bluera-knowledge 0.11.3 → 0.11.5

package/.claude-plugin/plugin.json

@@ -1,5 +1,5 @@
 {
   "name": "bluera-knowledge",
-  "version": "0.11.3",
+  "version": "0.11.5",
   "description": "Clone repos, crawl docs, search locally. Fast, authoritative answers for AI coding agents."
 }

package/.mcp.json

@@ -2,8 +2,9 @@
   "mcpServers": {
     "bluera-knowledge": {
       "command": "node",
-      "args": ["${CLAUDE_PLUGIN_ROOT}/dist/mcp/server.js"],
+      "args": ["./dist/mcp/server.js"],
       "env": {
+        "PROJECT_ROOT": "${PWD}",
         "DATA_DIR": ".bluera/bluera-knowledge/data",
         "CONFIG_PATH": ".bluera/bluera-knowledge/config.json"
       }

package/CHANGELOG.md

@@ -2,6 +2,38 @@
 
 All notable changes to this project will be documented in this file. See [commit-and-tag-version](https://github.com/absolute-version/commit-and-tag-version) for commit guidelines.
 
+## [0.11.5](https://github.com/blueraai/bluera-knowledge/compare/v0.10.0...v0.11.5) (2026-01-10)
+
+
+### Features
+
+* add file logging to background worker for visibility ([6d7a751](https://github.com/blueraai/bluera-knowledge/commit/6d7a751de59a566c34b03b434c772ecde3770b2c))
+* **analysis:** add custom language extensibility framework with ZIL adapter ([c4dc526](https://github.com/blueraai/bluera-knowledge/commit/c4dc526467c70dbc3fb28e7e5d7620a90cc3bf95))
+* require env vars with no defaults (fail fast) ([b404cd6](https://github.com/blueraai/bluera-knowledge/commit/b404cd60374e0a7c5ace89f1ef0235bfc5c799fa))
+* **sync:** add git-committable store definitions with sync command ([5cfa925](https://github.com/blueraai/bluera-knowledge/commit/5cfa92580397f193fda75ea61197fb4c9d9d4b0a))
+
+
+### Bug Fixes
+
+* **crawl:** handle Claude CLI structured_output wrapper in intelligent crawl ([54ea74b](https://github.com/blueraai/bluera-knowledge/commit/54ea74bca6d4b7263ef11a8290416e0d66b8d37f))
+* **test:** add timeout to flaky search test ([5848b76](https://github.com/blueraai/bluera-knowledge/commit/5848b7648a547510fc2333f283ae835a6ca9efef))
+
+## [0.11.4](https://github.com/blueraai/bluera-knowledge/compare/v0.10.0...v0.11.4) (2026-01-10)
+
+
+### Features
+
+* add file logging to background worker for visibility ([6d7a751](https://github.com/blueraai/bluera-knowledge/commit/6d7a751de59a566c34b03b434c772ecde3770b2c))
+* **analysis:** add custom language extensibility framework with ZIL adapter ([c4dc526](https://github.com/blueraai/bluera-knowledge/commit/c4dc526467c70dbc3fb28e7e5d7620a90cc3bf95))
+* require env vars with no defaults (fail fast) ([b404cd6](https://github.com/blueraai/bluera-knowledge/commit/b404cd60374e0a7c5ace89f1ef0235bfc5c799fa))
+* **sync:** add git-committable store definitions with sync command ([5cfa925](https://github.com/blueraai/bluera-knowledge/commit/5cfa92580397f193fda75ea61197fb4c9d9d4b0a))
+
+
+### Bug Fixes
+
+* **crawl:** handle Claude CLI structured_output wrapper in intelligent crawl ([54ea74b](https://github.com/blueraai/bluera-knowledge/commit/54ea74bca6d4b7263ef11a8290416e0d66b8d37f))
+* **test:** add timeout to flaky search test ([5848b76](https://github.com/blueraai/bluera-knowledge/commit/5848b7648a547510fc2333f283ae835a6ca9efef))
+
 ## [0.11.3](https://github.com/blueraai/bluera-knowledge/compare/v0.10.0...v0.11.3) (2026-01-10)
 
 

package/dist/{chunk-OLKG5576.js → chunk-AHS2EILR.js}

@@ -6,7 +6,7 @@ import {
   createServices,
   createStoreId,
   summarizePayload
-} from "./chunk-B3TR6OBU.js";
+} from "./chunk-UB3L33JF.js";
 
 // src/mcp/server.ts
 import { Server } from "@modelcontextprotocol/sdk/server/index.js";
@@ -2096,4 +2096,4 @@ export {
   createMCPServer,
   runMCPServer
 };
-//# sourceMappingURL=chunk-OLKG5576.js.map
+//# sourceMappingURL=chunk-AHS2EILR.js.map

package/dist/{chunk-SLLKH3VQ.js → chunk-TTV7P7HG.js}

@@ -3,7 +3,7 @@ import {
   createLogger,
   summarizePayload,
   truncateForLog
-} from "./chunk-B3TR6OBU.js";
+} from "./chunk-UB3L33JF.js";
 
 // src/crawl/intelligent-crawler.ts
 import { EventEmitter } from "events";
@@ -801,4 +801,4 @@ var IntelligentCrawler = class extends EventEmitter {
 export {
   IntelligentCrawler
 };
-//# sourceMappingURL=chunk-SLLKH3VQ.js.map
+//# sourceMappingURL=chunk-TTV7P7HG.js.map

package/dist/{chunk-B3TR6OBU.js → chunk-UB3L33JF.js}

@@ -4449,6 +4449,7 @@ async function destroyServices(services) {
 export {
   AdapterRegistry,
   createLogger,
+  shutdownLogger,
   summarizePayload,
   truncateForLog,
   PythonBridge,
@@ -4465,4 +4466,4 @@ export {
   createServices,
   destroyServices
 };
-//# sourceMappingURL=chunk-B3TR6OBU.js.map
+//# sourceMappingURL=chunk-UB3L33JF.js.map

package/dist/index.js

@@ -6,10 +6,10 @@ import {
   isRepoStoreDefinition,
   isWebStoreDefinition,
   runMCPServer
-} from "./chunk-OLKG5576.js";
+} from "./chunk-AHS2EILR.js";
 import {
   IntelligentCrawler
-} from "./chunk-SLLKH3VQ.js";
+} from "./chunk-TTV7P7HG.js";
 import {
   ASTParser,
   AdapterRegistry,
@@ -22,7 +22,7 @@ import {
   err,
   extractRepoName,
   ok
-} from "./chunk-B3TR6OBU.js";
+} from "./chunk-UB3L33JF.js";
 import "./chunk-6FHWC36B.js";
 
 // src/index.ts

package/dist/mcp/server.js

@@ -1,8 +1,8 @@
 import {
   createMCPServer,
   runMCPServer
-} from "../chunk-OLKG5576.js";
-import "../chunk-B3TR6OBU.js";
+} from "../chunk-AHS2EILR.js";
+import "../chunk-UB3L33JF.js";
 import "../chunk-6FHWC36B.js";
 export {
   createMCPServer,

package/dist/workers/background-worker-cli.js

@@ -1,17 +1,20 @@
 #!/usr/bin/env node
 import {
   IntelligentCrawler
-} from "../chunk-SLLKH3VQ.js";
+} from "../chunk-TTV7P7HG.js";
 import {
   JobService,
   createDocumentId,
+  createLogger,
   createServices,
-  createStoreId
-} from "../chunk-B3TR6OBU.js";
+  createStoreId,
+  shutdownLogger
+} from "../chunk-UB3L33JF.js";
 import "../chunk-6FHWC36B.js";
 
 // src/workers/background-worker.ts
 import { createHash } from "crypto";
+var logger = createLogger("background-worker");
 function calculateIndexProgress(current, total, scale = 100) {
   if (total === 0) return 0;
   return current / total * scale;
@@ -33,6 +36,7 @@ var BackgroundWorker = class {
       throw new Error(`Job ${jobId} not found`);
     }
     try {
+      logger.info({ jobId, type: job.type }, "Starting job execution");
       this.jobService.updateJob(jobId, {
         status: "running",
         message: `Starting ${job.type} operation...`,
@@ -59,6 +63,10 @@ var BackgroundWorker = class {
         details: { completedAt: (/* @__PURE__ */ new Date()).toISOString() }
       });
     } catch (error) {
+      logger.error(
+        { jobId, error: error instanceof Error ? error.message : String(error) },
+        "Job failed"
+      );
       const errorDetails = {
         completedAt: (/* @__PURE__ */ new Date()).toISOString()
       };
@@ -268,12 +276,13 @@ function buildPidFilePath(jobsDir, jobId) {
 }
 
 // src/workers/background-worker-cli.ts
+var logger2 = createLogger("background-worker-cli");
 async function main() {
   const jobId = process.argv[2];
   const dataDir = process.env["BLUERA_DATA_DIR"];
   if (jobId === void 0 || jobId === "") {
-    console.error("Error: Job ID required");
-    console.error("Usage: background-worker-cli <job-id>");
+    logger2.error("Job ID required. Usage: background-worker-cli <job-id>");
+    await shutdownLogger();
     process.exit(1);
   }
   const jobService = new JobService(dataDir);
@@ -286,22 +295,27 @@ async function main() {
   try {
     writePidFile(pidFile, process.pid);
   } catch (error) {
-    console.error(error instanceof Error ? error.message : String(error));
+    logger2.error(
+      { error: error instanceof Error ? error.message : String(error) },
+      "Failed to write PID file"
+    );
+    await shutdownLogger();
     process.exit(1);
   }
   process.on("SIGTERM", () => {
-    console.log(`[${jobId}] Received SIGTERM, cancelling job...`);
+    logger2.info({ jobId }, "Received SIGTERM, cancelling job");
     jobService.updateJob(jobId, {
       status: "cancelled",
       message: "Job cancelled by user"
     });
     const deleteResult = deletePidFile(pidFile, "sigterm");
     if (!deleteResult.success && deleteResult.error !== void 0) {
-      console.error(
-        `Warning: Could not remove PID file during SIGTERM: ${deleteResult.error.message}`
+      logger2.warn(
+        { jobId, error: deleteResult.error.message },
+        "Could not remove PID file during SIGTERM"
       );
     }
-    process.exit(0);
+    void shutdownLogger().finally(() => process.exit(0));
   });
   const worker = new BackgroundWorker(
     jobService,
@@ -314,25 +328,36 @@ async function main() {
     await worker.executeJob(jobId);
     const successCleanup = deletePidFile(pidFile, "success");
     if (!successCleanup.success && successCleanup.error !== void 0) {
-      console.error(
-        `Warning: Could not remove PID file after success: ${successCleanup.error.message}`
+      logger2.warn(
+        { jobId, error: successCleanup.error.message },
+        "Could not remove PID file after success"
       );
     }
-    console.log(`[${jobId}] Job completed successfully`);
+    logger2.info({ jobId }, "Job completed successfully");
+    await shutdownLogger();
     process.exit(0);
   } catch (error) {
-    console.error(`[${jobId}] Job failed:`, error);
+    logger2.error(
+      { jobId, error: error instanceof Error ? error.message : String(error) },
+      "Job failed"
+    );
     const failureCleanup = deletePidFile(pidFile, "failure");
     if (!failureCleanup.success && failureCleanup.error !== void 0) {
-      console.error(
-        `Warning: Could not remove PID file after failure: ${failureCleanup.error.message}`
+      logger2.warn(
+        { jobId, error: failureCleanup.error.message },
+        "Could not remove PID file after failure"
       );
     }
+    await shutdownLogger();
     process.exit(1);
   }
 }
-main().catch((error) => {
-  console.error("Fatal error in background worker:", error);
+main().catch(async (error) => {
+  logger2.error(
+    { error: error instanceof Error ? error.message : String(error) },
+    "Fatal error in background worker"
+  );
+  await shutdownLogger();
   process.exit(1);
 });
 //# sourceMappingURL=background-worker-cli.js.map

package/dist/workers/background-worker-cli.js.map

@@ -1 +1 @@
-{"version":3,"sources":["../../src/workers/background-worker.ts","../../src/workers/pid-file.ts","../../src/workers/background-worker-cli.ts"],"sourcesContent":["import { createHash } from 'node:crypto';\nimport { IntelligentCrawler, type CrawlProgress } from '../crawl/intelligent-crawler.js';\nimport { IndexService } from '../services/index.service.js';\nimport { JobService } from '../services/job.service.js';\nimport { StoreService } from '../services/store.service.js';\nimport { createStoreId, createDocumentId } from '../types/brands.js';\nimport type { EmbeddingEngine } from '../db/embeddings.js';\nimport type { LanceStore } from '../db/lance.js';\nimport type { Document } from '../types/document.js';\nimport type { Job } from '../types/job.js';\n\n/**\n * Calculate index progress as a percentage, handling division by zero.\n * @param current - Current number of items processed\n * @param total - Total number of items (may be 0)\n * @param scale - Scale factor for progress (default 100 for 0-100%)\n * @returns Progress value, or 0 if total is 0\n */\nexport function calculateIndexProgress(\n  current: number,\n  total: number,\n  scale: number = 100\n): number {\n  if (total === 0) return 0;\n  return (current / total) * scale;\n}\n\nexport class BackgroundWorker {\n  constructor(\n    private readonly jobService: JobService,\n    private readonly storeService: StoreService,\n    private readonly indexService: IndexService,\n    private readonly lanceStore: LanceStore,\n    private readonly embeddingEngine: EmbeddingEngine\n  ) {}\n\n  /**\n   * Execute a job based on its type\n   */\n  async executeJob(jobId: string): Promise<void> {\n    const job = this.jobService.getJob(jobId);\n\n    if (!job) {\n      throw new Error(`Job ${jobId} not found`);\n    }\n\n    try {\n      // Update to running status\n      this.jobService.updateJob(jobId, {\n        status: 'running',\n        message: `Starting ${job.type} operation...`,\n        progress: 0,\n        details: { startedAt: new Date().toISOString() },\n      });\n\n      // Execute based on job type\n      switch (job.type) {\n        case 'clone':\n          await this.executeCloneJob(job);\n          break;\n        case 'index':\n          await this.executeIndexJob(job);\n          break;\n        case 'crawl':\n          await this.executeCrawlJob(job);\n          break;\n        default:\n          throw new Error(`Unknown job type: ${String(job.type)}`);\n      }\n\n      // Mark as completed\n      this.jobService.updateJob(jobId, {\n        status: 'completed',\n        progress: 100,\n        message: `${job.type} operation completed successfully`,\n        details: { completedAt: new Date().toISOString() },\n      });\n    } catch (error) {\n      // Mark as failed\n      const errorDetails: Record<string, unknown> = {\n        completedAt: new Date().toISOString(),\n      };\n      if (error instanceof Error && error.stack !== undefined) {\n        errorDetails['error'] = error.stack;\n      } else {\n        errorDetails['error'] = String(error);\n      }\n      this.jobService.updateJob(jobId, {\n        status: 'failed',\n        message: error instanceof Error ? error.message : 'Unknown error',\n        details: errorDetails,\n      });\n      throw error;\n    }\n  }\n\n  /**\n   * Execute a clone job (git clone + initial indexing)\n   */\n  private async executeCloneJob(job: Job): Promise<void> {\n    const { storeId } = job.details;\n\n    if (storeId === undefined || typeof storeId !== 'string') {\n      throw new Error('Store ID required for clone job');\n    }\n\n    // Get the store\n    const store = await this.storeService.get(createStoreId(storeId));\n    if (!store) {\n      throw new Error(`Store ${storeId} not found`);\n    }\n\n    // Clone is already done by the time the job is created\n    // (happens in StoreService.create), so we just need to index\n\n    // Update progress - cloning considered done (30%)\n    this.jobService.updateJob(job.id, {\n      status: 'running',\n      message: 'Repository cloned, starting indexing...',\n      progress: 30,\n    });\n\n    // Index the repository with progress updates\n    const result = await this.indexService.indexStore(\n      store,\n      (event: { type: string; current: number; total: number; message: string }) => {\n        // Check if job was cancelled\n        const currentJob = this.jobService.getJob(job.id);\n        if (currentJob?.status === 'cancelled') {\n          throw new Error('Job cancelled by user');\n        }\n\n        // Indexing is 70% of total progress (30-100%)\n        const indexProgress = calculateIndexProgress(event.current, event.total, 70);\n        const totalProgress = 30 + indexProgress;\n\n        this.jobService.updateJob(job.id, {\n          message: `Indexed ${String(event.current)}/${String(event.total)} files`,\n          progress: Math.min(99, totalProgress), // Cap at 99 until fully complete\n          details: {\n            filesProcessed: event.current,\n            totalFiles: event.total,\n          },\n        });\n      }\n    );\n\n    if (!result.success) {\n      throw result.error;\n    }\n  }\n\n  /**\n   * Execute an index job (re-indexing existing store)\n   */\n  private async executeIndexJob(job: Job): Promise<void> {\n    const { storeId } = job.details;\n\n    if (storeId === undefined || typeof storeId !== 'string') {\n      throw new Error('Store ID required for index job');\n    }\n\n    // Get the store\n    const store = await this.storeService.getByIdOrName(createStoreId(storeId));\n    if (!store) {\n      throw new Error(`Store ${storeId} not found`);\n    }\n\n    // Index with progress updates\n    const result = await this.indexService.indexStore(\n      store,\n      (event: { type: string; current: number; total: number; message: string }) => {\n        // Check if job was cancelled\n        const currentJob = this.jobService.getJob(job.id);\n        if (currentJob?.status === 'cancelled') {\n          throw new Error('Job cancelled by user');\n        }\n\n        const progress = calculateIndexProgress(event.current, event.total);\n\n        this.jobService.updateJob(job.id, {\n          message: `Indexed ${String(event.current)}/${String(event.total)} files`,\n          progress: Math.min(99, progress), // Cap at 99 until fully complete\n          details: {\n            filesProcessed: event.current,\n            totalFiles: event.total,\n          },\n        });\n      }\n    );\n\n    if (!result.success) {\n      throw result.error;\n    }\n  }\n\n  /**\n   * Execute a crawl job (web crawling + indexing)\n   */\n  private async executeCrawlJob(job: Job): Promise<void> {\n    const { storeId, url, crawlInstruction, extractInstruction, maxPages, simple, useHeadless } =\n      job.details;\n\n    if (storeId === undefined || typeof storeId !== 'string') {\n      throw new Error('Store ID required for crawl job');\n    }\n    if (url === undefined || typeof url !== 'string') {\n      throw new Error('URL required for crawl job');\n    }\n\n    // Get the store\n    const store = await this.storeService.get(createStoreId(storeId));\n    if (store?.type !== 'web') {\n      throw new Error(`Web store ${storeId} not found`);\n    }\n\n    const resolvedMaxPages = typeof maxPages === 'number' ? maxPages : 50;\n    const crawler = new IntelligentCrawler();\n\n    // Listen for progress events\n    crawler.on('progress', (progress: CrawlProgress) => {\n      // Check if job was cancelled - just return early, for-await loop will throw and finally will cleanup\n      const currentJob = this.jobService.getJob(job.id);\n      if (currentJob?.status === 'cancelled') {\n        return;\n      }\n\n      // Crawling is 80% of total progress (0-80%)\n      const crawlProgress = (progress.pagesVisited / resolvedMaxPages) * 80;\n\n      this.jobService.updateJob(job.id, {\n        message:\n          progress.message ??\n          `Crawling page ${String(progress.pagesVisited)}/${String(resolvedMaxPages)}`,\n        progress: Math.min(80, crawlProgress),\n        details: { pagesCrawled: progress.pagesVisited },\n      });\n    });\n\n    try {\n      await this.lanceStore.initialize(store.id);\n      const docs: Document[] = [];\n\n      // Build crawl options, only including defined values\n      const crawlOptions: {\n        maxPages: number;\n        simple: boolean;\n        useHeadless: boolean;\n        crawlInstruction?: string;\n        extractInstruction?: string;\n      } = {\n        maxPages: resolvedMaxPages,\n        simple: simple ?? false,\n        useHeadless: useHeadless ?? true, // Default to headless for reliability\n      };\n      if (crawlInstruction !== undefined) {\n        crawlOptions.crawlInstruction = crawlInstruction;\n      }\n      if (extractInstruction !== undefined) {\n        crawlOptions.extractInstruction = extractInstruction;\n      }\n\n      // Crawl pages using IntelligentCrawler\n      for await (const result of crawler.crawl(url, crawlOptions)) {\n        // Check cancellation between pages\n        const currentJob = this.jobService.getJob(job.id);\n        if (currentJob?.status === 'cancelled') {\n          throw new Error('Job cancelled by user');\n        }\n\n        // Embed and index the content (use extracted if available, otherwise markdown)\n        const contentToEmbed = result.extracted ?? result.markdown;\n        const vector = await this.embeddingEngine.embed(contentToEmbed);\n\n        docs.push({\n          id: createDocumentId(`${store.id}-${createHash('md5').update(result.url).digest('hex')}`),\n          content: contentToEmbed,\n          vector,\n          metadata: {\n            type: 'web',\n            storeId: store.id,\n            url: result.url,\n            title: result.title,\n            extracted: result.extracted !== undefined,\n            depth: result.depth,\n            indexedAt: new Date(),\n          },\n        });\n      }\n\n      // Index all documents (remaining 20%)\n      if (docs.length > 0) {\n        this.jobService.updateJob(job.id, {\n          message: 'Indexing crawled documents...',\n          progress: 85,\n        });\n\n        await this.lanceStore.addDocuments(store.id, docs);\n        // Create FTS index for full-text search\n        await this.lanceStore.createFtsIndex(store.id);\n      }\n\n      this.jobService.updateJob(job.id, {\n        message: `Crawled and indexed ${String(docs.length)} pages`,\n        progress: 100,\n        details: { pagesCrawled: docs.length },\n      });\n    } finally {\n      await crawler.stop();\n    }\n  }\n}\n","import fs from 'fs';\nimport path from 'path';\n\n/**\n * Result of a PID file delete operation.\n * Delete operations are best-effort and should not throw.\n */\nexport interface PidFileResult {\n  success: boolean;\n  error?: Error;\n}\n\n/**\n * Context for PID file deletion - indicates when the delete is happening.\n * Used for logging/debugging purposes.\n */\nexport type PidFileDeleteContext = 'sigterm' | 'success' | 'failure';\n\n/**\n * Write PID file - CRITICAL operation that must succeed.\n *\n * If the PID file cannot be written, the job cannot be cancelled through\n * the job management system. This is a critical failure and the job\n * should not proceed.\n *\n * @param pidFile - Absolute path to the PID file\n * @param pid - Process ID to write\n * @throws Error if PID file cannot be written\n */\nexport function writePidFile(pidFile: string, pid: number): void {\n  try {\n    fs.writeFileSync(pidFile, pid.toString(), 'utf-8');\n  } catch (error) {\n    const message = error instanceof Error ? error.message : String(error);\n    throw new Error(\n      `CRITICAL: Failed to write PID file ${pidFile}. ` +\n        `Job cannot be cancelled without PID file. ` +\n        `Original error: ${message}`\n    );\n  }\n}\n\n/**\n * Delete PID file - best-effort cleanup during shutdown.\n *\n * This operation should NEVER throw. During process shutdown (SIGTERM,\n * job success, job failure), failing to delete a PID file should not\n * prevent the process from exiting cleanly.\n *\n * Stale PID files are cleaned up by JobService.cleanupOldJobs().\n *\n * @param pidFile - Absolute path to the PID file\n * @param _context - Context indicating when the delete is happening (for future logging)\n * @returns Result indicating success or failure with error details\n */\nexport function deletePidFile(pidFile: string, _context: PidFileDeleteContext): PidFileResult {\n  try {\n    fs.unlinkSync(pidFile);\n    return { success: true };\n  } catch (error) {\n    // ENOENT = file doesn't exist - that's success (nothing to delete)\n    if (error instanceof Error && 'code' in error && error.code === 'ENOENT') {\n      return { success: true };\n    }\n    // Any other error = failure (permission denied, etc.)\n    return {\n      success: false,\n      error: error instanceof Error ? error : new Error(String(error)),\n    };\n  }\n}\n\n/**\n * Build the path to a PID file for a given job.\n *\n * @param jobsDir - Directory where job files are stored\n * @param jobId - Job identifier\n * @returns Absolute path to the PID file\n */\nexport function buildPidFilePath(jobsDir: string, jobId: string): string {\n  return path.join(jobsDir, `${jobId}.pid`);\n}\n","#!/usr/bin/env node\nimport { BackgroundWorker } from './background-worker.js';\nimport { writePidFile, deletePidFile, buildPidFilePath } from './pid-file.js';\nimport { createServices } from '../services/index.js';\nimport { JobService } from '../services/job.service.js';\n\n/**\n * Background worker CLI entry point\n *\n * Usage: background-worker-cli <job-id>\n *\n * This process runs detached from the parent and executes a single job.\n */\n\nasync function main(): Promise<void> {\n  const jobId = process.argv[2];\n  const dataDir = process.env['BLUERA_DATA_DIR'];\n\n  if (jobId === undefined || jobId === '') {\n    console.error('Error: Job ID 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error.message : String(error) },\n        'Job failed'\n      );\n\n      // Mark as failed\n      const errorDetails: Record<string, unknown> = {\n        completedAt: new Date().toISOString(),\n      };\n      if (error instanceof Error && error.stack !== undefined) {\n        errorDetails['error'] = error.stack;\n      } else {\n        errorDetails['error'] = String(error);\n      }\n      this.jobService.updateJob(jobId, {\n        status: 'failed',\n        message: error instanceof Error ? error.message : 'Unknown error',\n        details: errorDetails,\n      });\n      throw error;\n    }\n  }\n\n  /**\n   * Execute a clone job (git clone + initial indexing)\n   */\n  private async executeCloneJob(job: Job): Promise<void> {\n    const { storeId } = job.details;\n\n    if (storeId === undefined || typeof storeId !== 'string') {\n      throw new Error('Store ID required for clone job');\n    }\n\n    // Get the store\n    const store = await this.storeService.get(createStoreId(storeId));\n    if (!store) {\n      throw new Error(`Store ${storeId} not found`);\n    }\n\n    // Clone is already done by the time the job is created\n    // (happens in StoreService.create), so we just need to index\n\n    // Update progress - cloning considered done (30%)\n    this.jobService.updateJob(job.id, {\n      status: 'running',\n      message: 'Repository cloned, starting indexing...',\n      progress: 30,\n    });\n\n    // Index the repository with progress updates\n    const result = await this.indexService.indexStore(\n      store,\n      (event: { type: string; current: number; total: number; message: string }) => {\n        // Check if job was cancelled\n        const currentJob = this.jobService.getJob(job.id);\n        if (currentJob?.status === 'cancelled') {\n          throw new Error('Job cancelled by user');\n        }\n\n        // Indexing is 70% of total progress (30-100%)\n        const indexProgress = calculateIndexProgress(event.current, event.total, 70);\n        const totalProgress = 30 + indexProgress;\n\n        this.jobService.updateJob(job.id, {\n          message: `Indexed ${String(event.current)}/${String(event.total)} files`,\n          progress: Math.min(99, totalProgress), // Cap at 99 until fully complete\n          details: {\n            filesProcessed: event.current,\n            totalFiles: event.total,\n          },\n        });\n      }\n    );\n\n    if (!result.success) {\n      throw result.error;\n    }\n  }\n\n  /**\n   * Execute an index job (re-indexing existing store)\n   */\n  private async executeIndexJob(job: Job): Promise<void> {\n    const { storeId } = job.details;\n\n    if (storeId === undefined || typeof storeId !== 'string') {\n      throw new Error('Store ID required for index job');\n    }\n\n    // Get the store\n    const store = await this.storeService.getByIdOrName(createStoreId(storeId));\n    if (!store) {\n      throw new Error(`Store ${storeId} not found`);\n    }\n\n    // Index with progress updates\n    const result = await this.indexService.indexStore(\n      store,\n      (event: { type: string; current: number; total: number; message: string }) => {\n        // Check if job was cancelled\n        const currentJob = this.jobService.getJob(job.id);\n        if (currentJob?.status === 'cancelled') {\n          throw new Error('Job cancelled by user');\n        }\n\n        const progress = calculateIndexProgress(event.current, event.total);\n\n        this.jobService.updateJob(job.id, {\n          message: `Indexed ${String(event.current)}/${String(event.total)} files`,\n          progress: Math.min(99, progress), // Cap at 99 until fully complete\n          details: {\n            filesProcessed: event.current,\n            totalFiles: event.total,\n          },\n        });\n      }\n    );\n\n    if (!result.success) {\n      throw result.error;\n    }\n  }\n\n  /**\n   * Execute a crawl job (web crawling + indexing)\n   */\n  private async executeCrawlJob(job: Job): Promise<void> {\n    const { storeId, url, crawlInstruction, extractInstruction, maxPages, simple, useHeadless } =\n      job.details;\n\n    if (storeId === undefined || typeof storeId !== 'string') {\n      throw new Error('Store ID required for crawl job');\n    }\n    if (url === undefined || typeof url !== 'string') {\n      throw new Error('URL required for crawl job');\n    }\n\n    // Get the store\n    const store = await this.storeService.get(createStoreId(storeId));\n    if (store?.type !== 'web') {\n      throw new Error(`Web store ${storeId} not found`);\n    }\n\n    const resolvedMaxPages = typeof maxPages === 'number' ? maxPages : 50;\n    const crawler = new IntelligentCrawler();\n\n    // Listen for progress events\n    crawler.on('progress', (progress: CrawlProgress) => {\n      // Check if job was cancelled - just return early, for-await loop will throw and finally will cleanup\n      const currentJob = this.jobService.getJob(job.id);\n      if (currentJob?.status === 'cancelled') {\n        return;\n      }\n\n      // Crawling is 80% of total progress (0-80%)\n      const crawlProgress = (progress.pagesVisited / resolvedMaxPages) * 80;\n\n      this.jobService.updateJob(job.id, {\n        message:\n          progress.message ??\n          `Crawling page ${String(progress.pagesVisited)}/${String(resolvedMaxPages)}`,\n        progress: Math.min(80, crawlProgress),\n        details: { pagesCrawled: progress.pagesVisited },\n      });\n    });\n\n    try {\n      await this.lanceStore.initialize(store.id);\n      const docs: Document[] = [];\n\n      // Build crawl options, only including defined values\n      const crawlOptions: {\n        maxPages: number;\n        simple: boolean;\n        useHeadless: boolean;\n        crawlInstruction?: string;\n        extractInstruction?: string;\n      } = {\n        maxPages: resolvedMaxPages,\n        simple: simple ?? false,\n        useHeadless: useHeadless ?? true, // Default to headless for reliability\n      };\n      if (crawlInstruction !== undefined) {\n        crawlOptions.crawlInstruction = crawlInstruction;\n      }\n      if (extractInstruction !== undefined) {\n        crawlOptions.extractInstruction = extractInstruction;\n      }\n\n      // Crawl pages using IntelligentCrawler\n      for await (const result of crawler.crawl(url, crawlOptions)) {\n        // Check cancellation between pages\n        const currentJob = this.jobService.getJob(job.id);\n        if (currentJob?.status === 'cancelled') {\n          throw new Error('Job cancelled by user');\n        }\n\n        // Embed and index the content (use extracted if available, otherwise markdown)\n        const contentToEmbed = result.extracted ?? result.markdown;\n        const vector = await this.embeddingEngine.embed(contentToEmbed);\n\n        docs.push({\n          id: createDocumentId(`${store.id}-${createHash('md5').update(result.url).digest('hex')}`),\n          content: contentToEmbed,\n          vector,\n          metadata: {\n            type: 'web',\n            storeId: store.id,\n            url: result.url,\n            title: result.title,\n            extracted: result.extracted !== undefined,\n            depth: result.depth,\n            indexedAt: new Date(),\n          },\n        });\n      }\n\n      // Index all documents (remaining 20%)\n      if (docs.length > 0) {\n        this.jobService.updateJob(job.id, {\n          message: 'Indexing crawled documents...',\n          progress: 85,\n        });\n\n        await this.lanceStore.addDocuments(store.id, docs);\n        // Create FTS index for full-text search\n        await this.lanceStore.createFtsIndex(store.id);\n      }\n\n      this.jobService.updateJob(job.id, {\n        message: `Crawled and indexed ${String(docs.length)} pages`,\n        progress: 100,\n        details: { pagesCrawled: docs.length },\n      });\n    } finally {\n      await crawler.stop();\n    }\n  }\n}\n","import fs from 'fs';\nimport path from 'path';\n\n/**\n * Result of a PID file delete operation.\n * Delete operations are best-effort and should not throw.\n */\nexport interface PidFileResult {\n  success: boolean;\n  error?: Error;\n}\n\n/**\n * Context for PID file deletion - indicates when the delete is happening.\n * Used for logging/debugging purposes.\n */\nexport type PidFileDeleteContext = 'sigterm' | 'success' | 'failure';\n\n/**\n * Write PID file - CRITICAL operation that must succeed.\n *\n * If the PID file cannot be written, the job cannot be cancelled through\n * the job management system. This is a critical failure and the job\n * should not proceed.\n *\n * @param pidFile - Absolute path to the PID file\n * @param pid - Process ID to write\n * @throws Error if PID file cannot be written\n */\nexport function writePidFile(pidFile: string, pid: number): void {\n  try {\n    fs.writeFileSync(pidFile, pid.toString(), 'utf-8');\n  } catch (error) {\n    const message = error instanceof Error ? error.message : String(error);\n    throw new Error(\n      `CRITICAL: Failed to write PID file ${pidFile}. ` +\n        `Job cannot be cancelled without PID file. ` +\n        `Original error: ${message}`\n    );\n  }\n}\n\n/**\n * Delete PID file - best-effort cleanup during shutdown.\n *\n * This operation should NEVER throw. During process shutdown (SIGTERM,\n * job success, job failure), failing to delete a PID file should not\n * prevent the process from exiting cleanly.\n *\n * Stale PID files are cleaned up by JobService.cleanupOldJobs().\n *\n * @param pidFile - Absolute path to the PID file\n * @param _context - Context indicating when the delete is happening (for future logging)\n * @returns Result indicating success or failure with error details\n */\nexport function deletePidFile(pidFile: string, _context: PidFileDeleteContext): PidFileResult {\n  try {\n    fs.unlinkSync(pidFile);\n    return { success: true };\n  } catch (error) {\n    // ENOENT = file doesn't exist - that's success (nothing to delete)\n    if (error instanceof Error && 'code' in error && error.code === 'ENOENT') {\n      return { success: true };\n    }\n    // Any other error = failure (permission denied, etc.)\n    return {\n      success: false,\n      error: error instanceof Error ? error : new Error(String(error)),\n    };\n  }\n}\n\n/**\n * Build the path to a PID file for a given job.\n *\n * @param jobsDir - Directory where job files are stored\n * @param jobId - Job identifier\n * @returns Absolute path to the PID file\n */\nexport function buildPidFilePath(jobsDir: string, jobId: string): string {\n  return path.join(jobsDir, `${jobId}.pid`);\n}\n","#!/usr/bin/env node\nimport { BackgroundWorker } from './background-worker.js';\nimport { writePidFile, deletePidFile, buildPidFilePath } from './pid-file.js';\nimport { createLogger, shutdownLogger } from '../logging/index.js';\nimport { createServices } from '../services/index.js';\nimport { JobService } from '../services/job.service.js';\n\nconst logger = createLogger('background-worker-cli');\n\n/**\n * Background worker CLI entry point\n *\n * Usage: background-worker-cli <job-id>\n *\n * This process runs detached from the parent and executes a single job.\n */\n\nasync function main(): Promise<void> {\n  const jobId = process.argv[2];\n  const dataDir = process.env['BLUERA_DATA_DIR'];\n\n  if (jobId === undefined || jobId === '') {\n    logger.error('Job ID required. Usage: background-worker-cli <job-id>');\n    await shutdownLogger();\n    process.exit(1);\n  }\n\n  // Initialize services\n  const jobService = new JobService(dataDir);\n  const services = await createServices(undefined, dataDir);\n\n  // Write PID file for job cancellation - CRITICAL: must succeed or job cannot be cancelled\n  const pidFile = buildPidFilePath(\n    jobService['jobsDir'], // Access private field for PID path\n    jobId\n  );\n\n  try {\n    writePidFile(pidFile, process.pid);\n  } catch (error) {\n    // CRITICAL: Cannot proceed without PID file - job would be uncancellable\n    logger.error(\n      { error: error instanceof Error ? error.message : String(error) },\n      'Failed to write PID file'\n    );\n    await shutdownLogger();\n    process.exit(1);\n  }\n\n  // Handle SIGTERM for graceful shutdown\n  process.on('SIGTERM', () => {\n    logger.info({ jobId }, 'Received SIGTERM, cancelling job');\n    jobService.updateJob(jobId, {\n      status: 'cancelled',\n      message: 'Job cancelled by user',\n    });\n\n    // Clean up PID file (best-effort - don't block shutdown)\n    const deleteResult = deletePidFile(pidFile, 'sigterm');\n    if (!deleteResult.success && deleteResult.error !== undefined) {\n      logger.warn(\n        { jobId, error: deleteResult.error.message },\n        'Could not remove PID file during SIGTERM'\n      );\n    }\n\n    // Flush logs before exit (best-effort, don't await in signal handler)\n    void shutdownLogger().finally(() => process.exit(0));\n  });\n\n  // Create worker and execute job\n  const worker = new BackgroundWorker(\n    jobService,\n    services.store,\n    services.index,\n    services.lance,\n    services.embeddings\n  );\n\n  try {\n    await worker.executeJob(jobId);\n\n    // Clean up PID file on success (best-effort - don't change exit code)\n    const successCleanup = deletePidFile(pidFile, 'success');\n    if (!successCleanup.success && successCleanup.error !== undefined) {\n      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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "bluera-knowledge",
-  "version": "0.11.3",
+  "version": "0.11.5",
   "description": "CLI tool for managing knowledge stores with semantic search",
   "type": "module",
   "bin": {

package/src/mcp/mcp-config.test.ts

@@ -0,0 +1,43 @@
+import { describe, it, expect } from 'vitest';
+import { readFileSync } from 'fs';
+import { join } from 'path';
+
+/**
+ * Tests to verify .mcp.json is correctly configured for project-level use.
+ * The MCP server should work when running from the project directory,
+ * not just when loaded as a Claude Code plugin.
+ */
+describe('MCP Configuration (.mcp.json)', () => {
+  const configPath = join(process.cwd(), '.mcp.json');
+  const config = JSON.parse(readFileSync(configPath, 'utf-8'));
+
+  it('does not use CLAUDE_PLUGIN_ROOT (only available in plugin mode)', () => {
+    const serverConfig = config.mcpServers['bluera-knowledge'];
+    const argsString = JSON.stringify(serverConfig.args);
+
+    // CLAUDE_PLUGIN_ROOT is only set when running as a Claude Code plugin
+    // .mcp.json is for project-level config, so it should use relative paths
+    expect(argsString).not.toContain('CLAUDE_PLUGIN_ROOT');
+  });
+
+  it('uses relative path for server entry point', () => {
+    const serverConfig = config.mcpServers['bluera-knowledge'];
+
+    // Should use ./dist/mcp/server.js or similar relative path
+    expect(serverConfig.args).toContain('./dist/mcp/server.js');
+  });
+
+  it('sets PROJECT_ROOT environment variable', () => {
+    const serverConfig = config.mcpServers['bluera-knowledge'];
+
+    // MCP server requires PROJECT_ROOT to function
+    expect(serverConfig.env).toHaveProperty('PROJECT_ROOT');
+  });
+
+  it('uses PWD for PROJECT_ROOT', () => {
+    const serverConfig = config.mcpServers['bluera-knowledge'];
+
+    // PROJECT_ROOT should be set to PWD (current working directory)
+    expect(serverConfig.env['PROJECT_ROOT']).toBe('${PWD}');
+  });
+});

package/src/workers/background-worker-cli.test.ts

@@ -0,0 +1,35 @@
+import { describe, it, expect } from 'vitest';
+import { readFileSync } from 'fs';
+import { join } from 'path';
+
+/**
+ * Tests to verify background-worker-cli.ts uses file logging instead of console.
+ * This prevents silent failures when the worker is spawned with stdio: 'ignore'.
+ */
+describe('BackgroundWorkerCLI Logging', () => {
+  const sourceFile = join(process.cwd(), 'src/workers/background-worker-cli.ts');
+  const source = readFileSync(sourceFile, 'utf-8');
+
+  it('imports createLogger from logging module', () => {
+    expect(source).toContain('createLogger');
+    expect(source).toContain("from '../logging/index.js'");
+  });
+
+  it('imports shutdownLogger for graceful exit', () => {
+    expect(source).toContain('shutdownLogger');
+  });
+
+  it('does not use console.log', () => {
+    // Filter out comments
+    const lines = source.split('\n').filter((line) => !line.trim().startsWith('//'));
+    const hasConsoleLog = lines.some((line) => /\bconsole\.log\b/.test(line));
+    expect(hasConsoleLog).toBe(false);
+  });
+
+  it('does not use console.error', () => {
+    // Filter out comments
+    const lines = source.split('\n').filter((line) => !line.trim().startsWith('//'));
+    const hasConsoleError = lines.some((line) => /\bconsole\.error\b/.test(line));
+    expect(hasConsoleError).toBe(false);
+  });
+});

package/src/workers/background-worker-cli.ts

@@ -1,9 +1,12 @@
 #!/usr/bin/env node
 import { BackgroundWorker } from './background-worker.js';
 import { writePidFile, deletePidFile, buildPidFilePath } from './pid-file.js';
+import { createLogger, shutdownLogger } from '../logging/index.js';
 import { createServices } from '../services/index.js';
 import { JobService } from '../services/job.service.js';
 
+const logger = createLogger('background-worker-cli');
+
 /**
  * Background worker CLI entry point
  *
@@ -17,8 +20,8 @@ async function main(): Promise<void> {
   const dataDir = process.env['BLUERA_DATA_DIR'];
 
   if (jobId === undefined || jobId === '') {
-    console.error('Error: Job ID required');
-    console.error('Usage: background-worker-cli <job-id>');
+    logger.error('Job ID required. Usage: background-worker-cli <job-id>');
+    await shutdownLogger();
     process.exit(1);
   }
 
@@ -36,13 +39,17 @@ async function main(): Promise<void> {
     writePidFile(pidFile, process.pid);
   } catch (error) {
     // CRITICAL: Cannot proceed without PID file - job would be uncancellable
-    console.error(error instanceof Error ? error.message : String(error));
+    logger.error(
+      { error: error instanceof Error ? error.message : String(error) },
+      'Failed to write PID file'
+    );
+    await shutdownLogger();
     process.exit(1);
   }
 
   // Handle SIGTERM for graceful shutdown
   process.on('SIGTERM', () => {
-    console.log(`[${jobId}] Received SIGTERM, cancelling job...`);
+    logger.info({ jobId }, 'Received SIGTERM, cancelling job');
     jobService.updateJob(jobId, {
       status: 'cancelled',
       message: 'Job cancelled by user',
@@ -51,12 +58,14 @@ async function main(): Promise<void> {
     // Clean up PID file (best-effort - don't block shutdown)
     const deleteResult = deletePidFile(pidFile, 'sigterm');
     if (!deleteResult.success && deleteResult.error !== undefined) {
-      console.error(
-        `Warning: Could not remove PID file during SIGTERM: ${deleteResult.error.message}`
+      logger.warn(
+        { jobId, error: deleteResult.error.message },
+        'Could not remove PID file during SIGTERM'
       );
     }
 
-    process.exit(0);
+    // Flush logs before exit (best-effort, don't await in signal handler)
+    void shutdownLogger().finally(() => process.exit(0));
   });
 
   // Create worker and execute job
@@ -74,30 +83,41 @@ async function main(): Promise<void> {
     // Clean up PID file on success (best-effort - don't change exit code)
     const successCleanup = deletePidFile(pidFile, 'success');
     if (!successCleanup.success && successCleanup.error !== undefined) {
-      console.error(
-        `Warning: Could not remove PID file after success: ${successCleanup.error.message}`
+      logger.warn(
+        { jobId, error: successCleanup.error.message },
+        'Could not remove PID file after success'
       );
     }
 
-    console.log(`[${jobId}] Job completed successfully`);
+    logger.info({ jobId }, 'Job completed successfully');
+    await shutdownLogger();
     process.exit(0);
   } catch (error) {
     // Job service already updated with failure status in BackgroundWorker
-    console.error(`[${jobId}] Job failed:`, error);
+    logger.error(
+      { jobId, error: error instanceof Error ? error.message : String(error) },
+      'Job failed'
+    );
 
     // Clean up PID file on failure (best-effort - exit code reflects job failure)
     const failureCleanup = deletePidFile(pidFile, 'failure');
     if (!failureCleanup.success && failureCleanup.error !== undefined) {
-      console.error(
-        `Warning: Could not remove PID file after failure: ${failureCleanup.error.message}`
+      logger.warn(
+        { jobId, error: failureCleanup.error.message },
+        'Could not remove PID file after failure'
       );
     }
 
+    await shutdownLogger();
     process.exit(1);
   }
 }
 
-main().catch((error: unknown) => {
-  console.error('Fatal error in background worker:', error);
+main().catch(async (error: unknown) => {
+  logger.error(
+    { error: error instanceof Error ? error.message : String(error) },
+    'Fatal error in background worker'
+  );
+  await shutdownLogger();
   process.exit(1);
 });

package/src/workers/background-worker.test.ts

@@ -191,3 +191,29 @@ describe('BackgroundWorker', () => {
     });
   });
 });
+
+/**
+ * Tests to verify background-worker.ts uses file logging for visibility.
+ * This ensures job execution is observable in log files.
+ */
+describe('BackgroundWorker Logging', () => {
+  const { readFileSync } = require('fs');
+  const source = readFileSync('src/workers/background-worker.ts', 'utf-8');
+
+  it('imports createLogger from logging module', () => {
+    expect(source).toContain('createLogger');
+    expect(source).toContain("from '../logging/index.js'");
+  });
+
+  it('logs job start with jobId and type', () => {
+    // Verify logger.info is called with job start pattern
+    expect(source).toContain('logger.info');
+    expect(source).toContain('Starting job');
+  });
+
+  it('logs job failure with error details', () => {
+    // Verify logger.error is called for failures
+    expect(source).toContain('logger.error');
+    expect(source).toContain('Job failed');
+  });
+});

package/src/workers/background-worker.ts

@@ -1,5 +1,6 @@
 import { createHash } from 'node:crypto';
 import { IntelligentCrawler, type CrawlProgress } from '../crawl/intelligent-crawler.js';
+import { createLogger } from '../logging/index.js';
 import { IndexService } from '../services/index.service.js';
 import { JobService } from '../services/job.service.js';
 import { StoreService } from '../services/store.service.js';
@@ -9,6 +10,8 @@ import type { LanceStore } from '../db/lance.js';
 import type { Document } from '../types/document.js';
 import type { Job } from '../types/job.js';
 
+const logger = createLogger('background-worker');
+
 /**
  * Calculate index progress as a percentage, handling division by zero.
  * @param current - Current number of items processed
@@ -45,6 +48,8 @@ export class BackgroundWorker {
     }
 
     try {
+      logger.info({ jobId, type: job.type }, 'Starting job execution');
+
       // Update to running status
       this.jobService.updateJob(jobId, {
         status: 'running',
@@ -76,6 +81,11 @@ export class BackgroundWorker {
         details: { completedAt: new Date().toISOString() },
       });
     } catch (error) {
+      logger.error(
+        { jobId, error: error instanceof Error ? error.message : String(error) },
+        'Job failed'
+      );
+
       // Mark as failed
       const errorDetails: Record<string, unknown> = {
         completedAt: new Date().toISOString(),