!Number.isSafeInteger(workerHeapMb) || workerHeapMb < 8 || workerHeapMb > 512) {
-        throw new RangeError('Parser worker heap must be an integer from 8 to 512 MiB');
+    if (!Number.isSafeInteger(workerHeapMb) ||
+        workerHeapMb < PARSER_WORKER_HEAP_MIN_MB ||
+        workerHeapMb > MAX_WORKER_HEAP_MB) {
+        throw new RangeError(`Parser worker heap must be an integer from ${PARSER_WORKER_HEAP_MIN_MB} to ${MAX_WORKER_HEAP_MB} MiB`);
     }
     // V8's process-level flags silently override Worker.resourceLimits. A claimed
     // per-worker ceiling would otherwise be false even when resourceLimits reports it.
@@ -96,14 +157,30 @@ export function createWorkerPool(workerUrl, poolSize, limits = {}, execution) {
                     owned.postMessage(message);
                 else
                     owned.child.send(message, (error) => {
-                        if (error)
-                            errorHandler(error);
+                        if (!error)
+                            return;
+                        // A write error means the worker is already gone. Reporting EPIPE
+                        // verbatim names the pipe, not the death — and settles the promise
+                        // before the 'exit' handler can supply the actual reason (T12312).
+                        const broken = /EPIPE|ERR_IPC_CHANNEL_CLOSED/.test(error.message);
+                        errorHandler(broken
+                            ? new Error(`Parse worker ${workerIndex} closed its channel while handling ` +
+                                `${inFlightDescription} (${error.message}). The write failed because the ` +
+                                `worker had already exited; the pipe is the symptom, not the cause. ` +
+                                `Every file parsed so far is discarded. Check the kernel log for an ` +
+                                `oom-kill naming this process, then raise ${WORKER_HEAP_ENV}=<MiB> or the ` +
+                                `cgroup ceiling (CLEO_TOOL_MEMORY_MAX_MB); a native parser crash on one ` +
+                                `file presents the same way.`, { cause: error })
+                            : error);
                     });
             };
             let settled = false;
             let ready = owned instanceof Worker;
             let subBatchTimer = null;
             let subBatchIdx = 0;
+            // Retained for diagnostics: a timeout that cannot name the file it was
+            // parsing sends the reader looking through 4 498 of them.
+            let inFlightDescription = '<not yet dispatched>';
             const cleanup = () => {
                 if (subBatchTimer) {
                     clearTimeout(subBatchTimer);
@@ -121,7 +198,11 @@ export function createWorkerPool(workerUrl, poolSize, limits = {}, execution) {
                     if (!settled) {
                         settled = true;
                         cleanup();
-                        reject(new Error(`E_PARSE_WORKER_TIMEOUT: Worker ${workerIndex} file timed out after ${timeoutMs}ms.`));
+                        reject(new Error(`E_PARSE_WORKER_TIMEOUT: worker ${workerIndex} exceeded ${timeoutMs}ms parsing ` +
+                            `${inFlightDescription}. Every file parsed so far in this run is discarded, so ` +
+                            `one slow file fails the whole index. Raise the per-file budget with ` +
+                            `${PARSE_TIMEOUT_ENV}=<ms> — a loaded machine or a network/FUSE mount can ` +
+                            `exceed the default, and a genuinely pathological file will still be bounded.`));
                     }
                 }, timeoutMs);
             };
@@ -133,6 +214,7 @@ export function createWorkerPool(workerUrl, poolSize, limits = {}, execution) {
                     return;
                 }
                 const subBatch = chunk.slice(start, start + SUB_BATCH_SIZE);
+                inFlightDescription = subBatch.map(describeWorkItem).join(', ');
                 subBatchIdx++;
                 resetSubBatchTimer();
                 send({ type: 'sub-batch', files: subBatch });
@@ -183,7 +265,18 @@ export function createWorkerPool(workerUrl, poolSize, limits = {}, execution) {
                 if (!settled) {
                     settled = true;
                     cleanup();
-                    reject(new Error(`Worker ${workerIndex} exited with code ${code}. Possible OOM or native module failure.`));
+                    reject(new Error(`Parse worker ${workerIndex} exited with code ${code} while handling ` +
+                        `${inFlightDescription}. Every file parsed so far is discarded. ` +
+                        (code === null
+                            ? `A null code means it was KILLED rather than returning — most often the ` +
+                                `${workerHeapMb}MiB V8 old-space cap, or a memory-cgroup ceiling when CLEO ` +
+                                `confines the run. Raise ${WORKER_HEAP_ENV}=<MiB>; if the kernel log shows ` +
+                                `an oom-kill with constraint=CONSTRAINT_MEMCG, raise CLEO_TOOL_MEMORY_MAX_MB ` +
+                                `or disable confinement with CLEO_NO_TOOL_CGROUP=1.`
+                            : `A non-null code means the worker THREW rather than being killed, so memory ` +
+                                `limits are not the cause and raising them will not help. The named file is ` +
+                                `the one dispatched to this worker; re-run with a single worker to confirm ` +
+                                `it is the trigger rather than a coincidence of timing.`)));
                 }
             };
             const abortHandler = () => {

package/dist/src/pipeline/workers/worker-pool.js.map

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