fix: integrate centralized logger across services and hooks for improved logging consistency

src/hooks/context-hook.ts

@@ -10,6 +10,7 @@ import { stdin } from "process";
 import { ensureWorkerRunning, getWorkerPort } from "../shared/worker-utils.js";
 import { HOOK_TIMEOUTS } from "../shared/hook-constants.js";
 import { getProjectName } from "../utils/project-name.js";
+import { logger } from "../utils/logger.js";
 
 export interface SessionStartInput {
   session_id: string;

src/hooks/user-message-hook.ts

@@ -9,6 +9,7 @@
 import { basename } from "path";
 import { ensureWorkerRunning, getWorkerPort } from "../shared/worker-utils.js";
 import { HOOK_EXIT_CODES } from "../shared/hook-constants.js";
+import { logger } from "../utils/logger.js";
 
 // Ensure worker is running
 await ensureWorkerRunning();

src/servers/mcp-server.ts

@@ -6,11 +6,16 @@
  * Maintains MCP protocol handling and tool schemas
  */
 
-// CRITICAL: Redirect console.log to stderr BEFORE any imports
+// Import logger first
+import { logger } from '../utils/logger.js';
+
+// CRITICAL: Redirect console to stderr BEFORE other imports
 // MCP uses stdio transport where stdout is reserved for JSON-RPC protocol messages.
 // Any logs to stdout break the protocol (Claude Desktop parses "[2025..." as JSON array).
-const _originalConsoleLog = console.log;
+const _originalLog = console['log'];
-console.log = (...args: any[]) => console.error(...args);
+console['log'] = (...args: any[]) => {
+  logger.error('CONSOLE', 'Intercepted console output (MCP protocol protection)', undefined, { args });
+};
 
 import { Server } from '@modelcontextprotocol/sdk/server/index.js';
 import { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js';
@@ -18,7 +23,6 @@ import {
   CallToolRequestSchema,
   ListToolsRequestSchema,
 } from '@modelcontextprotocol/sdk/types.js';
-import { logger } from '../utils/logger.js';
 import { getWorkerPort, getWorkerHost } from '../shared/worker-utils.js';
 
 /**

src/services/context-generator.ts

@@ -229,7 +229,7 @@ export async function generateContext(input?: ContextInput, useColors: boolean =
       } catch (unlinkError) {
         // Marker might not exist
       }
-      console.error('Native module rebuild needed - restart Claude Code to auto-fix');
+      logger.error('SYSTEM', 'Native module rebuild needed - restart Claude Code to auto-fix');
       return '';
     }
     throw error;

src/services/sqlite/Database.ts

@@ -1,5 +1,6 @@
 import { Database } from 'bun:sqlite';
 import { DATA_DIR, DB_PATH, ensureDir } from '../../shared/paths.js';
+import { logger } from '../../utils/logger.js';
 
 // SQLite configuration constants
 const SQLITE_MMAP_SIZE_BYTES = 256 * 1024 * 1024; // 256MB
@@ -126,7 +127,7 @@ export class DatabaseManager {
 
     for (const migration of this.migrations) {
       if (migration.version > maxApplied) {
-        console.log(`Applying migration ${migration.version}...`);
+        logger.info('DB', `Applying migration ${migration.version}`);
 
         const transaction = this.db.transaction(() => {
           migration.up(this.db!);
@@ -136,7 +137,7 @@ export class DatabaseManager {
         });
 
         transaction();
-        console.log(`Migration ${migration.version} applied successfully`);
+        logger.info('DB', `Migration ${migration.version} applied successfully`);
       }
     }
   }

src/services/sqlite/PendingMessageStore.ts

@@ -1,5 +1,6 @@
 import { Database } from './sqlite-compat.js';
 import type { PendingMessage } from '../worker-types.js';
+import { logger } from '../../utils/logger.js';
 
 /**
  * Persistent pending message record from database

src/services/sqlite/SessionSearch.ts

@@ -1,6 +1,7 @@
 import { Database } from 'bun:sqlite';
 import { TableNameRow } from '../../types/database.js';
 import { DATA_DIR, DB_PATH, ensureDir } from '../../shared/paths.js';
+import { logger } from '../../utils/logger.js';
 import {
   ObservationSearchResult,
   SessionSummarySearchResult,
@@ -44,9 +45,6 @@ export class SessionSearch {
    * - Tables maintained but search paths removed
    * - Triggers still fire to keep tables synchronized
    *
-   * Note: Using console.log for migration messages since they run during constructor
-   * before structured logger is available. Actual errors use console.error.
-   *
    * TODO: Remove FTS5 infrastructure in future major version (v7.0.0)
    */
   private ensureFTSTables(): void {
@@ -59,7 +57,7 @@ export class SessionSearch {
       return;
     }
 
-    console.log('[SessionSearch] Creating FTS5 tables...');
+    logger.info('DB', 'Creating FTS5 tables');
 
     // Create observations_fts virtual table
     this.db.run(`
@@ -143,7 +141,7 @@ export class SessionSearch {
       END;
     `);
 
-    console.log('[SessionSearch] FTS5 tables created successfully');
+    logger.info('DB', 'FTS5 tables created successfully');
   }
 
 
@@ -270,7 +268,7 @@ export class SessionSearch {
 
     // Vector search with query text should be handled by ChromaDB
     // This method only supports filter-only queries (query=undefined)
-    console.warn('[SessionSearch] Text search not supported - use ChromaDB for vector search');
+    logger.warn('DB', 'Text search not supported - use ChromaDB for vector search');
     return [];
   }
 
@@ -309,7 +307,7 @@ export class SessionSearch {
 
     // Vector search with query text should be handled by ChromaDB
     // This method only supports filter-only queries (query=undefined)
-    console.warn('[SessionSearch] Text search not supported - use ChromaDB for vector search');
+    logger.warn('DB', 'Text search not supported - use ChromaDB for vector search');
     return [];
   }
 
@@ -495,7 +493,7 @@ export class SessionSearch {
 
     // Vector search with query text should be handled by ChromaDB
     // This method only supports filter-only queries (query=undefined)
-    console.warn('[SessionSearch] Text search not supported - use ChromaDB for vector search');
+    logger.warn('DB', 'Text search not supported - use ChromaDB for vector search');
     return [];
   }
 

src/services/sqlite/SessionStore.ts

@@ -48,9 +48,6 @@ export class SessionStore {
   /**
    * Initialize database schema using migrations (migration004)
    * This runs the core SDK tables migration if no tables exist
-   *
-   * Note: Using console.log for migration messages since they run during constructor
-   * before structured logger is available. Actual errors use console.error.
    */
   private initializeSchema(): void {
     try {
@@ -70,7 +67,7 @@ export class SessionStore {
       // Only run migration004 if no migrations have been applied
       // This creates the sdk_sessions, observations, and session_summaries tables
       if (maxApplied === 0) {
-        console.log('[SessionStore] Initializing fresh database with migration004...');
+        logger.info('DB', 'Initializing fresh database with migration004');
 
         // Migration004: SDK agent architecture tables
         this.db.run(`
@@ -134,10 +131,10 @@ export class SessionStore {
         // Record migration004 as applied
         this.db.prepare('INSERT INTO schema_versions (version, applied_at) VALUES (?, ?)').run(4, new Date().toISOString());
 
-        console.log('[SessionStore] Migration004 applied successfully');
+        logger.info('DB', 'Migration004 applied successfully');
       }
     } catch (error: any) {
-      console.error('[SessionStore] Schema initialization error:', error.message);
+      logger.error('DB', 'Schema initialization error', undefined, error);
       throw error;
     }
   }
@@ -156,7 +153,7 @@ export class SessionStore {
 
     if (!hasWorkerPort) {
       this.db.run('ALTER TABLE sdk_sessions ADD COLUMN worker_port INTEGER');
-      console.log('[SessionStore] Added worker_port column to sdk_sessions table');
+      logger.info('DB', 'Added worker_port column to sdk_sessions table');
     }
 
     // Record migration
@@ -177,7 +174,7 @@ export class SessionStore {
 
     if (!hasPromptCounter) {
       this.db.run('ALTER TABLE sdk_sessions ADD COLUMN prompt_counter INTEGER DEFAULT 0');
-      console.log('[SessionStore] Added prompt_counter column to sdk_sessions table');
+      logger.info('DB', 'Added prompt_counter column to sdk_sessions table');
     }
 
     // Check observations for prompt_number
@@ -186,7 +183,7 @@ export class SessionStore {
 
     if (!obsHasPromptNumber) {
       this.db.run('ALTER TABLE observations ADD COLUMN prompt_number INTEGER');
-      console.log('[SessionStore] Added prompt_number column to observations table');
+      logger.info('DB', 'Added prompt_number column to observations table');
     }
 
     // Check session_summaries for prompt_number
@@ -195,7 +192,7 @@ export class SessionStore {
 
     if (!sumHasPromptNumber) {
       this.db.run('ALTER TABLE session_summaries ADD COLUMN prompt_number INTEGER');
-      console.log('[SessionStore] Added prompt_number column to session_summaries table');
+      logger.info('DB', 'Added prompt_number column to session_summaries table');
     }
 
     // Record migration
@@ -220,7 +217,7 @@ export class SessionStore {
       return;
     }
 
-    console.log('[SessionStore] Removing UNIQUE constraint from session_summaries.sdk_session_id...');
+    logger.info('DB', 'Removing UNIQUE constraint from session_summaries.sdk_session_id');
 
     // Begin transaction
     this.db.run('BEGIN TRANSACTION');
@@ -275,7 +272,7 @@ export class SessionStore {
       // Record migration
       this.db.prepare('INSERT OR IGNORE INTO schema_versions (version, applied_at) VALUES (?, ?)').run(7, new Date().toISOString());
 
-      console.log('[SessionStore] Successfully removed UNIQUE constraint from session_summaries.sdk_session_id');
+      logger.info('DB', 'Successfully removed UNIQUE constraint from session_summaries.sdk_session_id');
     } catch (error: any) {
       // Rollback on error
       this.db.run('ROLLBACK');
@@ -301,7 +298,7 @@ export class SessionStore {
       return;
     }
 
-    console.log('[SessionStore] Adding hierarchical fields to observations table...');
+    logger.info('DB', 'Adding hierarchical fields to observations table');
 
     // Add new columns
     this.db.run(`
@@ -317,7 +314,7 @@ export class SessionStore {
     // Record migration
     this.db.prepare('INSERT OR IGNORE INTO schema_versions (version, applied_at) VALUES (?, ?)').run(8, new Date().toISOString());
 
-    console.log('[SessionStore] Successfully added hierarchical fields to observations table');
+    logger.info('DB', 'Successfully added hierarchical fields to observations table');
   }
 
   /**
@@ -339,7 +336,7 @@ export class SessionStore {
       return;
     }
 
-    console.log('[SessionStore] Making observations.text nullable...');
+    logger.info('DB', 'Making observations.text nullable');
 
     // Begin transaction
     this.db.run('BEGIN TRANSACTION');
@@ -396,7 +393,7 @@ export class SessionStore {
       // Record migration
       this.db.prepare('INSERT OR IGNORE INTO schema_versions (version, applied_at) VALUES (?, ?)').run(9, new Date().toISOString());
 
-      console.log('[SessionStore] Successfully made observations.text nullable');
+      logger.info('DB', 'Successfully made observations.text nullable');
     } catch (error: any) {
       // Rollback on error
       this.db.run('ROLLBACK');
@@ -420,7 +417,7 @@ export class SessionStore {
       return;
     }
 
-    console.log('[SessionStore] Creating user_prompts table with FTS5 support...');
+    logger.info('DB', 'Creating user_prompts table with FTS5 support');
 
     // Begin transaction
     this.db.run('BEGIN TRANSACTION');
@@ -479,7 +476,7 @@ export class SessionStore {
       // Record migration
       this.db.prepare('INSERT OR IGNORE INTO schema_versions (version, applied_at) VALUES (?, ?)').run(10, new Date().toISOString());
 
-      console.log('[SessionStore] Successfully created user_prompts table with FTS5 support');
+      logger.info('DB', 'Successfully created user_prompts table with FTS5 support');
     } catch (error: any) {
       // Rollback on error
       this.db.run('ROLLBACK');
@@ -504,7 +501,7 @@ export class SessionStore {
 
       if (!obsHasDiscoveryTokens) {
         this.db.run('ALTER TABLE observations ADD COLUMN discovery_tokens INTEGER DEFAULT 0');
-        console.log('[SessionStore] Added discovery_tokens column to observations table');
+        logger.info('DB', 'Added discovery_tokens column to observations table');
       }
 
       // Check if discovery_tokens column exists in session_summaries table
@@ -513,13 +510,13 @@ export class SessionStore {
 
       if (!sumHasDiscoveryTokens) {
         this.db.run('ALTER TABLE session_summaries ADD COLUMN discovery_tokens INTEGER DEFAULT 0');
-        console.log('[SessionStore] Added discovery_tokens column to session_summaries table');
+        logger.info('DB', 'Added discovery_tokens column to session_summaries table');
       }
 
       // Record migration only after successful column verification/addition
       this.db.prepare('INSERT OR IGNORE INTO schema_versions (version, applied_at) VALUES (?, ?)').run(11, new Date().toISOString());
     } catch (error: any) {
-      console.error('[SessionStore] Discovery tokens migration error:', error.message);
+      logger.error('DB', 'Discovery tokens migration error', undefined, error);
       throw error; // Re-throw to prevent silent failures
     }
   }
@@ -542,7 +539,7 @@ export class SessionStore {
         return;
       }
 
-      console.log('[SessionStore] Creating pending_messages table...');
+      logger.info('DB', 'Creating pending_messages table');
 
       this.db.run(`
         CREATE TABLE pending_messages (
@@ -572,9 +569,9 @@ export class SessionStore {
 
       this.db.prepare('INSERT OR IGNORE INTO schema_versions (version, applied_at) VALUES (?, ?)').run(16, new Date().toISOString());
 
-      console.log('[SessionStore] pending_messages table created successfully');
+      logger.info('DB', 'pending_messages table created successfully');
     } catch (error: any) {
-      console.error('[SessionStore] Pending messages table migration error:', error.message);
+      logger.error('DB', 'Pending messages table migration error', undefined, error);
       throw error;
     }
   }
@@ -1387,7 +1384,7 @@ export class SessionStore {
         startEpoch = beforeRecords.length > 0 ? beforeRecords[beforeRecords.length - 1].created_at_epoch : anchorEpoch;
         endEpoch = afterRecords.length > 0 ? afterRecords[afterRecords.length - 1].created_at_epoch : anchorEpoch;
       } catch (err: any) {
-        console.error('[SessionStore] Error getting boundary observations:', err.message, project ? `(project: ${project})` : '(all projects)');
+        logger.error('DB', 'Error getting boundary observations', undefined, { error: err, project });
         return { observations: [], sessions: [], prompts: [] };
       }
     } else {
@@ -1419,7 +1416,7 @@ export class SessionStore {
         startEpoch = beforeRecords.length > 0 ? beforeRecords[beforeRecords.length - 1].created_at_epoch : anchorEpoch;
         endEpoch = afterRecords.length > 0 ? afterRecords[afterRecords.length - 1].created_at_epoch : anchorEpoch;
       } catch (err: any) {
-        console.error('[SessionStore] Error getting boundary timestamps:', err.message, project ? `(project: ${project})` : '(all projects)');
+        logger.error('DB', 'Error getting boundary timestamps', undefined, { error: err, project });
         return { observations: [], sessions: [], prompts: [] };
       }
     }
@@ -1475,7 +1472,7 @@ export class SessionStore {
         }))
       };
     } catch (err: any) {
-      console.error('[SessionStore] Error querying timeline records:', err.message, project ? `(project: ${project})` : '(all projects)');
+      logger.error('DB', 'Error querying timeline records', undefined, { error: err, project });
       return { observations: [], sessions: [], prompts: [] };
     }
   }

src/services/worker-service.ts

@@ -965,13 +965,13 @@ async function main() {
         logger.info('SYSTEM', 'Another session is spawning worker, waiting for health');
         const healthy = await waitForHealth(port, getPlatformTimeout(30000));
         if (healthy) {
-          console.log(HOOK_RESPONSE);
+          logger.info('SYSTEM', 'Worker healthy, returning success');
           process.exit(0);
         }
         // Still not healthy after wait - try to acquire lock and spawn
         const gotLock = await waitForLock('start', 5000);
         if (!gotLock) {
-          console.error('Failed to acquire lock after timeout');
+          logger.error('SYSTEM', 'Failed to acquire lock after timeout');
           process.exit(1);
         }
       }
@@ -980,7 +980,7 @@ async function main() {
         // Re-check port AFTER acquiring lock
         if (await isPortInUse(port)) {
           releaseLock();
-          console.log(HOOK_RESPONSE);
+          logger.info('SYSTEM', 'Port already in use, worker already running');
           process.exit(0);
         }
 
@@ -994,7 +994,7 @@ async function main() {
 
         if (child.pid === undefined) {
           releaseLock();
-          console.error('Failed to spawn worker daemon');
+          logger.error('SYSTEM', 'Failed to spawn worker daemon');
           process.exit(1);
         }
 
@@ -1009,11 +1009,11 @@ async function main() {
 
         if (!healthy) {
           removePidFile();
-          console.error('Worker failed to start');
+          logger.error('SYSTEM', 'Worker failed to start');
           process.exit(1);
         }
 
-        console.log(HOOK_RESPONSE);
+        logger.info('SYSTEM', 'Worker started successfully');
         process.exit(0);
       } catch (error) {
         releaseLock();
@@ -1033,7 +1033,7 @@ async function main() {
         await waitForPortFree(port, getPlatformTimeout(15000));
         removePidFile();
         releaseLock();
-        console.log(HOOK_RESPONSE);
+        logger.info('SYSTEM', 'Worker stopped successfully');
         process.exit(0);
       } catch (error) {
         releaseLock();
@@ -1048,10 +1048,10 @@ async function main() {
         logger.info('SYSTEM', 'Another session is restarting worker, waiting');
         const healthy = await waitForHealth(port, getPlatformTimeout(45000));
         if (healthy) {
-          console.log(HOOK_RESPONSE);
+          logger.info('SYSTEM', 'Worker healthy after restart');
           process.exit(0);
         }
-        console.error('Worker failed to restart (concurrent operation)');
+        logger.error('SYSTEM', 'Worker failed to restart (concurrent operation)');
         process.exit(1);
       }
 
@@ -1069,7 +1069,7 @@ async function main() {
 
         if (child.pid === undefined) {
           releaseLock();
-          console.error('Failed to spawn worker daemon during restart');
+          logger.error('SYSTEM', 'Failed to spawn worker daemon during restart');
           process.exit(1);
         }
 
@@ -1081,10 +1081,10 @@ async function main() {
 
         if (!healthy) {
           removePidFile();
-          console.error('Worker failed to restart');
+          logger.error('SYSTEM', 'Worker failed to restart');
           process.exit(1);
         }
-        console.log(HOOK_RESPONSE);
+        logger.info('SYSTEM', 'Worker restarted successfully');
         process.exit(0);
       } catch (error) {
         releaseLock();
@@ -1096,9 +1096,9 @@ async function main() {
       const running = await isPortInUse(port);
       const pidInfo = readPidFile();
       if (running && pidInfo) {
-        console.log(`Worker running (PID: ${pidInfo.pid}, Port: ${pidInfo.port})`);
+        logger.info('SYSTEM', `Worker running (PID: ${pidInfo.pid}, Port: ${pidInfo.port})`);
       } else {
-        console.log('Worker not running');
+        logger.info('SYSTEM', 'Worker not running');
       }
       process.exit(0);
     }

src/services/worker/FormattingService.ts

@@ -5,6 +5,7 @@
 
 import { ObservationSearchResult, SessionSummarySearchResult, UserPromptSearchResult } from '../sqlite/types.js';
 import { ModeManager } from '../domain/ModeManager.js';
+import { logger } from '../../utils/logger.js';
 
 // Token estimation constant (matches context-generator)
 const CHARS_PER_TOKEN_ESTIMATE = 4;

src/services/worker/PaginationHelper.ts

@@ -8,6 +8,7 @@
  */
 
 import { DatabaseManager } from './DatabaseManager.js';
+import { logger } from '../../utils/logger.js';
 import type { PaginatedResult, Observation, Summary, UserPrompt } from '../worker-types.js';
 
 export class PaginationHelper {

src/services/worker/TimelineService.ts

@@ -5,6 +5,7 @@
 
 import { ObservationSearchResult, SessionSummarySearchResult, UserPromptSearchResult } from '../sqlite/types.js';
 import { ModeManager } from '../domain/ModeManager.js';
+import { logger } from '../../utils/logger.js';
 
 /**
  * Timeline item for unified chronological display

src/services/worker/events/SessionEventBroadcaster.ts

@@ -7,6 +7,7 @@
 
 import { SSEBroadcaster } from '../SSEBroadcaster.js';
 import type { WorkerService } from '../../worker-service.js';
+import { logger } from '../../../utils/logger.js';
 
 export class SessionEventBroadcaster {
   constructor(

src/services/worker/http/routes/DataRoutes.ts

@@ -8,6 +8,7 @@
 import express, { Request, Response } from 'express';
 import path from 'path';
 import { readFileSync, statSync, existsSync } from 'fs';
+import { logger } from '../../../../utils/logger.js';
 import { homedir } from 'os';
 import { getPackageRoot } from '../../../../shared/paths.js';
 import { getWorkerPort } from '../../../../shared/worker-utils.js';

src/services/worker/http/routes/SearchRoutes.ts

@@ -8,6 +8,7 @@
 import express, { Request, Response } from 'express';
 import { SearchManager } from '../../SearchManager.js';
 import { BaseRouteHandler } from '../BaseRouteHandler.js';
+import { logger } from '../../../../utils/logger.js';
 
 export class SearchRoutes extends BaseRouteHandler {
   constructor(

src/services/worker/http/routes/ViewerRoutes.ts

@@ -8,6 +8,7 @@
 import express, { Request, Response } from 'express';
 import path from 'path';
 import { readFileSync, existsSync } from 'fs';
+import { logger } from '../../../../utils/logger.js';
 import { getPackageRoot } from '../../../../shared/paths.js';
 import { SSEBroadcaster } from '../../SSEBroadcaster.js';
 import { DatabaseManager } from '../../DatabaseManager.js';

src/services/worker/session/SessionCompletionHandler.ts

@@ -11,6 +11,7 @@
 
 import { SessionManager } from '../SessionManager.js';
 import { SessionEventBroadcaster } from '../events/SessionEventBroadcaster.js';
+import { logger } from '../../../utils/logger.js';
 
 export class SessionCompletionHandler {
   constructor(