@cleocode/core 2026.8.9 → 2026.9.1

package/dist/shutdown-deadline.js

@@ -0,0 +1,187 @@
+/**
+ * Deadlines and a last-resort exit backstop for CLI teardown.
+ *
+ * ## Why this module exists (T12115 — the 12.9-hour `cleo` process)
+ *
+ * {@link ../shutdown.ts | shutdownCliRuntime} tears down the process-lifetime
+ * workers so a one-shot CLI command can drain its event loop and exit rc:0.
+ * Every step was best-effort — wrapped so a *throw* could not abort the rest —
+ * but nothing bounded a step that never settles at all. A promise that simply
+ * does not resolve is not an error, so `safely()` waited on it forever.
+ *
+ * Measured on a live box 2026-09-12: `cleo update T1690` sat in `ep_poll` for
+ * **12.9 hours**, holding ~100 MB RSS and open SQLite descriptors on two
+ * databases. Its envelope had been printed hours earlier; the command was DONE.
+ * Sibling `cleo add` / `cleo update` processes from other agent sessions had
+ * been resident 9.3 hours each. Thirty-one such processes held 3.25 GiB between
+ * them while the host ran 13 GiB into swap with 3 GiB free of 62 GiB.
+ *
+ * The descriptors are the tell: `closeAllDatabases()` is step 3 of 4, so if the
+ * DB handles are still open the teardown never got past step 1 or 2 — both of
+ * which await a worker thread. A hang there is invisible: the envelope is on
+ * stdout, the exit code is never written, and the caller cannot distinguish
+ * "still working" from "wedged forever" (issues #1228, #1229, #1237, #1241).
+ *
+ * ## The two guarantees
+ *
+ * 1. {@link withDeadline} — no single teardown step can stall the exit path.
+ *    A step that misses its deadline is abandoned, not awaited. Abandoning is
+ *    safe here precisely because teardown is best-effort: the worst case is a
+ *    worker thread that outlives us by microseconds before the process exits.
+ *
+ * 2. {@link armExitBackstop} — an **unref'd** timer that force-exits if the
+ *    loop is still alive after the grace period. Unref'd means the timer does
+ *    not itself hold the loop open, so a process that drains promptly exits
+ *    naturally and never reaches it.
+ *
+ *    It does NOT mean the timer only fires on leaks. An unref'd timer still
+ *    *fires* if the loop is alive for any other reason when the grace period
+ *    elapses — including legitimate unawaited work. `cleo memory observe`
+ *    schedules a fire-and-forget embedding whose first call loads a ~22 MB
+ *    model, which will not finish inside the grace window on a cold cache. So
+ *    the backstop can and does cut short work that was going to succeed. That
+ *    is an accepted trade: a bounded exit with a named remedy beats an
+ *    unbounded hang. It is why the message below says what was abandoned
+ *    rather than claiming the process was idle.
+ *
+ * Neither is a substitute for fixing a leak. Both exist so that the next leak
+ * costs a log line instead of a wedged host.
+ *
+ * @module
+ * @task T12115
+ */
+/** Per-step teardown budget, in ms. */
+export const STEP_DEADLINE_MS = 2_000;
+/** Grace period after teardown before the backstop force-exits, in ms. */
+export const EXIT_BACKSTOP_MS = 3_000;
+/**
+ * Run a teardown step, abandoning it if it outlives `deadlineMs`.
+ *
+ * Swallows rejections as well as stalls — a teardown step must never be able to
+ * abort the exit path, whether by throwing or by never settling.
+ *
+ * @param label - step name for diagnostics.
+ * @param step - the teardown work.
+ * @param deadlineMs - budget before the step is abandoned.
+ * @returns what happened, for the caller's diagnostics.
+ *
+ * @example
+ * ```ts
+ * const outcome = await withDeadline('brain-writer', () => shutdownBrainWriter());
+ * if (!outcome.settled) console.error('brain-writer did not stop in time');
+ * ```
+ */
+export async function withDeadline(label, step, deadlineMs = STEP_DEADLINE_MS) {
+    const startedAt = Date.now();
+    let timer;
+    let threw = false;
+    const settled = await Promise.race([
+        (async () => {
+            try {
+                await step();
+            }
+            catch {
+                // Best-effort teardown — a throwing step is still a settled step and
+                // must not abort the exit path. RECORDED rather than swallowed, so a
+                // teardown failing on every invocation is discoverable.
+                //
+                // Deliberately not logged here. `closeLogger` is itself step 4 of this
+                // sequence, so a catch that reaches for the logger can run against a
+                // subsystem that is mid-teardown or already closed — turning a recorded
+                // failure into a second, worse one. The caller surfaces `threw` on
+                // stderr instead, where nothing is being torn down.
+                threw = true;
+            }
+            return true;
+        })(),
+        new Promise((resolve) => {
+            timer = setTimeout(() => resolve(false), deadlineMs);
+            // Do not let the deadline timer itself hold the loop open.
+            timer.unref();
+        }),
+    ]);
+    if (timer)
+        clearTimeout(timer);
+    return { label, settled, threw, durationMs: Date.now() - startedAt };
+}
+/**
+ * Names of the resources currently keeping the event loop alive.
+ *
+ * Wraps `process.getActiveResourcesInfo()`, which is the only supported way to
+ * answer "what is holding this process open" without a native inspector. Values
+ * are coarse type names (`'Timeout'`, `'MessagePort'`, `'TCPSocketWrap'`), which
+ * is exactly the granularity needed to route the next report to a subsystem.
+ *
+ * @returns a tally of active-handle type names, most frequent first.
+ */
+export function activeHandleSummary() {
+    const info = process.getActiveResourcesInfo?.();
+    if (!info || info.length === 0)
+        return 'none';
+    const tally = new Map();
+    for (const name of info)
+        tally.set(name, (tally.get(name) ?? 0) + 1);
+    return [...tally.entries()]
+        .sort((a, b) => b[1] - a[1])
+        .map(([name, count]) => (count > 1 ? `${name}×${count}` : name))
+        .join(', ');
+}
+/**
+ * Arm the last-resort exit backstop.
+ *
+ * Call once, AFTER the envelope has been written and teardown has been
+ * attempted. The returned timer is unref'd, so a healthy process that drains
+ * its loop exits normally and never reaches this code path.
+ *
+ * When it does fire, it writes one diagnostic line to **stderr** — never stdout,
+ * which must carry exactly one LAFS envelope per call (ADR-086) — naming what
+ * kept the loop alive and warning that unawaited background work was cut short,
+ * then exits with `code`.
+ *
+ * The exit code stays the command's own result. A killed *tail* is not a failed
+ * *command*: the envelope on stdout is already correct and the row is already
+ * written. Exiting non-zero here would turn a slow-but-correct invocation into
+ * a failure, which is the false-red defect (gh#1270) in a new place.
+ *
+ * @param code - exit code to use; the command's own result, not an error code.
+ * @param graceMs - how long to let the loop try to drain on its own.
+ * @returns the armed timer, so tests can inspect or clear it.
+ *
+ * @example
+ * ```ts
+ * await shutdownCliRuntime();
+ * armExitBackstop();    // inherits process.exitCode; healthy commands never reach it
+ * ```
+ */
+export function armExitBackstop(code, graceMs = EXIT_BACKSTOP_MS) {
+    const timer = setTimeout(() => {
+        if (process.env.CLEO_NO_EXIT_BACKSTOP === '1')
+            return;
+        // Resolve the exit code at FIRE time, and inherit `process.exitCode` when
+        // the caller did not name one.
+        //
+        // The first version of this hardcoded 0, which silently discarded the
+        // result of any command that reports failure by SETTING `process.exitCode`
+        // and returning normally rather than calling `process.exit()`. There are
+        // ~199 such call sites (`add-batch`, `agent`, …), and they are not the
+        // error branches that bypass this path — a failed `cleo add-batch` returns
+        // through the success-path `finally`, so a backstop that forces 0 tells the
+        // caller the command succeeded while its own envelope says it failed.
+        //
+        // That is the exact inversion this module exists to prevent, so the
+        // backstop must never manufacture an exit code it was not given. Reading at
+        // fire time rather than arm time also catches a code set after arming.
+        const resolved = code ?? (typeof process.exitCode === 'number' ? process.exitCode : 0);
+        process.stderr.write(`cleo: event loop still alive ${graceMs}ms after teardown ` +
+            `(held by: ${activeHandleSummary()}); exiting rc:${resolved}.\n` +
+            `cleo: any unawaited background work was abandoned. The command's own ` +
+            `result stands — its envelope is already written. Deferred BRAIN ` +
+            `embeddings are recoverable with \`cleo brain maintenance\`. If this ` +
+            `recurs on a fast command it is a resource leak; please report it with ` +
+            `the command you ran.\n`);
+        process.exit(resolved);
+    }, graceMs);
+    timer.unref();
+    return timer;
+}
+//# sourceMappingURL=shutdown-deadline.js.map

package/dist/shutdown-deadline.js.map

@@ -0,0 +1 @@
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package/dist/shutdown.d.ts

@@ -51,6 +51,7 @@
  * @module
  * @task T11568
  */
+import { type StepOutcome } from './shutdown-deadline.js';
 /**
  * Tear down every process-lifetime resource that would otherwise keep the libuv
  * event loop alive after a short-lived CLI command resolves.
@@ -74,7 +75,9 @@
  * Every step is best-effort and idempotent — safe to call once per process at
  * exit, and harmless if a given subsystem was never initialized.
  *
- * @returns A promise that resolves once all teardown steps have settled.
+ * @returns One {@link StepOutcome} per step, in run order. A step with
+ *          `settled: false` blew its deadline and was abandoned — the caller
+ *          should surface that, because it means something leaked.
  *
  * @example
  * ```ts
@@ -87,5 +90,5 @@
  *
  * @task T11568
  */
-export declare function shutdownCliRuntime(): Promise<void>;
+export declare function shutdownCliRuntime(): Promise<StepOutcome[]>;
 //# sourceMappingURL=shutdown.d.ts.map

package/dist/shutdown.d.ts.map

@@ -1 +1 @@
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package/dist/shutdown.js

@@ -54,18 +54,19 @@
 import { closeLogger } from './logger.js';
 import { shutdownBrainWriter } from './memory/brain-writer-thread.js';
 import { resetEmbeddingQueue } from './memory/embedding-queue.js';
+import { withDeadline } from './shutdown-deadline.js';
 import { closeAllDatabases } from './store/sqlite.js';
 /**
- * Run a teardown step, swallowing any error so a single failure cannot abort
- * the remaining teardown steps. Best-effort by design.
+ * Run a teardown step under a deadline, swallowing both errors and stalls.
+ *
+ * T12115: the original helper swallowed only *throws*. A step that never
+ * settles is not a throw, so a stalled worker handshake hung the exit path
+ * forever — measured at 12.9 hours on a live host, with the process still
+ * holding its SQLite descriptors because teardown never reached step 3.
+ * Bounding each step is what makes "best-effort" actually best-effort.
  */
-async function safely(step) {
-    try {
-        await step();
-    }
-    catch {
-        // Best-effort teardown — never let cleanup throw out of the CLI exit path.
-    }
+async function safely(label, step) {
+    return withDeadline(label, step);
 }
 /**
  * Tear down every process-lifetime resource that would otherwise keep the libuv
@@ -90,7 +91,9 @@ async function safely(step) {
  * Every step is best-effort and idempotent — safe to call once per process at
  * exit, and harmless if a given subsystem was never initialized.
  *
- * @returns A promise that resolves once all teardown steps have settled.
+ * @returns One {@link StepOutcome} per step, in run order. A step with
+ *          `settled: false` blew its deadline and was abandoned — the caller
+ *          should surface that, because it means something leaked.
  *
  * @example
  * ```ts
@@ -106,15 +109,17 @@ async function safely(step) {
 export async function shutdownCliRuntime() {
     // 1. BRAIN single-writer worker thread — the live MessagePort that hangs
     //    `cleo memory observe` / `cleo docs add` / any brain.db write path.
-    await safely(() => shutdownBrainWriter());
+    const outcomes = [];
+    outcomes.push(await safely('brain-writer', () => shutdownBrainWriter()));
     // 2. Embedding queue worker thread (T11655) — the second live MessagePort.
     //    Flushes in-flight batches then terminates the worker, so an opportunistic
     //    embed enqueued during the command cannot keep the loop alive at exit.
-    await safely(() => resetEmbeddingQueue());
+    outcomes.push(await safely('embedding-queue', () => resetEmbeddingQueue()));
     // 3. Close DB singletons (dual-scope cleo.db + brain/nexus native handles).
     //    Releases SQLite file handles — required before tmpdir cleanup on Windows.
-    await safely(() => closeAllDatabases());
+    outcomes.push(await safely('databases', () => closeAllDatabases()));
     // 4. Flush + terminate the pino-roll transport worker thread.
-    await safely(() => closeLogger());
+    outcomes.push(await safely('logger', () => closeLogger()));
+    return outcomes;
 }
 //# sourceMappingURL=shutdown.js.map

package/dist/shutdown.js.map

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package/dist/spawn/branch-lock.d.ts.map

@@ -1 +1 @@
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package/dist/spawn/branch-lock.js

@@ -536,6 +536,39 @@ export function completeAgentWorktreeViaMerge(taskId, projectRoot, opts = {}) {
     }
     const worktreeRoot = resolveAgentWorktreeRoot(projectRoot);
     const worktreePath = join(worktreeRoot, taskId);
+    // T12153 (GH #1223) — distinguish "nothing to integrate" from "integration
+    // failed" BEFORE delegating.
+    //
+    // Most tasks are worked on a feature branch and merged by PR, so no
+    // `task/<id>` branch and no agent worktree ever exist. The NAPI helper
+    // reports that as `merged: false` with `error: "task branch … does not
+    // exist"`, which is the only shape it has — and the caller then logs a WARN
+    // naming a mergeError for a task where nothing failed. That is a routine,
+    // correct outcome reported as a failure, on most completions.
+    //
+    // Detected here rather than by string-matching the Rust error, which would
+    // couple this to a message in another language that is free to change.
+    const branchExists = gitSync(['branch', '--list', branch], gitRoot).trim().length > 0;
+    if (!branchExists && !existsSync(worktreePath)) {
+        return {
+            taskId,
+            targetBranch,
+            merged: false,
+            mergeCommit: '',
+            commitCount: 0,
+            rebased: false,
+            worktreeRemoved: false,
+            branchDeleted: false,
+            // `error` is kept as a human-readable MESSAGE, while
+            // `nothingToIntegrate` is the machine-readable CLASSIFICATION. Dropping
+            // the string made `orchestrate worktree-complete` fall back to
+            // "unknown merge failure" (it renders `integration.error ?? …`), which
+            // is strictly less informative than the truth. A caller distinguishes
+            // no-work from failure by the FLAG, never by the presence of a string.
+            error: `no task branch '${branch}' and no worktree — nothing to integrate`,
+            nothingToIntegrate: true,
+        };
+    }
     // T11124: Delegate to Rust NAPI SSoT
     const result = integrateWorktree({
         repoRoot: gitRoot,

package/dist/spawn/branch-lock.js.map

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package/dist/store/sqlite-data-accessor.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"sqlite-data-accessor.d.ts","sourceRoot":"","sources":["../../src/store/sqlite-data-accessor.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAYH,OAAO,KAAK,EAEV,YAAY,EAOb,MAAM,oBAAoB,CAAC;AAyG5B,yDAAyD;AACzD,wBAAsB,YAAY,CAChC,GAAG,EAAE,MAAM,GAAG,SAAS,EACvB,GAAG,EAAE,MAAM,EACX,KAAK,EAAE,OAAO,GACb,OAAO,CAAC,IAAI,CAAC,CAWf;AAID;;;;;;;;GAQG;AACH,wBAAsB,wBAAwB,CAAC,GAAG,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,YAAY,CAAC,CA2tClF"}
+{"version":3,"file":"sqlite-data-accessor.d.ts","sourceRoot":"","sources":["../../src/store/sqlite-data-accessor.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAYH,OAAO,KAAK,EAEV,YAAY,EAOb,MAAM,oBAAoB,CAAC;AAyG5B,yDAAyD;AACzD,wBAAsB,YAAY,CAChC,GAAG,EAAE,MAAM,GAAG,SAAS,EACvB,GAAG,EAAE,MAAM,EACX,KAAK,EAAE,OAAO,GACb,OAAO,CAAC,IAAI,CAAC,CAWf;AAID;;;;;;;;GAQG;AACH,wBAAsB,wBAAwB,CAAC,GAAG,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,YAAY,CAAC,CA0uClF"}

package/dist/store/sqlite-data-accessor.js

@@ -547,6 +547,20 @@ export async function createSqliteDataAccessor(cwd) {
                 conditions.push(eq(schema.tasks.type, filters.type));
             if (filters.phase)
                 conditions.push(eq(schema.tasks.phase, filters.phase));
+            // T12120 (GH #1245) — severity/kind are ADR-066 first-class axes that
+            // `cleo add` persists but no read path ever filtered on, so
+            // `list --severity P0` silently returned every task. Both accept a
+            // single value or an array; values are validated upstream by
+            // `assertTaskAxisFilters` so an unknown value can never reach SQL and
+            // widen the result set.
+            if (filters.severity) {
+                const severities = Array.isArray(filters.severity) ? filters.severity : [filters.severity];
+                conditions.push(inArray(schema.tasks.severity, severities));
+            }
+            if (filters.kind) {
+                const kinds = Array.isArray(filters.kind) ? filters.kind : [filters.kind];
+                conditions.push(inArray(schema.tasks.kind, kinds));
+            }
             if (filters.parentId !== undefined) {
                 if (filters.parentId === null) {
                     conditions.push(isNull(schema.tasks.parentId));