@cleocode/core 2026.4.38 → 2026.4.40

package/dist/init.d.ts

@@ -182,4 +182,19 @@ export declare function ensureInitialized(projectRoot?: string): Promise<{
 export declare function getVersion(projectRoot?: string): Promise<{
     version: string;
 }>;
+/**
+ * Deploy the starter CANT bundle (team + agents) to a project's `.cleo/cant/`.
+ *
+ * Idempotent: skips deployment if `.cleo/cant/` already contains `.cant` files.
+ * Does not overwrite existing files. Resolves the starter bundle from
+ * `@cleocode/cleo-os/starter-bundle` or workspace fallback paths.
+ *
+ * Called by both `initProject()` and `runUpgrade()` to ensure every project
+ * gets a working team topology for the CANT bridge.
+ *
+ * @param cleoDir - Absolute path to the project's `.cleo/` directory.
+ * @param created - Array to push created-file descriptions into.
+ * @param warnings - Array to push warning messages into.
+ */
+export declare function deployStarterBundle(cleoDir: string, created: string[], warnings: string[]): Promise<void>;
 //# sourceMappingURL=init.d.ts.map

package/dist/init.d.ts.map

@@ -1 +1 @@
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package/dist/internal.d.ts

@@ -234,6 +234,7 @@ export { initCoreSkills } from './init.js';
 export { extractFromTranscript } from './memory/auto-extract.js';
 export { initDefaultProvider } from './memory/brain-embedding.js';
 export type { BrainAnchor, BrainConsolidationObservationRow, BrainDecisionNode, BrainFtsRow, BrainIdCheckRow, BrainKnnRow, BrainNarrativeRow, BrainSearchHit, BrainTimelineNeighborRow, } from './memory/brain-row-types.js';
+export { autoLinkMemories, linkMemoryToCode, listCodeLinks, queryCodeForMemory, queryMemoriesForCode, } from './memory/graph-memory-bridge.js';
 export type { ExtractedMemory, ExtractFromTranscriptOptions, ExtractionReport, ExtractionType, } from './memory/llm-extraction.js';
 export { extractFromTranscript as llmExtractFromTranscript } from './memory/llm-extraction.js';
 export { generateContextAwareContent, refreshMemoryBridge, writeMemoryBridge, } from './memory/memory-bridge.js';

package/dist/internal.d.ts.map

@@ -1 +1 @@
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package/dist/memory/brain-lifecycle.d.ts

@@ -113,6 +113,8 @@ export interface RunConsolidationResult {
     edgesStrengthened: number;
     /** Summary nodes generated. */
     summariesGenerated: number;
+    /** Code↔memory graph links created. */
+    graphLinksCreated?: number;
 }
 /**
  * Run the full sleep-time consolidation pipeline.

package/dist/memory/brain-lifecycle.d.ts.map

@@ -1 +1 @@
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package/dist/tasks/complete.d.ts.map

@@ -1 +1 @@
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package/dist/upgrade.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"upgrade.d.ts","sourceRoot":"","sources":["../src/upgrade.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AAmCH,2CAA2C;AAC3C,MAAM,WAAW,aAAa;IAC5B,MAAM,EAAE,MAAM,CAAC;IACf,MAAM,EAAE,SAAS,GAAG,SAAS,GAAG,SAAS,GAAG,OAAO,CAAC;IACpD,OAAO,EAAE,MAAM,CAAC;IAChB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,GAAG,CAAC,EAAE,MAAM,CAAC;CACd;AAED,2BAA2B;AAC3B,MAAM,WAAW,aAAa;IAC5B,OAAO,EAAE,OAAO,CAAC;IACjB,QAAQ,EAAE,OAAO,CAAC;IAClB,MAAM,EAAE,OAAO,CAAC;IAChB,OAAO,EAAE,aAAa,EAAE,CAAC;IACzB,OAAO,EAAE,MAAM,CAAC;IAChB,MAAM,EAAE,MAAM,EAAE,CAAC;IACjB,2EAA2E;IAC3E,OAAO,CAAC,EAAE,cAAc,CAAC;IACzB,iEAAiE;IACjE,gBAAgB,CAAC,EAAE;QACjB,QAAQ,EAAE,OAAO,CAAC;QAClB,aAAa,EAAE,MAAM,CAAC;QACtB,gBAAgB,EAAE,MAAM,CAAC;QACzB,gBAAgB,EAAE,MAAM,CAAC;QACzB,QAAQ,EAAE,MAAM,EAAE,CAAC;KACpB,CAAC;CACH;AAED,sDAAsD;AACtD,MAAM,WAAW,cAAc;IAC7B,OAAO,EAAE,MAAM,CAAC;IAChB,OAAO,EAAE,MAAM,CAAC;IAChB,OAAO,EAAE,MAAM,CAAC;IAChB,MAAM,EAAE,MAAM,CAAC;IACf,QAAQ,EAAE,MAAM,EAAE,CAAC;CACpB;AAED,mDAAmD;AACnD,MAAM,WAAW,eAAe;IAC9B,KAAK,EAAE,MAAM,CAAC;IACd,MAAM,EAAE,IAAI,GAAG,SAAS,GAAG,OAAO,CAAC;IACnC,OAAO,EAAE,MAAM,CAAC;IAChB,GAAG,CAAC,EAAE,MAAM,CAAC;CACd;AAED,qCAAqC;AACrC,MAAM,WAAW,cAAc;IAC7B,OAAO,EAAE,OAAO,CAAC;IACjB,QAAQ,EAAE,eAAe,EAAE,CAAC;IAC5B,OAAO,EAAE;QAAE,EAAE,EAAE,MAAM,CAAC;QAAC,QAAQ,EAAE,MAAM,CAAC;QAAC,MAAM,EAAE,MAAM,CAAA;KAAE,CAAC;CAC3D;AAED;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAsB,UAAU,CAC9B,OAAO,GAAE;IACP,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,aAAa,CAAC,EAAE,OAAO,CAAC;IACxB,WAAW,CAAC,EAAE,OAAO,CAAC;IACtB,WAAW,CAAC,EAAE,OAAO,CAAC;IACtB,WAAW,CAAC,EAAE,OAAO,CAAC;IACtB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,GAAG,CAAC,EAAE,MAAM,CAAC;CACT,GACL,OAAO,CAAC,aAAa,CAAC,CAi7BxB;AAED;;;;;;;;;;;;;;GAcG;AACH,wBAAsB,eAAe,CAAC,OAAO,GAAE;IAAE,GAAG,CAAC,EAAE,MAAM,CAAA;CAAO,GAAG,OAAO,CAAC,cAAc,CAAC,CA0O7F"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@cleocode/core",
-  "version": "2026.4.38",
+  "version": "2026.4.40",
   "description": "CLEO core business logic kernel — tasks, sessions, memory, orchestration, lifecycle, with bundled SQLite store",
   "type": "module",
   "main": "./dist/index.js",
@@ -48,13 +48,13 @@
     "write-file-atomic": "^7.0.1",
     "yaml": "^2.8.3",
     "zod": "^4.3.6",
-    "@cleocode/caamp": "2026.4.38",
-    "@cleocode/adapters": "2026.4.38",
-    "@cleocode/contracts": "2026.4.38",
-    "@cleocode/lafs": "2026.4.38",
-    "@cleocode/agents": "2026.4.36",
-    "@cleocode/nexus": "2026.4.38",
-    "@cleocode/skills": "2026.4.36"
+    "@cleocode/caamp": "2026.4.40",
+    "@cleocode/adapters": "2026.4.40",
+    "@cleocode/agents": "2026.4.40",
+    "@cleocode/contracts": "2026.4.40",
+    "@cleocode/nexus": "2026.4.40",
+    "@cleocode/lafs": "2026.4.40",
+    "@cleocode/skills": "2026.4.40"
   },
   "engines": {
     "node": ">=24.0.0"

package/src/init.ts

@@ -832,65 +832,7 @@ export async function initProject(opts: InitOptions = {}): Promise<InitResult> {
   // This gives the CANT bridge a working team topology on first `cleoos` run.
   // Only deploys if .cleo/cant/ does not already contain .cant files (idempotent).
   try {
-    const cantDir = join(cleoDir, 'cant');
-    const cantAgentsDir = join(cantDir, 'agents');
-    const hasCantFiles =
-      existsSync(cantDir) &&
-      readdirSync(cantDir, { recursive: true }).some(
-        (f) => typeof f === 'string' && f.endsWith('.cant'),
-      );
-
-    if (!hasCantFiles) {
-      // Resolve the starter-bundle from @cleocode/cleo-os package
-      let starterBundleSrc: string | null = null;
-      try {
-        const { createRequire } = await import('node:module');
-        const req = createRequire(import.meta.url);
-        const cleoOsPkgMain = req.resolve('@cleocode/cleo-os/package.json');
-        const cleoOsPkgRoot = dirname(cleoOsPkgMain);
-        const candidate = join(cleoOsPkgRoot, 'starter-bundle');
-        if (existsSync(candidate)) {
-          starterBundleSrc = candidate;
-        }
-      } catch {
-        // Not resolvable via require.resolve — try workspace fallbacks
-      }
-
-      if (!starterBundleSrc) {
-        const packageRoot = getPackageRoot();
-        const fallbacks = [
-          join(packageRoot, '..', 'cleo-os', 'starter-bundle'),
-          join(packageRoot, '..', '..', 'packages', 'cleo-os', 'starter-bundle'),
-        ];
-        starterBundleSrc = fallbacks.find((p) => existsSync(p)) ?? null;
-      }
-
-      if (starterBundleSrc) {
-        await mkdir(cantDir, { recursive: true });
-        await mkdir(cantAgentsDir, { recursive: true });
-
-        // Copy team.cant
-        const teamSrc = join(starterBundleSrc, 'team.cant');
-        const teamDst = join(cantDir, 'team.cant');
-        if (existsSync(teamSrc) && !existsSync(teamDst)) {
-          await copyFile(teamSrc, teamDst);
-        }
-
-        // Copy agent .cant files
-        const agentsSrc = join(starterBundleSrc, 'agents');
-        if (existsSync(agentsSrc)) {
-          const agentFiles = readdirSync(agentsSrc).filter((f) => f.endsWith('.cant'));
-          for (const agentFile of agentFiles) {
-            const dst = join(cantAgentsDir, agentFile);
-            if (!existsSync(dst)) {
-              await copyFile(join(agentsSrc, agentFile), dst);
-            }
-          }
-        }
-
-        created.push('starter-bundle: team + agent .cant files deployed to .cleo/cant/');
-      }
-    }
+    await deployStarterBundle(cleoDir, created, warnings);
   } catch (err) {
     warnings.push(`Starter bundle deploy: ${err instanceof Error ? err.message : String(err)}`);
   }
@@ -1068,3 +1010,92 @@ export async function getVersion(projectRoot?: string): Promise<{ version: strin
 
   return { version: '0.0.0' };
 }
+
+// ---------------------------------------------------------------------------
+// Starter bundle deployment (T441) — shared between init and upgrade
+// ---------------------------------------------------------------------------
+
+/**
+ * Deploy the starter CANT bundle (team + agents) to a project's `.cleo/cant/`.
+ *
+ * Idempotent: skips deployment if `.cleo/cant/` already contains `.cant` files.
+ * Does not overwrite existing files. Resolves the starter bundle from
+ * `@cleocode/cleo-os/starter-bundle` or workspace fallback paths.
+ *
+ * Called by both `initProject()` and `runUpgrade()` to ensure every project
+ * gets a working team topology for the CANT bridge.
+ *
+ * @param cleoDir - Absolute path to the project's `.cleo/` directory.
+ * @param created - Array to push created-file descriptions into.
+ * @param warnings - Array to push warning messages into.
+ */
+export async function deployStarterBundle(
+  cleoDir: string,
+  created: string[],
+  warnings: string[],
+): Promise<void> {
+  const cantDir = join(cleoDir, 'cant');
+  const cantAgentsDir = join(cantDir, 'agents');
+  const hasCantFiles =
+    existsSync(cantDir) &&
+    readdirSync(cantDir, { recursive: true }).some(
+      (f) => typeof f === 'string' && f.endsWith('.cant'),
+    );
+
+  if (hasCantFiles) return; // Already deployed — idempotent
+
+  // Resolve the starter-bundle from @cleocode/cleo-os package
+  let starterBundleSrc: string | null = null;
+  try {
+    const { createRequire } = await import('node:module');
+    const req = createRequire(import.meta.url);
+    const cleoOsPkgMain = req.resolve('@cleocode/cleo-os/package.json');
+    const cleoOsPkgRoot = dirname(cleoOsPkgMain);
+    const candidate = join(cleoOsPkgRoot, 'starter-bundle');
+    if (existsSync(candidate)) {
+      starterBundleSrc = candidate;
+    }
+  } catch {
+    // Not resolvable via require.resolve — try workspace fallbacks
+  }
+
+  if (!starterBundleSrc) {
+    const packageRoot = getPackageRoot();
+    const fallbacks = [
+      join(packageRoot, '..', 'cleo-os', 'starter-bundle'),
+      join(packageRoot, '..', '..', 'packages', 'cleo-os', 'starter-bundle'),
+    ];
+    starterBundleSrc = fallbacks.find((p) => existsSync(p)) ?? null;
+  }
+
+  if (!starterBundleSrc) {
+    warnings.push(
+      'Starter bundle not found — .cleo/cant/ will remain empty. Run cleo init in a project with @cleocode/cleo-os installed.',
+    );
+    return;
+  }
+
+  await mkdir(cantDir, { recursive: true });
+  await mkdir(cantAgentsDir, { recursive: true });
+
+  // Copy team.cant
+  const teamSrc = join(starterBundleSrc, 'team.cant');
+  const teamDst = join(cantDir, 'team.cant');
+  if (existsSync(teamSrc) && !existsSync(teamDst)) {
+    await copyFile(teamSrc, teamDst);
+  }
+
+  // Copy agent .cant files
+  const agentsSrc = join(starterBundleSrc, 'agents');
+  if (existsSync(agentsSrc)) {
+    const agentFiles = readdirSync(agentsSrc).filter((f) => f.endsWith('.cant'));
+    for (const agentFile of agentFiles) {
+      const dst = join(cantAgentsDir, agentFile);
+      if (!existsSync(dst)) {
+        await copyFile(join(agentsSrc, agentFile), dst);
+      }
+    }
+  }
+
+  created.push('starter-bundle: team + agent .cant files deployed to .cleo/cant/');
+}

package/src/internal.ts

@@ -897,6 +897,13 @@ export type {
   BrainSearchHit,
   BrainTimelineNeighborRow,
 } from './memory/brain-row-types.js';
+export {
+  autoLinkMemories,
+  linkMemoryToCode,
+  listCodeLinks,
+  queryCodeForMemory,
+  queryMemoriesForCode,
+} from './memory/graph-memory-bridge.js';
 // Memory — LLM extraction gate (additional)
 export type {
   ExtractedMemory,

package/src/memory/__tests__/{graph-memory-bridge.test.ts → graph-memory-bridge-integration.test.ts}

@@ -12,7 +12,22 @@
 import { mkdir, mkdtemp, rm } from 'node:fs/promises';
 import { tmpdir } from 'node:os';
 import { join } from 'node:path';
-import { afterEach, beforeEach, describe, expect, it } from 'vitest';
+import { afterEach, beforeEach, describe, expect, it, vi } from 'vitest';
+
+// Force-pass-through the real modules so that any leaked mocks from other
+// test files in the same vitest shard cannot pollute this integration test.
+// vitest resolves mocks at file-load time; vi.unmock is not sufficient when
+// another file's vi.mock('../../paths.js') already poisoned the module registry.
+vi.mock('../../paths.js', async () => await vi.importActual('../../paths.js'));
+vi.mock(
+  '../../store/brain-sqlite.js',
+  async () => await vi.importActual('../../store/brain-sqlite.js'),
+);
+vi.mock(
+  '../../store/nexus-sqlite.js',
+  async () => await vi.importActual('../../store/nexus-sqlite.js'),
+);
+vi.mock('../../config.js', async () => await vi.importActual('../../config.js'));
 
 let tempDir: string;
 
@@ -21,6 +36,9 @@ describe('graph-memory-bridge', () => {
     tempDir = await mkdtemp(join(tmpdir(), 'cleo-gmb-'));
     await mkdir(join(tempDir, '.cleo'), { recursive: true });
     process.env['CLEO_DIR'] = join(tempDir, '.cleo');
+    // nexus.db is global (ADR-036) — point CLEO_HOME to temp dir so
+    // getNexusDb() creates it here instead of ~/.cleo/ on CI.
+    process.env['CLEO_HOME'] = join(tempDir, '.cleo');
   });
 
   afterEach(async () => {
@@ -29,6 +47,7 @@ describe('graph-memory-bridge', () => {
     closeBrainDb();
     resetNexusDbState();
     delete process.env['CLEO_DIR'];
+    delete process.env['CLEO_HOME'];
     await rm(tempDir, { recursive: true, force: true });
   });
 

package/src/memory/__tests__/observer-reflector.test.ts

@@ -26,12 +26,14 @@ const {
   mockStoreLearning,
   mockStorePattern,
   mockLoadConfig,
+  mockResolveKey,
 } = vi.hoisted(() => ({
   mockGetBrainDb: vi.fn().mockResolvedValue({}),
   mockGetBrainNativeDb: vi.fn(),
   mockStoreLearning: vi.fn().mockResolvedValue({ id: 'L-test-001' }),
   mockStorePattern: vi.fn().mockResolvedValue({ id: 'P-test-001' }),
   mockLoadConfig: vi.fn(),
+  mockResolveKey: vi.fn().mockReturnValue(null),
 }));
 
 vi.mock('../../store/brain-sqlite.js', () => ({
@@ -56,6 +58,13 @@ vi.mock('../../config.js', () => ({
   loadConfig: mockLoadConfig,
 }));
 
+// Mock the key resolver so tests don't depend on filesystem state
+// (~/.claude/.credentials.json, ~/.local/share/cleo/anthropic-key).
+vi.mock('../anthropic-key-resolver.js', () => ({
+  resolveAnthropicApiKey: (...args: unknown[]) => mockResolveKey(...args),
+  clearAnthropicKeyCache: vi.fn(),
+}));
+
 // ============================================================================
 // Import module under test (after all mocks)
 // ============================================================================
@@ -69,11 +78,7 @@ import { runObserver, runReflector } from '../observer-reflector.js';
 const FAKE_API_KEY = 'sk-ant-test-key';
 
 function setApiKey(key: string | undefined): void {
-  if (key === undefined) {
-    delete process.env['ANTHROPIC_API_KEY'];
-  } else {
-    process.env['ANTHROPIC_API_KEY'] = key;
-  }
+  mockResolveKey.mockReturnValue(key ?? null);
 }
 
 type RawObs = {

package/src/memory/__tests__/sleep-consolidation.test.ts

@@ -171,7 +171,11 @@ function buildMockNativeDb(options: {
     return { run: mockRun, all: mockAll, get: vi.fn().mockReturnValue({ cnt: 0 }) };
   });
 
-  const stmtMock = { run: mockRun, all: vi.fn().mockReturnValue([]), get: vi.fn().mockReturnValue({ cnt: 0 }) };
+  const stmtMock = {
+    run: mockRun,
+    all: vi.fn().mockReturnValue([]),
+    get: vi.fn().mockReturnValue({ cnt: 0 }),
+  };
   return { prepare, _stmtMock: stmtMock };
 }
 

package/src/memory/brain-lifecycle.ts

@@ -579,6 +579,8 @@ export interface RunConsolidationResult {
   edgesStrengthened: number;
   /** Summary nodes generated. */
   summariesGenerated: number;
+  /** Code↔memory graph links created. */
+  graphLinksCreated?: number;
 }
 
 /**
@@ -671,6 +673,17 @@ export async function runConsolidation(projectRoot: string): Promise<RunConsolid
     console.warn('[consolidation] Step 7 summary generation failed:', err);
   }
 
+  // Step 8: Link memory nodes to code graph (graph-memory-bridge, T555)
+  // Scans brain entries for entity references and creates code_reference
+  // edges connecting memory to nexus-indexed symbols.
+  try {
+    const { autoLinkMemories } = await import('./graph-memory-bridge.js');
+    const bridgeResult = await autoLinkMemories(projectRoot);
+    result.graphLinksCreated = bridgeResult.linked;
+  } catch (err) {
+    console.warn('[consolidation] Step 8 graph memory bridge failed:', err);
+  }
+
   return result;
 }
 

package/src/tasks/complete.ts

@@ -334,6 +334,26 @@ export async function completeTask(
       /* Graph population is best-effort */
     });
 
+  // Dispatch PostToolUse hook — triggers observer, quality feedback, and memory bridge refresh.
+  // This is the missing link between "task completed" and "brain processes it" (T555).
+  try {
+    const { hooks } = await import('../hooks/registry.js');
+    await hooks
+      .dispatch('PostToolUse', cwd ?? process.cwd(), {
+        timestamp: new Date().toISOString(),
+        taskId: options.taskId,
+        taskTitle: task.title,
+        previousStatus: before.status,
+        newStatus: 'done',
+        unblockedCount: unblockedTasks.length,
+      })
+      .catch(() => {
+        /* Hooks are best-effort — never block task completion */
+      });
+  } catch {
+    /* Hook registry unavailable — non-fatal */
+  }
+
   return {
     task,
     ...(autoCompleted.length > 0 && { autoCompleted }),

package/src/upgrade.ts

@@ -900,7 +900,30 @@ export async function runUpgrade(
       /* best-effort */
     }
 
-    // (Step skipped — CLI dispatch only)
+    // Deploy starter CANT bundle (team + agents) to .cleo/cant/ if missing.
+    // Ensures existing projects get agent definitions on upgrade, not just init. (T555)
+    try {
+      const { deployStarterBundle } = await import('./init.js');
+      const cantCreated: string[] = [];
+      const cantWarnings: string[] = [];
+      await deployStarterBundle(cleoDir, cantCreated, cantWarnings);
+      if (cantCreated.length > 0) {
+        actions.push({
+          action: 'cant_starter_bundle',
+          status: 'applied',
+          details: cantCreated.join(', '),
+        });
+      }
+      for (const w of cantWarnings) {
+        actions.push({
+          action: 'cant_starter_bundle',
+          status: 'skipped',
+          details: w,
+        });
+      }
+    } catch {
+      /* best-effort */
+    }
 
     // Install core skills
     try {