@cleocode/core 2026.8.9 → 2026.9.1

package/dist/tasks/tool-cache.js

@@ -37,6 +37,7 @@ import { ExitCode } from '@cleocode/contracts';
 import { CleoError } from '../errors.js';
 import { withLock } from '../store/lock.js';
 import { heavyToolEnv } from './heavy-tool-env.js';
+import { withMemoryLimit } from './heavy-tool-limit.js';
 import { acquireGlobalSlot } from './tool-semaphore.js';
 // ---------------------------------------------------------------------------
 // Wall-clock deadline resolution (T12105 / gh#1193)
@@ -53,6 +54,64 @@ import { acquireGlobalSlot } from './tool-semaphore.js';
  * @task T12105
  */
 export const DEFAULT_SPAWN_TIMEOUT_MS = 300_000;
+/**
+ * Wall-clock deadline for the HEAVY tool classes (`test`, `build`), in ms.
+ *
+ * ## Why these need their own default (gh#1221)
+ *
+ * A test suite is categorically not a linter. The single 300s default was
+ * below a real monorepo suite — measured ~10 min in the gh#1221 report — so
+ * EVERY run was killed before finishing, and the timeout path deliberately
+ * caches nothing (T12025, correct: an unfinished run is not a result). The
+ * cache could therefore never hit, not because the key moved but because no
+ * entry was ever produced, on a path that always fired. Each attempt still ran
+ * the suite at full parallelism for the full 300s before discarding it — the
+ * worst possible shape, and the load multiplier that wedged shared hosts.
+ *
+ * 30 min is 3x the measured ~10 min suite, so a project whose suite triples
+ * still completes on the default rather than discovering an env var after
+ * burning 5 CPU-minutes to learn its name. It is a ceiling on a pathological
+ * hang, not a budget anyone should plan to use.
+ *
+ * ## Why a longer rope is safe now, and was not before
+ *
+ * Raising a deadline means a runaway suite runs LONGER before anything stops
+ * it, and the 300s kill was accidentally acting as a crude memory
+ * circuit-breaker. Heavy tools are now spawned inside a memory-bounded scope
+ * with swap denied (T12116), so duration no longer converts into unbounded
+ * host memory: a runaway dies inside its own boundary and CLEO reports a
+ * failed run. A failed test run is a result; a frozen workstation is not.
+ *
+ * `lint`, `typecheck`, `audit` and `security-scan` deliberately do NOT inherit
+ * this — they are single-process and CPU-bound, and a lint that has run for 5
+ * minutes is hung, not busy.
+ *
+ * @task T12126 (gh#1221)
+ */
+export const HEAVY_TOOL_SPAWN_TIMEOUT_MS = 1_800_000;
+/**
+ * Canonical tools that get {@link HEAVY_TOOL_SPAWN_TIMEOUT_MS}.
+ *
+ * Matches the memory-bound heavy classes rather than being a second, separate
+ * opinion about which tools are expensive — the two must not drift.
+ *
+ * @task T12126 (gh#1221)
+ */
+const HEAVY_TIMEOUT_TOOLS = new Set(['test', 'build']);
+/**
+ * The default wall-clock deadline for a canonical tool, before any env
+ * override.
+ *
+ * @param canonical - Canonical tool name from the resolver.
+ * @returns Deadline in milliseconds.
+ *
+ * @task T12126 (gh#1221)
+ */
+export function defaultSpawnTimeoutMs(canonical) {
+    return HEAVY_TIMEOUT_TOOLS.has(canonical)
+        ? HEAVY_TOOL_SPAWN_TIMEOUT_MS
+        : DEFAULT_SPAWN_TIMEOUT_MS;
+}
 /**
  * Resolve the wall-clock child-process deadline for a canonical tool.
  *
@@ -76,19 +135,20 @@ export const DEFAULT_SPAWN_TIMEOUT_MS = 300_000;
  */
 export function resolveSpawnTimeoutMs(canonical, env = process.env) {
     const envKey = `CLEO_TOOL_TIMEOUT_${canonical.toUpperCase().replace(/-/g, '_')}`;
+    const fallback = defaultSpawnTimeoutMs(canonical);
     const raw = env[envKey];
     if (raw === undefined || raw.trim() === '')
-        return DEFAULT_SPAWN_TIMEOUT_MS;
+        return fallback;
     const trimmed = raw.trim();
     if (!/^\d+$/.test(trimmed)) {
         throw new CleoError(ExitCode.VALIDATION_ERROR, `${envKey} must be a positive integer (milliseconds), got "${raw}".`, {
-            fix: `Set ${envKey} to a millisecond value such as 600000 (10 min), or unset it to use the ${DEFAULT_SPAWN_TIMEOUT_MS}ms default.`,
+            fix: `Set ${envKey} to a millisecond value such as 600000 (10 min), or unset it to use the ${fallback}ms default.`,
         });
     }
     const parsed = Number.parseInt(trimmed, 10);
     if (parsed <= 0) {
         throw new CleoError(ExitCode.VALIDATION_ERROR, `${envKey} must be greater than zero, got ${parsed}.`, {
-            fix: `Set ${envKey} to a positive millisecond value such as 600000 (10 min), or unset it to use the ${DEFAULT_SPAWN_TIMEOUT_MS}ms default.`,
+            fix: `Set ${envKey} to a positive millisecond value such as 600000 (10 min), or unset it to use the ${fallback}ms default.`,
         });
     }
     return parsed;
@@ -300,25 +360,51 @@ export async function captureHead(projectRoot) {
     return r.stdout.trim() || null;
 }
 /**
- * Capture a fingerprint of the uncommitted tree by sha256-hashing
- * `git status --porcelain=v1`. Returns `null` for non-git roots.
+ * Capture a fingerprint of the uncommitted TRACKED tree by sha256-hashing
+ * `git status --porcelain=v1 --untracked-files=no`. Returns `null` for
+ * non-git roots.
  *
  * Two repos with identical tracked content but different uncommitted edits
- * produce different fingerprints — so editing a file before re-verifying
- * always invalidates the cache for tools sensitive to that file.
+ * produce different fingerprints — so editing a tracked file before
+ * re-verifying always invalidates the cache for tools sensitive to that file.
+ *
+ * ## Why untracked files are excluded (gh#1221)
+ *
+ * The fingerprint is captured BEFORE the tool spawns and is the key the
+ * result is stored under. When untracked files were included, a tool that
+ * emitted any untracked artifact changed the fingerprint that the NEXT call
+ * computes — so the tool invalidated its own cache entry simply by running,
+ * and the cache could never hit. This is not hypothetical or
+ * multi-agent-specific: in this repo `coverage/`, `.vitest/` and `*.log` are
+ * not gitignored, so a single suite run is enough. A one-line marker file is
+ * enough.
+ *
+ * Excluding untracked files fixes that at the root, rather than maintaining a
+ * per-project list of build-output paths that rots as tooling changes.
+ *
+ * TRADEOFF (deliberate): a brand-new UNTRACKED source or test file no longer
+ * invalidates the cache either, so `cleo verify` can return a cached pass
+ * that did not exercise it. Commit the file (HEAD moves, the key moves) or
+ * force a fresh run with {@link RunToolOptions.bypassCache} — surfaced as
+ * `CLEO_EVIDENCE_FRESH=1`. The alternative — a maintained exclude list — trades
+ * a loud, documented staleness for a silent, per-project one.
  *
  * The cache directory itself (`.cleo/cache/`) and other CLEO-managed runtime
- * state (`.cleo/tasks.db`, `.cleo/brain.db`, journal/log files) are excluded
- * from the fingerprint via pathspec. Without this exclusion the cache would
- * invalidate itself on every write — call #1 writes its entry, call #2 sees
- * the new file in `git status` and records a different fingerprint.
+ * state (`.cleo/tasks.db`, `.cleo/brain.db`, journal/log files) remain
+ * excluded via pathspec so a tracked-and-modified CLEO file cannot reintroduce
+ * the same self-invalidation.
  *
  * @task T1534
+ * @task T12112 (gh#1221)
  */
 export async function captureDirtyFingerprint(projectRoot) {
     const r = await spawnCmd('git', [
         'status',
         '--porcelain=v1',
+        // gh#1221: untracked files are the tool's own output as often as they
+        // are the operator's input; including them made every tool invalidate
+        // its own cache entry. See the docblock TRADEOFF note.
+        '--untracked-files=no',
         '--',
         '.',
         ':(exclude).cleo/cache',
@@ -428,11 +514,22 @@ export async function runToolCached(command, projectRoot, opts = {}) {
     // T12105 / gh#1193: an explicit opts value (tests) wins; otherwise the
     // CLEO_TOOL_TIMEOUT_<CANONICAL> env override, else the 5 min default.
     const spawnTimeoutMs = opts.spawnTimeoutMs ?? resolveSpawnTimeoutMs(command.canonical);
-    const head = await captureHead(projectRoot);
-    const dirtyFingerprint = await captureDirtyFingerprint(projectRoot);
+    // gh#1220/#1226/#1230: the tool runs in — and is fingerprinted against —
+    // the caller's tree, which is NOT necessarily the store root. The cache
+    // ENTRY still lives under `projectRoot` so every worktree shares one cache;
+    // that is sound because the key is content-addressed (HEAD + tracked
+    // fingerprint), so two trees only collide when they hold the same code.
+    const executionRoot = opts.executionRoot ?? projectRoot;
+    // gh#1221 escape hatch. The fingerprint covers TRACKED content only, so an
+    // uncommitted NEW file does not invalidate the cache; this is the
+    // documented way to force a measured run without committing first.
+    // An explicit option always wins over the env var.
+    const bypassCache = opts.bypassCache ?? process.env['CLEO_EVIDENCE_FRESH'] === '1';
+    const head = await captureHead(executionRoot);
+    const dirtyFingerprint = await captureDirtyFingerprint(executionRoot);
     const key = computeCacheKey(command, head, dirtyFingerprint);
     // Fast path — fresh cache hit
-    if (!opts.bypassCache) {
+    if (!bypassCache) {
         const existing = readCacheEntry(projectRoot, key);
         if (existing) {
             return {
@@ -443,6 +540,7 @@ export async function runToolCached(command, projectRoot, opts = {}) {
                 cacheHit: true,
                 timedOut: false,
                 lockBusy: false,
+                executionRoot,
                 entry: existing,
             };
         }
@@ -472,7 +570,7 @@ export async function runToolCached(command, projectRoot, opts = {}) {
         return await withLock(cachePath, async () => {
             // Inside the lock — re-check the cache. If another process beat us to
             // it, prefer its result.
-            if (!opts.bypassCache) {
+            if (!bypassCache) {
                 const fresh = readCacheEntry(projectRoot, key);
                 if (fresh) {
                     return {
@@ -483,13 +581,23 @@ export async function runToolCached(command, projectRoot, opts = {}) {
                         cacheHit: true,
                         timedOut: false,
                         lockBusy: false,
+                        executionRoot,
                         entry: fresh,
                     };
                 }
             }
             // Spawn the tool ourselves.
+            //
+            // T12116: `test` and `build` run inside a transient systemd scope with
+            // a hard `MemoryMax` and `MemorySwapMax=0`, so the kernel bounds the
+            // ENTIRE process tree — a `pnpm -r` fan-out into fifteen packages is
+            // still one cgroup, which is the multiplier the semaphore could not
+            // see. Denying swap is the point: the failure this guards against was
+            // a throttle-and-thrash host freeze, not an OOM kill. Degrades to an
+            // unwrapped spawn off Linux or without a user systemd manager.
+            const limited = withMemoryLimit(command.canonical, command.cmd, command.args);
             const startedAt = Date.now();
-            const result = await spawnCmd(command.cmd, command.args, projectRoot, spawnTimeoutMs, heavyToolEnv(command.canonical));
+            const result = await spawnCmd(limited.cmd, [...limited.args], executionRoot, spawnTimeoutMs, heavyToolEnv(command.canonical));
             const durationMs = Date.now() - startedAt;
             // T12025: when the child exceeded its wall-clock deadline, do NOT
             // persist a cache entry — the run produced no real result. The lock
@@ -504,6 +612,7 @@ export async function runToolCached(command, projectRoot, opts = {}) {
                     cacheHit: false,
                     timedOut: true,
                     lockBusy: false,
+                    executionRoot,
                     entry: {
                         schemaVersion: 1,
                         key,
@@ -547,6 +656,7 @@ export async function runToolCached(command, projectRoot, opts = {}) {
                 cacheHit: false,
                 timedOut: false,
                 lockBusy: false,
+                executionRoot,
                 entry,
             };
         }, { stale: lockStaleMs, retries: 3 });
@@ -569,6 +679,7 @@ export async function runToolCached(command, projectRoot, opts = {}) {
                     cacheHit: false,
                     timedOut: false,
                     lockBusy: true,
+                    executionRoot,
                     entry: {
                         schemaVersion: 1,
                         key,

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package/dist/tasks/tool-semaphore.d.ts

@@ -198,6 +198,97 @@ export declare function pressureScaleSlots(canonical: CanonicalTool, staticMax:
  * @task T1534
  */
 export declare function semaphoreDir(canonical: CanonicalTool): string;
+/**
+ * Identity of the process currently holding a semaphore slot.
+ *
+ * `proper-lockfile` decides staleness from the lock's **mtime**, which it
+ * refreshes on a timer while the holder lives. That makes a slot held by a
+ * process which died without releasing indistinguishable from one held by a
+ * legitimately long-running suite: both simply wait out `staleMs` (10 min by
+ * default). On a box where evidence runs are frequent, one orphan therefore
+ * blocks every later verify for ten minutes with `E_EVIDENCE_TOOL_BUSY` and
+ * no indication of who is holding it (gh#1222).
+ *
+ * Recording the holder turns that into a decidable question: a slot whose
+ * owner is a dead pid on this host is orphaned NOW, not in ten minutes, and
+ * the operator can be told which process to look at.
+ *
+ * @task T12113 (gh#1222)
+ */
+export interface SlotHolder {
+    /** OS process id of the holder. */
+    pid: number;
+    /** Host that pid is meaningful on. Liveness is only decided on a match. */
+    host: string;
+    /** ISO 8601 timestamp of acquisition — lets the operator judge "stuck vs slow". */
+    acquiredAt: string;
+    /** Canonical tool the slot belongs to. */
+    canonical: string;
+    /** Slot file this holder record describes. */
+    slot: string;
+}
+/**
+ * Read a slot's holder record. Returns `null` when absent or unparseable —
+ * both mean "we cannot say who holds this", which is treated as alive.
+ *
+ * @internal
+ * @task T12113 (gh#1222)
+ */
+export declare function readHolder(slotPath: string): SlotHolder | null;
+/**
+ * Is a slot's recorded holder still running?
+ *
+ * Fails SAFE: an unknown holder, a holder on another host, or any error is
+ * reported as ALIVE. Reaping a live holder's slot would let two heavy suites
+ * run against one bound — the exact oversubscription the semaphore exists to
+ * prevent — so uncertainty must never authorise a reap.
+ *
+ * @param holder - Holder record, or `null` when none could be read.
+ * @returns `true` when the slot must be treated as legitimately held.
+ *
+ * @task T12113 (gh#1222)
+ */
+export declare function isHolderAlive(holder: SlotHolder | null): boolean;
+/**
+ * Release a slot whose recorded holder is gone.
+ *
+ * Removes `proper-lockfile`'s lock directory directly — the same thing its own
+ * stale recovery does, but decided by process liveness instead of by a 10
+ * minute mtime timeout.
+ *
+ * @param slotPath - Slot lock file path.
+ * @returns `true` when an orphaned slot was actually reaped.
+ *
+ * @task T12113 (gh#1222)
+ */
+export declare function reapSlotIfOrphaned(slotPath: string): boolean;
+/**
+ * Enumerate every slot of a canonical tool with its holder and liveness.
+ *
+ * Backs the operator-facing lock inspection surface requested in gh#1222 —
+ * "who is holding this, and is it even alive?" — which previously required
+ * reading `~/.local/share/cleo/locks/` by hand.
+ *
+ * @param canonical - Canonical tool name.
+ * @returns One row per existing slot file.
+ *
+ * @task T12113 (gh#1222)
+ */
+export declare function listSlotHolders(canonical: CanonicalTool): Array<{
+    slot: string;
+    held: boolean;
+    holder: SlotHolder | null;
+    alive: boolean;
+}>;
+/**
+ * Reap every orphaned slot of a canonical tool.
+ *
+ * @param canonical - Canonical tool name.
+ * @returns Paths of the slots actually reaped.
+ *
+ * @task T12113 (gh#1222)
+ */
+export declare function reapOrphanedSlots(canonical: CanonicalTool): string[];
 /**
  * Acquire one slot from the global semaphore for a canonical tool. Blocks
  * until a slot becomes free or `timeoutMs` elapses.

package/dist/tasks/tool-semaphore.d.ts.map

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