@cleocode/core 2026.3.76 → 2026.4.2

package/src/hooks/handlers/__tests__/hook-automation-e2e.test.ts

@@ -38,8 +38,8 @@ import * as configModule from '../../../config.js';
 import * as brainRetrieval from '../../../memory/brain-retrieval.js';
 import { handleSubagentStart, handleSubagentStop } from '../agent-hooks.js';
 import { handlePostCompact, handlePreCompact } from '../context-hooks.js';
-import { handleSystemNotification } from '../mcp-hooks.js';
 import * as bridgeRefresh from '../memory-bridge-refresh.js';
+import { handleSystemNotification } from '../notification-hooks.js';
 import { handleSessionEnd, handleSessionStart } from '../session-hooks.js';
 import { handleToolComplete, handleToolStart } from '../task-hooks.js';
 import { handleWorkPromptSubmit, handleWorkResponseComplete } from '../work-capture-hooks.js';
@@ -62,7 +62,7 @@ function makeConfig(
     captureMcp?: boolean;
     autoRefresh?: boolean;
   } = {},
-): Record<string, unknown> {
+): Awaited<ReturnType<typeof configModule.loadConfig>> {
   return {
     brain: {
       autoCapture: overrides.autoCapture ?? true,
@@ -73,7 +73,7 @@ function makeConfig(
       embedding: { enabled: false, provider: 'local' },
       summarization: { enabled: false },
     },
-  };
+  } as Awaited<ReturnType<typeof configModule.loadConfig>>;
 }
 
 const PROJECT_ROOT = '/tmp/e2e-test-project';
@@ -85,7 +85,9 @@ const TIMESTAMP = '2026-03-24T00:00:00.000Z';
 
 describe('hook automation E2E', () => {
   beforeEach(() => {
-    observeBrainMock.mockReset().mockResolvedValue(undefined);
+    observeBrainMock
+      .mockReset()
+      .mockResolvedValue({ id: 'O-test', type: 'observation', createdAt: '2026-01-01 00:00:00' });
     loadConfigMock.mockReset().mockResolvedValue(makeConfig());
     maybeRefreshMemoryBridgeMock.mockReset().mockResolvedValue(undefined);
     // Clear work-capture env var

package/src/hooks/handlers/index.ts

@@ -13,7 +13,7 @@ import './session-hooks.js';
 import './task-hooks.js';
 import './error-hooks.js';
 import './file-hooks.js';
-import './mcp-hooks.js';
+import './notification-hooks.js';
 import './work-capture-hooks.js';
 import './agent-hooks.js';
 import './context-hooks.js';
@@ -22,11 +22,7 @@ export { handleSubagentStart, handleSubagentStop } from './agent-hooks.js';
 export { handlePostCompact, handlePreCompact } from './context-hooks.js';
 export { handleError } from './error-hooks.js';
 export { handleFileChange } from './file-hooks.js';
-export {
-  handlePromptSubmit,
-  handleResponseComplete,
-  handleSystemNotification,
-} from './mcp-hooks.js';
+export { handleSystemNotification } from './notification-hooks.js';
 // Re-export handler functions for explicit use
 export { handleSessionEnd, handleSessionStart } from './session-hooks.js';
 export { handleToolComplete, handleToolStart } from './task-hooks.js';

package/src/hooks/handlers/notification-hooks.ts

@@ -0,0 +1,65 @@
+/**
+ * System Notification Hook Handler
+ *
+ * Captures message-bearing system notifications as BRAIN observations.
+ * File-change notifications (filePath + changeType) are handled by
+ * file-hooks.ts; this module only handles Notification payloads with
+ * a `message` field.
+ *
+ * Gated behind brain.autoCapture config. Never throws.
+ * Auto-registers on module load.
+ *
+ * @task T166
+ */
+
+import { hooks } from '../registry.js';
+import type { NotificationPayload } from '../types.js';
+import { isAutoCaptureEnabled, isMissingBrainSchemaError } from './handler-helpers.js';
+
+/**
+ * Handle Notification — capture system notifications as BRAIN observations.
+ *
+ * Only fires for Notification payloads that carry a message field (i.e. system
+ * notifications). File-change notifications (filePath + changeType) are
+ * handled exclusively by file-hooks.ts and are skipped here to avoid
+ * double-capture.
+ *
+ * Gated behind brain.autoCapture config. Never throws.
+ *
+ * @param projectRoot - Absolute path to the project root directory.
+ * @param payload     - Notification event payload.
+ *
+ * @task T166
+ */
+export async function handleSystemNotification(
+  projectRoot: string,
+  payload: NotificationPayload,
+): Promise<void> {
+  // File-change notifications are handled by file-hooks.ts
+  if (payload.filePath || payload.changeType) return;
+  // Only handle message-bearing system notifications
+  if (!payload.message) return;
+  if (!(await isAutoCaptureEnabled(projectRoot))) return;
+
+  const { observeBrain } = await import('../../memory/brain-retrieval.js');
+
+  try {
+    await observeBrain(projectRoot, {
+      text: `System notification: ${payload.message}`,
+      title: `Notification: ${payload.message.slice(0, 60)}`,
+      type: 'discovery',
+      sourceSessionId: payload.sessionId,
+      sourceType: 'agent',
+    });
+  } catch (err) {
+    if (!isMissingBrainSchemaError(err)) throw err;
+  }
+}
+
+// Lower priority (90) so file-hooks.ts (100) runs first for Notification events
+hooks.register({
+  id: 'brain-system-notification',
+  event: 'Notification',
+  handler: handleSystemNotification,
+  priority: 90,
+});

package/src/index.ts

@@ -33,6 +33,7 @@ export * as admin from './admin/index.js';
 export * as adrs from './adrs/index.js';
 export * as agents from './agents/index.js';
 export * as caamp from './caamp/index.js';
+export * as code from './code/index.js';
 export * as codebaseMap from './codebase-map/index.js';
 export * as compliance from './compliance/index.js';
 export * as conduit from './conduit/index.js';
@@ -43,7 +44,7 @@ export * as intelligence from './intelligence/index.js';
 export * as issue from './issue/index.js';
 export * as lib from './lib/index.js';
 export * as lifecycle from './lifecycle/index.js';
-export * as coreMcp from './mcp/index.js';
+// (removed: former coreMcp export — Phase 2 production readiness)
 export * as memory from './memory/index.js';
 export * as metrics from './metrics/index.js';
 export * as migration from './migration/index.js';

package/src/init.ts

@@ -1,8 +1,8 @@
 /**
  * Core init logic - project initialization and maintenance.
  *
- * Single source of truth for all init operations. Both CLI and MCP
- * delegate here (shared-core pattern).
+ * Single source of truth for all init operations. CLI delegates here
+ * (shared-core pattern).
  *
  * Handles:
  *   1. .cleo/ directory structure creation
@@ -11,7 +11,7 @@
  *   4. Sequence counter (SQLite schema_meta)
  *   5. Project info (.cleo/project-info.json)
  *   6. CAAMP injection into agent instruction files (AGENTS.md hub pattern)
- *   7. MCP server installation to detected providers
+ *   7. (removed — was MCP server installation)
  *   8. Agent definition installation (cleo-subagent)
  *   9. Core skill installation via CAAMP
  *  10. NEXUS project registration
@@ -169,55 +169,15 @@ export async function initAgentDefinition(created: string[], warnings: string[])
 }
 
 /**
- * Install MCP server config to all detected providers via CAAMP.
+ * No-op. Kept for API compatibility.
  * @task T4706
  */
 export async function initMcpServer(
-  projectRoot: string,
-  created: string[],
-  warnings: string[],
+  _projectRoot: string,
+  _created: string[],
+  _warnings: string[],
 ): Promise<void> {
-  try {
-    const { detectEnvMode, generateMcpServerEntry, getMcpServerName } = await import(
-      './mcp/index.js'
-    );
-    const { getInstalledProviders, installMcpServerToAll } = await import('@cleocode/caamp');
-    type McpServerConfig = import('@cleocode/caamp').McpServerConfig;
-
-    const env = detectEnvMode();
-    const serverEntry = generateMcpServerEntry(env) as McpServerConfig;
-    const serverName = getMcpServerName(env);
-    const providers = getInstalledProviders();
-
-    if (providers.length === 0) {
-      return;
-    }
-
-    // MCP server config is a system-level tool setup by default.
-    // Project-level CLEO data still lives in per-project .cleo/.
-    const results = await installMcpServerToAll(
-      providers,
-      serverName,
-      serverEntry,
-      'global',
-      projectRoot,
-    );
-
-    const successes = results.filter((r) => r.success);
-    const failures = results.filter((r) => !r.success);
-
-    if (successes.length > 0) {
-      created.push(`MCP server: ${successes.map((r) => r.provider.id).join(', ')}`);
-    }
-
-    for (const f of failures) {
-      if (f.error) {
-        warnings.push(`MCP install to ${f.provider.id}: ${f.error}`);
-      }
-    }
-  } catch (err) {
-    warnings.push(`MCP server install: ${err instanceof Error ? err.message : String(err)}`);
-  }
+  // No-op: removed
 }
 
 /**
@@ -464,7 +424,7 @@ export async function updateDocs(): Promise<InitResult> {
  * Run full project initialization.
  *
  * Creates the .cleo/ directory structure, installs schemas, templates,
- * agent definitions, MCP server configs, skills, and registers with NEXUS.
+ * agent definitions, skills, and registers with NEXUS.
  *
  * @task T4681
  * @task T4682
@@ -694,15 +654,15 @@ export async function initProject(opts: InitOptions = {}): Promise<InitResult> {
     warnings.push(`CAAMP injection: ${err instanceof Error ? err.message : String(err)}`);
   }
 
-  // ADR-029: Contributor project MCP registration
+  // ADR-029: Contributor project dev channel setup
   try {
     const { ensureContributorMcp } = await import('./scaffold.js');
-    const mcpResult = await ensureContributorMcp(projRoot);
-    if (mcpResult.action !== 'skipped') {
-      created.push(`contributor MCP: ${mcpResult.details ?? mcpResult.action}`);
+    const devResult = await ensureContributorMcp(projRoot);
+    if (devResult.action !== 'skipped') {
+      created.push(`contributor dev channel: ${devResult.details ?? devResult.action}`);
     }
   } catch (err) {
-    warnings.push(`Contributor MCP setup: ${err instanceof Error ? err.message : String(err)}`);
+    warnings.push(`Contributor dev channel: ${err instanceof Error ? err.message : String(err)}`);
   }
 
   // T4685: Agent definition (cleo-subagent)

package/src/injection.ts

@@ -336,9 +336,10 @@ export function checkInjection(projectRoot: string): InjectionCheckResult {
 
     for (const ref of refs) {
       const rawPath = ref.slice(1).trim();
-      const resolvedPath = rawPath.startsWith('~/')
-        ? join(homedir(), rawPath.slice(2))
-        : join(projectRoot, rawPath);
+      const resolvedPath =
+        rawPath.startsWith('~/') || rawPath.startsWith('~\\')
+          ? join(homedir(), rawPath.slice(2))
+          : join(projectRoot, rawPath);
 
       if (!existsSync(resolvedPath)) {
         missing.push(rawPath);

package/src/internal.ts

@@ -3,7 +3,7 @@
  *
  * This entry point is a SUPERSET of the public API. It re-exports everything
  * from `@cleocode/core` plus additional symbols needed by the dispatch layer,
- * CLI commands, MCP gateways, and engine adapters inside @cleocode/cleo.
+ * CLI commands, and engine adapters inside @cleocode/cleo.
  *
  * External consumers should import from `@cleocode/core` (the public API).
  * Only @cleocode/cleo should import from `@cleocode/core/internal`.
@@ -40,9 +40,13 @@ export type { BootstrapContext, BootstrapOptions } from './bootstrap.js';
 // Bootstrap (global setup)
 export {
   bootstrapGlobalCleo,
-  installMcpToProviders,
   installSkillsGlobally,
 } from './bootstrap.js';
+export { smartOutline } from './code/outline.js';
+// Code analysis (Smart Explore)
+export { batchParse, isTreeSitterAvailable, parseFile } from './code/parser.js';
+export { type SmartSearchOptions, smartSearch } from './code/search.js';
+export { smartUnfold } from './code/unfold.js';
 export type { ViolationLogEntry } from './compliance/protocol-enforcement.js';
 // Compliance
 export { ProtocolEnforcer, protocolEnforcer } from './compliance/protocol-enforcement.js';
@@ -133,8 +137,6 @@ export {
 } from './lifecycle/index.js';
 export { instantiateTessera, showTessera } from './lifecycle/tessera-engine.js';
 
-// MCP helpers
-export { detectEnvMode, generateMcpServerEntry, getMcpServerName } from './mcp/index.js';
 // Memory — brain lifecycle (temporal decay + consolidation)
 export type { ConsolidationResult, DecayResult } from './memory/brain-lifecycle.js';
 export { applyTemporalDecay, consolidateMemories } from './memory/brain-lifecycle.js';
@@ -144,6 +146,7 @@ export type {
   BrainMaintenanceDecayResult,
   BrainMaintenanceEmbeddingsResult,
   BrainMaintenanceOptions,
+  BrainMaintenanceReconciliationResult,
   BrainMaintenanceResult,
 } from './memory/brain-maintenance.js';
 export { runBrainMaintenance } from './memory/brain-maintenance.js';
@@ -805,4 +808,3 @@ export { createConduit } from './conduit/factory.js';
 export { HttpTransport } from './conduit/http-transport.js';
 export { decrypt, encrypt } from './crypto/credentials.js';
 export { AgentRegistryAccessor } from './store/agent-registry-accessor.js';
-export { agentCredentials } from './store/tasks-schema.js';

package/src/lib/index.ts

@@ -14,3 +14,11 @@ export {
   type RetryOptions,
   withRetry,
 } from './retry.js';
+
+export {
+  detectLanguage,
+  grammarPackage,
+  SUPPORTED_EXTENSIONS,
+  SUPPORTED_LANGUAGES,
+  type TreeSitterLanguage,
+} from './tree-sitter-languages.js';

package/src/lib/tree-sitter-languages.ts

@@ -0,0 +1,88 @@
+/**
+ * Tree-sitter language detection and grammar resolution.
+ *
+ * Maps file extensions to tree-sitter grammar packages for use by
+ * the Smart Explore code analysis pipeline.
+ *
+ * @task T148
+ */
+
+/** Supported tree-sitter language identifiers. */
+export type TreeSitterLanguage =
+  | 'typescript'
+  | 'tsx'
+  | 'javascript'
+  | 'python'
+  | 'go'
+  | 'rust'
+  | 'java'
+  | 'c'
+  | 'cpp'
+  | 'ruby';
+
+/** Map from file extension (without dot) to tree-sitter language. */
+const EXTENSION_MAP: Record<string, TreeSitterLanguage> = {
+  ts: 'typescript',
+  tsx: 'tsx',
+  mts: 'typescript',
+  cts: 'typescript',
+  js: 'javascript',
+  jsx: 'javascript',
+  mjs: 'javascript',
+  cjs: 'javascript',
+  py: 'python',
+  pyi: 'python',
+  go: 'go',
+  rs: 'rust',
+  java: 'java',
+  c: 'c',
+  h: 'c',
+  cpp: 'cpp',
+  cc: 'cpp',
+  cxx: 'cpp',
+  hpp: 'cpp',
+  hh: 'cpp',
+  rb: 'ruby',
+};
+
+/** Map from language to its npm grammar package name. */
+const GRAMMAR_PACKAGE_MAP: Record<TreeSitterLanguage, string> = {
+  typescript: 'tree-sitter-typescript',
+  tsx: 'tree-sitter-typescript',
+  javascript: 'tree-sitter-javascript',
+  python: 'tree-sitter-python',
+  go: 'tree-sitter-go',
+  rust: 'tree-sitter-rust',
+  java: 'tree-sitter-java',
+  c: 'tree-sitter-c',
+  cpp: 'tree-sitter-cpp',
+  ruby: 'tree-sitter-ruby',
+};
+
+/**
+ * Detect tree-sitter language from a file path.
+ *
+ * @param filePath - Path to a source file
+ * @returns The detected language, or undefined if unsupported
+ */
+export function detectLanguage(filePath: string): TreeSitterLanguage | undefined {
+  const ext = filePath.split('.').pop()?.toLowerCase();
+  if (!ext) return undefined;
+  return EXTENSION_MAP[ext];
+}
+
+/**
+ * Get the npm grammar package name for a language.
+ *
+ * @param language - A tree-sitter language identifier
+ * @returns The npm package name containing the grammar
+ */
+export function grammarPackage(language: TreeSitterLanguage): string {
+  return GRAMMAR_PACKAGE_MAP[language];
+}
+
+/** All supported file extensions. */
+export const SUPPORTED_EXTENSIONS = Object.keys(EXTENSION_MAP);
+
+/** All supported languages. */
+export const SUPPORTED_LANGUAGES: TreeSitterLanguage[] = [...new Set(Object.values(EXTENSION_MAP))];

package/src/logger.ts

@@ -5,8 +5,8 @@
  * Custom formatters for uppercase level labels and ISO timestamps.
  * Context via child loggers (getLogger('subsystem')).
  *
- * MCP safety: all diagnostic logging goes to files — stdout is reserved
- * for the MCP protocol. Fallback stderr logger if not yet initialized.
+ * All diagnostic logging goes to files — stdout is reserved for structured
+ * CLI output. Fallback stderr logger if not yet initialized.
  */
 
 import { existsSync } from 'node:fs';
@@ -59,7 +59,7 @@ export function initLogger(
   // transport has mkdir: true as a safety net for edge cases where the
   // logger is initialized before scaffold (e.g. early startup fallback).
   if (!existsSync(currentLogDir)) {
-    // Emit to stderr — safe for MCP (protocol is stdout only)
+    // Emit to stderr — stdout is reserved for structured output
     process.stderr.write(
       `[cleo:logger] Log directory missing: ${currentLogDir} — pino-roll will create it\n`,
     );
@@ -122,11 +122,11 @@ export function initLogger(
  * Safe to call before initLogger — returns a stderr fallback logger
  * so early startup code and tests never crash.
  *
- * @param subsystem - Logical subsystem name (e.g. 'audit', 'mcp', 'migration')
+ * @param subsystem - Logical subsystem name (e.g. 'audit', 'dispatch', 'migration')
  */
 export function getLogger(subsystem: string): pino.Logger {
   if (!rootLogger) {
-    // Fallback: stderr logger (safe for MCP — protocol is stdout)
+    // Fallback: stderr logger (stdout reserved for structured output)
     return pino(
       {
         level: 'warn',

package/src/memory/__tests__/brain-links.test.js

@@ -16,10 +16,23 @@ describe('Brain Memory Links', () => {
         cleoDir = join(tempDir, '.cleo');
         await mkdir(cleoDir, { recursive: true });
         process.env['CLEO_DIR'] = cleoDir;
+        // Initialize tasks.db with test task IDs for cross-db write-guard validation
+        const { getDb } = await import('../../store/sqlite.js');
+        const { tasks } = await import('../../store/tasks-schema.js');
+        const db = await getDb(tempDir);
+        for (const id of ['T1000', 'T2000', 'T9999']) {
+            await db
+                .insert(tasks)
+                .values({ id, title: `Test task ${id}`, status: 'pending', type: 'task', position: 0 })
+                .onConflictDoNothing()
+                .run();
+        }
     });
     afterEach(async () => {
         const { closeBrainDb } = await import('../../store/brain-sqlite.js');
+        const { resetDbState } = await import('../../store/sqlite.js');
         closeBrainDb();
+        resetDbState();
         delete process.env['CLEO_DIR'];
         await rm(tempDir, { recursive: true, force: true });
     });

package/src/memory/__tests__/brain-links.test.js.map

@@ -1 +1 @@
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package/src/memory/__tests__/brain-links.test.ts

@@ -19,11 +19,25 @@ describe('Brain Memory Links', () => {
     cleoDir = join(tempDir, '.cleo');
     await mkdir(cleoDir, { recursive: true });
     process.env['CLEO_DIR'] = cleoDir;
+
+    // Initialize tasks.db with test task IDs for cross-db write-guard validation
+    const { getDb } = await import('../../store/sqlite.js');
+    const { tasks } = await import('../../store/tasks-schema.js');
+    const db = await getDb(tempDir);
+    for (const id of ['T1000', 'T2000', 'T9999']) {
+      await db
+        .insert(tasks)
+        .values({ id, title: `Test task ${id}`, status: 'pending', type: 'task', position: 0 })
+        .onConflictDoNothing()
+        .run();
+    }
   });
 
   afterEach(async () => {
     const { closeBrainDb } = await import('../../store/brain-sqlite.js');
+    const { resetDbState } = await import('../../store/sqlite.js');
     closeBrainDb();
+    resetDbState();
     delete process.env['CLEO_DIR'];
     await rm(tempDir, { recursive: true, force: true });
   });

package/src/memory/__tests__/brain-retrieval.test.js

@@ -18,6 +18,15 @@ describe('Brain Retrieval', () => {
         cleoDir = join(tempDir, '.cleo');
         await mkdir(cleoDir, { recursive: true });
         process.env['CLEO_DIR'] = cleoDir;
+        // Initialize tasks.db with test session for cross-db write-guard validation
+        const { getDb } = await import('../../store/sqlite.js');
+        const { sessions } = await import('../../store/tasks-schema.js');
+        const db = await getDb(tempDir);
+        await db
+            .insert(sessions)
+            .values({ id: 'S-123', name: 'test-session', status: 'active' })
+            .onConflictDoNothing()
+            .run();
     });
     afterEach(async () => {
         try {