@cleocode/core 2026.10.25 → 2026.10.26

package/dist/memory/brain-writer-thread.d.ts

@@ -203,6 +203,36 @@ export type WriterResponseEnvelope = {
     ok: false;
     error: string;
 };
+/**
+ * Ask the writer worker to finish its background work (scheduled embeddings)
+ * before it is terminated (T14069). It answers {@link WriterDrainedMessage}.
+ */
+export interface WriterDrainMessage {
+    drain: true;
+}
+/** The writer worker finished its background work and may be terminated (T14069). */
+export interface WriterDrainedMessage {
+    drained: true;
+}
+/**
+ * How long {@link drainAndTerminateWriter} waits for the worker's background
+ * work before it terminates the worker anyway (T14069).
+ */
+export declare const WRITER_DRAIN_TIMEOUT_MS = 10000;
+/**
+ * Stop a brain writer worker without cutting through its background work
+ * (T14069): ask it to drain, wait for its answer (at most `timeoutMs`), then
+ * terminate it. The worker embeds new observations inline, which loads the
+ * native onnxruntime addon; terminating the isolate mid-load or mid-inference
+ * can abort the whole process, and vitest reports that as "Worker exited
+ * unexpectedly".
+ *
+ * @param worker - The writer worker.
+ * @param timeoutMs - Longest wait for the drain. @defaultValue {@link WRITER_DRAIN_TIMEOUT_MS}
+ *
+ * @task T14069
+ */
+export declare function drainAndTerminateWriter(worker: import('node:worker_threads').Worker, timeoutMs?: number): Promise<void>;
 /**
  * Opt this process in to the worker-thread brain writer.
  *

package/dist/memory/brain-writer-thread.d.ts.map

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package/dist/memory/brain-writer-thread.js

@@ -64,6 +64,48 @@ import { getLogger } from '../logger.js';
 import { resolveDualScopeDbPath } from '../store/dual-scope-db.js';
 import { acquireWriterLease, assertWriterLeaseHeld, resolveLeaseMode, } from '../store/writer-lease.js';
 import { _resetLongLivedBrainHostForTests, isLongLivedBrainHost, markLongLivedBrainHost, } from './brain-host.js';
+/**
+ * How long {@link drainAndTerminateWriter} waits for the worker's background
+ * work before it terminates the worker anyway (T14069).
+ */
+export const WRITER_DRAIN_TIMEOUT_MS = 10_000;
+/**
+ * Stop a brain writer worker without cutting through its background work
+ * (T14069): ask it to drain, wait for its answer (at most `timeoutMs`), then
+ * terminate it. The worker embeds new observations inline, which loads the
+ * native onnxruntime addon; terminating the isolate mid-load or mid-inference
+ * can abort the whole process, and vitest reports that as "Worker exited
+ * unexpectedly".
+ *
+ * @param worker - The writer worker.
+ * @param timeoutMs - Longest wait for the drain. @defaultValue {@link WRITER_DRAIN_TIMEOUT_MS}
+ *
+ * @task T14069
+ */
+export async function drainAndTerminateWriter(worker, timeoutMs = WRITER_DRAIN_TIMEOUT_MS) {
+    await new Promise((resolve) => {
+        const done = () => {
+            clearTimeout(timer);
+            worker.off('message', onMessage);
+            worker.off('exit', done);
+            resolve();
+        };
+        const onMessage = (msg) => {
+            if (typeof msg === 'object' && msg !== null && 'drained' in msg)
+                done();
+        };
+        const timer = setTimeout(done, timeoutMs);
+        worker.on('message', onMessage);
+        worker.once('exit', done);
+        try {
+            worker.postMessage({ drain: true });
+        }
+        catch {
+            done();
+        }
+    });
+    await worker.terminate();
+}
 // ============================================================================
 // Bypass mode (CLEO_BRAIN_BYPASS_WRITER_THREAD=1)
 // ============================================================================
@@ -173,6 +215,8 @@ class BrainWriterManager {
             throw new BrainWriterShutDownError('observe');
         const worker = new Worker(workerPath);
         worker.on('message', (msg) => {
+            if ('drained' in msg)
+                return; // answered to drainAndTerminateWriter
             this.handleWorkerMessage(msg);
         });
         worker.on('error', (err) => {
@@ -257,7 +301,8 @@ class BrainWriterManager {
         }
         if (this.worker) {
             try {
-                await this.worker.terminate();
+                // T14069: let its scheduled embeddings finish before terminating it.
+                await drainAndTerminateWriter(this.worker);
             }
             catch {
                 // ignore — worker may already be gone

package/dist/memory/brain-writer-thread.js.map

@@ -1 +1 @@
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package/dist/memory/brain-writer-worker.js

@@ -15,6 +15,7 @@
 import { parentPort } from 'node:worker_threads';
 import { markBrainWriterIsolate, markLongLivedBrainHost } from './brain-host.js';
 import { handleWriteOp } from './brain-writer-handlers.js';
+import { drainScheduledEmbeddings } from './embedding-backfill.js';
 if (!parentPort) {
     throw new Error('brain-writer-worker.ts must be run as a worker thread');
 }
@@ -55,9 +56,19 @@ async function processEnvelope(envelope) {
 // we additionally serialize the *handling* so the DB writes never interleave.
 // ---------------------------------------------------------------------------
 let processingChain = Promise.resolve();
-port.on('message', (envelope) => {
+port.on('message', (msg) => {
+    // T14069: before it is terminated, finish the ops queued so far and the
+    // embeddings they scheduled, so termination never cuts through the native
+    // onnxruntime addon mid-load or mid-inference.
+    if ('drain' in msg) {
+        processingChain = processingChain
+            .then(() => drainScheduledEmbeddings())
+            .catch(() => undefined)
+            .then(() => port.postMessage({ drained: true }));
+        return;
+    }
     // Chain each new request to the tail of the current processing chain so
     // ops execute strictly sequentially.
-    processingChain = processingChain.then(() => processEnvelope(envelope)).catch(() => undefined); // chain marker is failure-tolerant
+    processingChain = processingChain.then(() => processEnvelope(msg)).catch(() => undefined); // chain marker is failure-tolerant
 });
 //# sourceMappingURL=brain-writer-worker.js.map

package/dist/memory/brain-writer-worker.js.map

@@ -1 +1 @@
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+{"version":3,"file":"brain-writer-worker.js","sourceRoot":"","sources":["../../src/memory/brain-writer-worker.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AAEH,OAAO,EAAE,UAAU,EAAE,MAAM,qBAAqB,CAAC;AACjD,OAAO,EAAE,sBAAsB,EAAE,sBAAsB,EAAE,MAAM,iBAAiB,CAAC;AACjF,OAAO,EAAE,aAAa,EAAE,MAAM,4BAA4B,CAAC;AAO3D,OAAO,EAAE,wBAAwB,EAAE,MAAM,yBAAyB,CAAC;AAEnE,IAAI,CAAC,UAAU,EAAE,CAAC;IAChB,MAAM,IAAI,KAAK,CAAC,uDAAuD,CAAC,CAAC;AAC3E,CAAC;AAED,MAAM,IAAI,GAAG,UAAU,CAAC;AAExB,iFAAiF;AACjF,2EAA2E;AAC3E,gFAAgF;AAChF,sBAAsB,EAAE,CAAC;AACzB,uEAAuE;AACvE,sBAAsB,EAAE,CAAC;AAEzB;;;;GAIG;AACH,KAAK,UAAU,eAAe,CAAC,QAA+B;IAC5D,IAAI,CAAC;QACH,MAAM,MAAM,GAAG,MAAM,aAAa,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC;QAChD,MAAM,QAAQ,GAA2B;YACvC,GAAG,EAAE,QAAQ,CAAC,GAAG;YACjB,EAAE,EAAE,IAAI;YACR,MAAM;SACP,CAAC;QACF,IAAI,CAAC,WAAW,CAAC,QAAQ,CAAC,CAAC;IAC7B,CAAC;IAAC,OAAO,GAAG,EAAE,CAAC;QACb,MAAM,QAAQ,GAA2B;YACvC,GAAG,EAAE,QAAQ,CAAC,GAAG;YACjB,EAAE,EAAE,KAAK;YACT,KAAK,EAAE,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC;SACxD,CAAC;QACF,IAAI,CAAC,WAAW,CAAC,QAAQ,CAAC,CAAC;IAC7B,CAAC;AACH,CAAC;AAED,8EAA8E;AAC9E,6EAA6E;AAC7E,gFAAgF;AAChF,8EAA8E;AAC9E,8EAA8E;AAE9E,IAAI,eAAe,GAAqB,OAAO,CAAC,OAAO,EAAE,CAAC;AAE1D,IAAI,CAAC,EAAE,CAAC,SAAS,EAAE,CAAC,GAA+C,EAAE,EAAE;IACrE,wEAAwE;IACxE,0EAA0E;IAC1E,+CAA+C;IAC/C,IAAI,OAAO,IAAI,GAAG,EAAE,CAAC;QACnB,eAAe,GAAG,eAAe;aAC9B,IAAI,CAAC,GAAG,EAAE,CAAC,wBAAwB,EAAE,CAAC;aACtC,KAAK,CAAC,GAAG,EAAE,CAAC,SAAS,CAAC;aACtB,IAAI,CAAC,GAAG,EAAE,CAAC,IAAI,CAAC,WAAW,CAAC,EAAE,OAAO,EAAE,IAAI,EAAiC,CAAC,CAAC,CAAC;QAClF,OAAO;IACT,CAAC;IACD,wEAAwE;IACxE,qCAAqC;IACrC,eAAe,GAAG,eAAe,CAAC,IAAI,CAAC,GAAG,EAAE,CAAC,eAAe,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,GAAG,EAAE,CAAC,SAAS,CAAC,CAAC,CAAC,mCAAmC;AAChI,CAAC,CAAC,CAAC"}

package/dist/memory/embedding-backfill.d.ts

@@ -97,4 +97,16 @@ export declare function runBoundedEmbeddingBackfill(projectRoot: string, options
  * @task T13740
  */
 export declare function scheduleEmbedding(projectRoot: string, id: string, text: string): void;
+/**
+ * Stop scheduling embeddings in this isolate and wait for the ones in flight
+ * (T14069). The brain writer worker calls it before it is terminated: an
+ * embedding loads `@huggingface/transformers` and its native onnxruntime addon,
+ * and terminating the isolate mid-load or mid-inference can abort the WHOLE
+ * process (`terminate called after throwing an instance of Napi::Error`).
+ *
+ * @returns Once every scheduled embedding has settled.
+ *
+ * @task T14069
+ */
+export declare function drainScheduledEmbeddings(): Promise<void>;
 //# sourceMappingURL=embedding-backfill.d.ts.map

package/dist/memory/embedding-backfill.d.ts.map

@@ -1 +1 @@
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package/dist/memory/embedding-backfill.js

@@ -137,6 +137,10 @@ export async function runBoundedEmbeddingBackfill(projectRoot, options = {}) {
         await admission.release();
     }
 }
+/** Embeddings {@link scheduleEmbedding} started that have not finished (T14069). */
+const _scheduledEmbeddings = new Set();
+/** Set by {@link drainScheduledEmbeddings}: no new embedding starts in this isolate. */
+let _embeddingsDrained = false;
 /**
  * Embed one freshly written memory row in the background — long-lived hosts only.
  *
@@ -153,39 +157,55 @@ export async function runBoundedEmbeddingBackfill(projectRoot, options = {}) {
  * @task T13740
  */
 export function scheduleEmbedding(projectRoot, id, text) {
-    if (!isLongLivedBrainHost())
+    if (!isLongLivedBrainHost() || _embeddingsDrained)
         return;
-    setImmediate(() => {
-        void (async () => {
-            try {
-                // T12314: registration is free; availability is checked by embedText.
-                if (!(await ensureEmbeddingProvider(projectRoot)))
-                    return;
-                const model = getEmbeddingProvider()?.model;
-                const vector = await embedText(text);
-                if (!vector || !model)
-                    return;
-                // T13230: inside the writer isolate the open handle IS the chokepoint's,
-                // so write directly (enqueueBrainWrite there would start a nested
-                // manager). Anywhere else (a main thread whose host ran the write
-                // inline, or any other worker thread, T13246) the op has already
-                // released the lease and the mutex, so the write goes back through
-                // the chokepoint.
-                if (isBrainWriterIsolate()) {
-                    const { getBrainNativeDb } = await import('../store/memory-sqlite.js');
-                    const { upsertEmbeddingRowsNative } = await import('../store/memory-accessor.js');
-                    const nativeDb = getBrainNativeDb(projectRoot);
-                    if (nativeDb)
-                        upsertEmbeddingRowsNative(nativeDb, model, [{ id, vector }]);
-                    return;
-                }
-                const { enqueueBrainWrite } = await import('./brain-writer-thread.js');
-                await enqueueBrainWrite({ kind: 'embed', projectRoot, model, rows: [{ id, vector }] });
+    const task = new Promise((resolve) => setImmediate(resolve)).then(async () => {
+        try {
+            // T12314: registration is free; availability is checked by embedText.
+            if (!(await ensureEmbeddingProvider(projectRoot)))
+                return;
+            const model = getEmbeddingProvider()?.model;
+            const vector = await embedText(text);
+            if (!vector || !model)
+                return;
+            // T13230: inside the writer isolate the open handle IS the chokepoint's,
+            // so write directly (enqueueBrainWrite there would start a nested
+            // manager). Anywhere else (a main thread whose host ran the write
+            // inline, or any other worker thread, T13246) the op has already
+            // released the lease and the mutex, so the write goes back through
+            // the chokepoint.
+            if (isBrainWriterIsolate()) {
+                const { getBrainNativeDb } = await import('../store/memory-sqlite.js');
+                const { upsertEmbeddingRowsNative } = await import('../store/memory-accessor.js');
+                const nativeDb = getBrainNativeDb(projectRoot);
+                if (nativeDb)
+                    upsertEmbeddingRowsNative(nativeDb, model, [{ id, vector }]);
+                return;
             }
-            catch {
-                // Embedding is enrichment — the row is already persisted.
-            }
-        })();
+            const { enqueueBrainWrite } = await import('./brain-writer-thread.js');
+            await enqueueBrainWrite({ kind: 'embed', projectRoot, model, rows: [{ id, vector }] });
+        }
+        catch {
+            // Embedding is enrichment — the row is already persisted.
+        }
     });
+    _scheduledEmbeddings.add(task);
+    void task.finally(() => _scheduledEmbeddings.delete(task));
+}
+/**
+ * Stop scheduling embeddings in this isolate and wait for the ones in flight
+ * (T14069). The brain writer worker calls it before it is terminated: an
+ * embedding loads `@huggingface/transformers` and its native onnxruntime addon,
+ * and terminating the isolate mid-load or mid-inference can abort the WHOLE
+ * process (`terminate called after throwing an instance of Napi::Error`).
+ *
+ * @returns Once every scheduled embedding has settled.
+ *
+ * @task T14069
+ */
+export async function drainScheduledEmbeddings() {
+    _embeddingsDrained = true;
+    while (_scheduledEmbeddings.size > 0)
+        await Promise.allSettled([..._scheduledEmbeddings]);
 }
 //# sourceMappingURL=embedding-backfill.js.map

package/dist/memory/embedding-backfill.js.map

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package/dist/orchestrate/include-deps.d.ts

@@ -0,0 +1,58 @@
+/**
+ * `cleo orchestrate spawn --include-deps` (T14045): the base a task branch
+ * starts from when it builds on dependencies whose branches have not landed.
+ *
+ * The orchestrator merges each dependency's `task/<id>` branch, `--no-ff`, into
+ * a commit made in a TEMPORARY integration worktree under the project's
+ * canonical worktree root; the primary checkout is never touched. The merge
+ * commit is then handed to the `--base` path (T14027), so the resolved-sha
+ * guard and the lifecycle audit apply as for any explicit base. Nothing is
+ * cherry-picked or rewritten: every dependency commit stays reachable.
+ *
+ * @task T14045
+ */
+/** One dependency branch folded into the integration commit. */
+export interface IncludedDependency {
+    /** Dependency task id. */
+    taskId: string;
+    /** Its branch, `task/<id>`. */
+    branch: string;
+    /** The commit the branch pointed to when it was merged. */
+    sha: string;
+}
+/** The integration commit, or why none could be built. */
+export type DependencyIntegration = {
+    ok: true;
+    /** Commit the task branch is created from (the last merge, or the base). */
+    sha: string;
+    /** The base the merges started from, as named (`HEAD` when none). */
+    baseRef: string;
+    /** The commit `baseRef` resolved to. */
+    baseSha: string;
+    /** Every dependency merged, in dependency order. */
+    dependencies: IncludedDependency[];
+} | {
+    ok: false;
+    /** `E_INCLUDE_DEPS_MISSING`, `E_INCLUDE_DEPS_DIVERGED` or `E_WORKTREE_BASE_INVALID`. */
+    code: string;
+    message: string;
+    fix: string;
+};
+/**
+ * Build the integration commit for `taskId` from its dependencies' branches.
+ *
+ * A dependency with no `task/<id>` branch is refused (its work cannot be
+ * shown to be in the base), as is one sharing no history with the base or
+ * one whose merge conflicts. On success the base ref, its sha and each
+ * dependency sha are appended to `.cleo/audit/worktree-integration.jsonl`.
+ * The temporary worktree is always removed; no existing worktree is touched.
+ *
+ * @param projectRoot - The project's git checkout.
+ * @param taskId - The task being spawned.
+ * @param dependencies - Its dependency task ids, in order.
+ * @param baseRef - Ref the merges start from (`--base`); HEAD when omitted.
+ * @returns The integration commit, or the refusal.
+ * @task T14045
+ */
+export declare function buildDependencyIntegration(projectRoot: string, taskId: string, dependencies: readonly string[], baseRef?: string): Promise<DependencyIntegration>;
+//# sourceMappingURL=include-deps.d.ts.map

package/dist/orchestrate/include-deps.d.ts.map

@@ -0,0 +1 @@
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package/dist/orchestrate/include-deps.js

@@ -0,0 +1,138 @@
+/**
+ * `cleo orchestrate spawn --include-deps` (T14045): the base a task branch
+ * starts from when it builds on dependencies whose branches have not landed.
+ *
+ * The orchestrator merges each dependency's `task/<id>` branch, `--no-ff`, into
+ * a commit made in a TEMPORARY integration worktree under the project's
+ * canonical worktree root; the primary checkout is never touched. The merge
+ * commit is then handed to the `--base` path (T14027), so the resolved-sha
+ * guard and the lifecycle audit apply as for any explicit base. Nothing is
+ * cherry-picked or rewritten: every dependency commit stays reachable.
+ *
+ * @task T14045
+ */
+import { execFileSync } from 'node:child_process';
+import { appendFileSync, mkdirSync, rmSync } from 'node:fs';
+import { join } from 'node:path';
+import { addTransientWorktree, removeTransientWorktree } from '@cleocode/worktree';
+import { resolveAgentWorktreeRoot } from '../spawn/branch-lock.js';
+function git(cwd, args) {
+    return execFileSync('git', args, {
+        cwd,
+        encoding: 'utf-8',
+        stdio: ['ignore', 'pipe', 'pipe'],
+    }).trim();
+}
+function tryGit(cwd, args) {
+    try {
+        return git(cwd, args);
+    }
+    catch {
+        return null;
+    }
+}
+/**
+ * Build the integration commit for `taskId` from its dependencies' branches.
+ *
+ * A dependency with no `task/<id>` branch is refused (its work cannot be
+ * shown to be in the base), as is one sharing no history with the base or
+ * one whose merge conflicts. On success the base ref, its sha and each
+ * dependency sha are appended to `.cleo/audit/worktree-integration.jsonl`.
+ * The temporary worktree is always removed; no existing worktree is touched.
+ *
+ * @param projectRoot - The project's git checkout.
+ * @param taskId - The task being spawned.
+ * @param dependencies - Its dependency task ids, in order.
+ * @param baseRef - Ref the merges start from (`--base`); HEAD when omitted.
+ * @returns The integration commit, or the refusal.
+ * @task T14045
+ */
+export async function buildDependencyIntegration(projectRoot, taskId, dependencies, baseRef) {
+    const base = baseRef ?? 'HEAD';
+    const baseSha = tryGit(projectRoot, ['rev-parse', '--verify', '--quiet', `${base}^{commit}`]);
+    if (!baseSha) {
+        return {
+            ok: false,
+            // @sync-invariant none:input-shape a --base that does not resolve is refused before any write
+            code: 'E_WORKTREE_BASE_INVALID',
+            message: `base '${base}' does not resolve to a commit`,
+            fix: 'Pass --base a branch, tag or sha that exists.',
+        };
+    }
+    const included = [];
+    for (const dep of dependencies) {
+        const branch = `task/${dep}`;
+        const sha = tryGit(projectRoot, ['rev-parse', '--verify', '--quiet', `refs/heads/${branch}`]);
+        if (!sha) {
+            return {
+                ok: false,
+                // @sync-invariant none:input-shape a dependency with no branch is refused before any write
+                code: 'E_INCLUDE_DEPS_MISSING',
+                message: `dependency ${dep} has no branch '${branch}' to include`,
+                fix: `Spawn without --include-deps when ${dep} has already landed in the base, or restore its branch.`,
+            };
+        }
+        if (tryGit(projectRoot, ['merge-base', baseSha, sha]) === null) {
+            return {
+                ok: false,
+                // @sync-invariant none:input-shape a dependency that cannot merge onto the base is refused before any write
+                code: 'E_INCLUDE_DEPS_DIVERGED',
+                message: `dependency branch '${branch}' shares no history with ${base}`,
+                fix: `Rebuild ${branch} from the base, or spawn without --include-deps.`,
+            };
+        }
+        included.push({ taskId: dep, branch, sha });
+    }
+    const scratch = join(resolveAgentWorktreeRoot(projectRoot), `.integration-${taskId}-${process.pid}-${Date.now()}`);
+    let sha = baseSha;
+    try {
+        mkdirSync(join(scratch, '..'), { recursive: true });
+        await addTransientWorktree({ projectRoot, worktreePath: scratch, baseRef: baseSha });
+        for (const dep of included) {
+            try {
+                git(scratch, [
+                    'merge',
+                    '--no-ff',
+                    '--no-edit',
+                    '-m',
+                    `Integrate ${dep.branch} into the base of ${taskId} (--include-deps)`,
+                    dep.sha,
+                ]);
+            }
+            catch {
+                tryGit(scratch, ['merge', '--abort']);
+                return {
+                    ok: false,
+                    // @sync-invariant none:input-shape a dependency that cannot merge onto the base is refused before any write
+                    code: 'E_INCLUDE_DEPS_DIVERGED',
+                    message: `dependency branch '${dep.branch}' does not merge cleanly onto ${base} and the dependencies before it`,
+                    fix: `Resolve the conflict on ${dep.branch} (rebase it on the base), then retry.`,
+                };
+            }
+        }
+        sha = git(scratch, ['rev-parse', 'HEAD']);
+    }
+    finally {
+        await removeTransientWorktree(projectRoot, scratch).catch(() => undefined);
+        rmSync(scratch, { recursive: true, force: true });
+    }
+    try {
+        const auditDir = join(projectRoot, '.cleo', 'audit');
+        mkdirSync(auditDir, { recursive: true });
+        appendFileSync(join(auditDir, 'worktree-integration.jsonl'), `${JSON.stringify({
+            timestamp: new Date().toISOString(),
+            action: 'include-deps',
+            taskId,
+            baseRef: base,
+            baseSha,
+            integrationSha: sha,
+            dependencies: included,
+            agent: process.env['CLEO_AGENT_ID'] ?? 'cleo',
+        })}\n`, 'utf-8');
+    }
+    catch {
+        // Audit is best-effort, as for every worktree-integration row.
+    }
+    return { ok: true, sha, baseRef: base, baseSha, dependencies: included };
+}
+//# sourceMappingURL=include-deps.js.map

package/dist/orchestrate/include-deps.js.map

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