bluera-knowledge 0.9.32 → 0.9.36

package/dist/index.js

@@ -1,10 +1,10 @@
 #!/usr/bin/env node
 import {
   runMCPServer
-} from "./chunk-WT2DAEO7.js";
+} from "./chunk-Z2KKVH45.js";
 import {
   IntelligentCrawler
-} from "./chunk-RST4XGRL.js";
+} from "./chunk-DC7CGSGT.js";
 import {
   ASTParser,
   ChunkingService,
@@ -16,312 +16,238 @@ import {
   err,
   extractRepoName,
   ok
-} from "./chunk-6PBP5DVD.js";
-import "./chunk-L2YVNC63.js";
+} from "./chunk-WFNPNAAP.js";
+import "./chunk-6FHWC36B.js";
 
 // src/index.ts
 import { homedir as homedir2 } from "os";
 import { join as join4 } from "path";
 
-// src/cli/program.ts
+// src/cli/commands/crawl.ts
+import { createHash } from "crypto";
 import { Command } from "commander";
-import { readFileSync } from "fs";
-import { fileURLToPath } from "url";
-import { dirname, join } from "path";
-function getVersion() {
-  const __filename2 = fileURLToPath(import.meta.url);
-  const __dirname2 = dirname(__filename2);
-  const content = readFileSync(join(__dirname2, "../package.json"), "utf-8");
-  const pkg = JSON.parse(content);
-  return pkg.version;
-}
-var version = getVersion();
-function createProgram() {
-  const program2 = new Command();
-  program2.name("bluera-knowledge").description("CLI tool for managing knowledge stores with semantic search").version(version);
-  program2.option("-c, --config <path>", "Path to config file").option("-d, --data-dir <path>", "Data directory").option("-p, --project-root <path>", "Project root directory (for resolving relative paths)").option("-f, --format <format>", "Output format: json | table | plain", "table").option("-q, --quiet", "Suppress non-essential output").option("-v, --verbose", "Enable verbose logging");
-  return program2;
-}
-function getGlobalOptions(program2) {
-  const opts = program2.opts();
-  return {
-    config: opts.config,
-    dataDir: opts.dataDir,
-    projectRoot: opts.projectRoot,
-    format: opts.format,
-    quiet: opts.quiet,
-    verbose: opts.verbose
-  };
-}
-
-// src/cli/commands/store.ts
-import { Command as Command2 } from "commander";
-function createStoreCommand(getOptions) {
-  const store = new Command2("store").description("Manage knowledge stores (collections of indexed documents)");
-  store.command("list").description("Show all stores with their type (file/repo/web) and ID").option("-t, --type <type>", "Filter by type: file, repo, or web").action(async (options) => {
-    const globalOpts = getOptions();
-    const services = await createServices(globalOpts.config, globalOpts.dataDir);
-    try {
-      const stores = await services.store.list(options.type);
-      if (globalOpts.format === "json") {
-        console.log(JSON.stringify(stores, null, 2));
-      } else if (globalOpts.quiet === true) {
-        for (const s of stores) {
-          console.log(s.name);
+import ora from "ora";
+function createCrawlCommand(getOptions) {
+  return new Command("crawl").description("Crawl web pages with natural language control and index into store").argument("<url>", "URL to crawl").argument("<store>", "Target web store to add crawled content to").option(
+    "--crawl <instruction>",
+    'Natural language instruction for what to crawl (e.g., "all Getting Started pages")'
+  ).option(
+    "--extract <instruction>",
+    'Natural language instruction for what to extract (e.g., "extract API references")'
+  ).option("--simple", "Use simple BFS mode instead of intelligent crawling").option("--max-pages <number>", "Maximum number of pages to crawl", "50").option("--headless", "Use headless browser for JavaScript-rendered sites").action(
+    async (url, storeIdOrName, cmdOptions) => {
+      const globalOpts = getOptions();
+      const services = await createServices(globalOpts.config, globalOpts.dataDir);
+      let store;
+      let storeCreated = false;
+      const existingStore = await services.store.getByIdOrName(storeIdOrName);
+      if (!existingStore) {
+        const result = await services.store.create({
+          name: storeIdOrName,
+          type: "web",
+          url
+        });
+        if (!result.success) {
+          await destroyServices(services);
+          throw new Error(`Failed to create store: ${result.error.message}`);
         }
-      } else {
-        if (stores.length === 0) {
-          console.log("No stores found.");
-        } else {
-          console.log("\nStores:\n");
-          for (const s of stores) {
-            console.log(`  ${s.name} (${s.type}) - ${s.id}`);
-          }
-          console.log("");
+        const createdStore = result.data;
+        if (createdStore.type !== "web") {
+          throw new Error("Unexpected store type after creation");
         }
-      }
-    } finally {
-      await destroyServices(services);
-    }
-  });
-  store.command("create <name>").description("Create a new store pointing to a local path or URL").requiredOption("-t, --type <type>", "Store type: file (local dir), repo (git), web (crawled site)").requiredOption("-s, --source <path>", "Local path for file/repo stores, URL for web stores").option("-d, --description <desc>", "Optional description for the store").option("--tags <tags>", "Comma-separated tags for filtering").action(async (name, options) => {
-    const globalOpts = getOptions();
-    const services = await createServices(globalOpts.config, globalOpts.dataDir);
-    let exitCode = 0;
-    try {
-      const isUrl = options.source.startsWith("http://") || options.source.startsWith("https://");
-      const result = await services.store.create({
-        name,
-        type: options.type,
-        path: options.type === "file" || options.type === "repo" && !isUrl ? options.source : void 0,
-        url: options.type === "web" || options.type === "repo" && isUrl ? options.source : void 0,
-        description: options.description,
-        tags: options.tags?.split(",").map((t) => t.trim())
-      });
-      if (result.success) {
-        if (globalOpts.format === "json") {
-          console.log(JSON.stringify(result.data, null, 2));
-        } else {
-          console.log(`
-Created store: ${result.data.name} (${result.data.id})
-`);
+        store = createdStore;
+        storeCreated = true;
+        if (globalOpts.quiet !== true && globalOpts.format !== "json") {
+          console.log(`Created web store: ${store.name}`);
         }
+      } else if (existingStore.type !== "web") {
+        await destroyServices(services);
+        throw new Error(
+          `Store "${storeIdOrName}" exists but is not a web store (type: ${existingStore.type})`
+        );
       } else {
-        console.error(`Error: ${result.error.message}`);
-        exitCode = 1;
-      }
-    } finally {
-      await destroyServices(services);
-    }
-    if (exitCode !== 0) {
-      process.exit(exitCode);
-    }
-  });
-  store.command("info <store>").description("Show store details: ID, type, path/URL, timestamps").action(async (storeIdOrName) => {
-    const globalOpts = getOptions();
-    const services = await createServices(globalOpts.config, globalOpts.dataDir);
-    try {
-      const s = await services.store.getByIdOrName(storeIdOrName);
-      if (s === void 0) {
-        console.error(`Error: Store not found: ${storeIdOrName}`);
-        process.exit(3);
-      }
-      if (globalOpts.format === "json") {
-        console.log(JSON.stringify(s, null, 2));
-      } else {
-        console.log(`
-Store: ${s.name}`);
-        console.log(`  ID: ${s.id}`);
-        console.log(`  Type: ${s.type}`);
-        if ("path" in s) console.log(`  Path: ${s.path}`);
-        if ("url" in s && s.url !== void 0) console.log(`  URL: ${s.url}`);
-        if (s.description !== void 0) console.log(`  Description: ${s.description}`);
-        console.log(`  Created: ${s.createdAt.toISOString()}`);
-        console.log(`  Updated: ${s.updatedAt.toISOString()}`);
-        console.log("");
+        store = existingStore;
       }
-    } finally {
-      await destroyServices(services);
-    }
-  });
-  store.command("delete <store>").description("Remove store and its indexed documents from LanceDB").option("-f, --force", "Delete without confirmation prompt").option("-y, --yes", "Alias for --force").action(async (storeIdOrName, options) => {
-    const globalOpts = getOptions();
-    const services = await createServices(globalOpts.config, globalOpts.dataDir);
-    try {
-      const s = await services.store.getByIdOrName(storeIdOrName);
-      if (s === void 0) {
-        console.error(`Error: Store not found: ${storeIdOrName}`);
-        process.exit(3);
+      const maxPages = cmdOptions.maxPages !== void 0 ? parseInt(cmdOptions.maxPages) : 50;
+      const isInteractive = process.stdout.isTTY && globalOpts.quiet !== true && globalOpts.format !== "json";
+      let spinner;
+      if (isInteractive) {
+        const mode = cmdOptions.simple === true ? "simple" : "intelligent";
+        spinner = ora(`Crawling ${url} (${mode} mode)`).start();
+      } else if (globalOpts.quiet !== true && globalOpts.format !== "json") {
+        console.log(`Crawling ${url}`);
       }
-      const skipConfirmation = options.force === true || options.yes === true;
-      if (!skipConfirmation) {
-        if (!process.stdin.isTTY) {
-          console.error("Error: Use --force or -y to delete without confirmation in non-interactive mode");
-          process.exit(1);
+      const crawler = new IntelligentCrawler();
+      const webChunker = ChunkingService.forContentType("web");
+      let pagesIndexed = 0;
+      let chunksCreated = 0;
+      let exitCode = 0;
+      crawler.on("progress", (progress) => {
+        if (spinner) {
+          if (progress.type === "strategy") {
+            spinner.text = progress.message ?? "Analyzing crawl strategy...";
+          } else if (progress.type === "page") {
+            const url2 = progress.currentUrl ?? "unknown";
+            spinner.text = `Crawling ${String(progress.pagesVisited + 1)}/${String(maxPages)} - ${url2}`;
+          } else if (progress.type === "extraction") {
+            const url2 = progress.currentUrl ?? "unknown";
+            spinner.text = `Extracting from ${url2}...`;
+          } else if (progress.type === "error" && progress.message !== void 0) {
+            spinner.warn(progress.message);
+          }
         }
-        const readline = await import("readline");
-        const rl = readline.createInterface({
-          input: process.stdin,
-          output: process.stdout
-        });
-        const answer = await new Promise((resolve) => {
-          rl.question(`Delete store "${s.name}"? [y/N] `, resolve);
-        });
-        rl.close();
-        if (answer.toLowerCase() !== "y" && answer.toLowerCase() !== "yes") {
-          console.log("Cancelled.");
-          process.exit(0);
+      });
+      try {
+        await services.lance.initialize(store.id);
+        const docs = [];
+        for await (const result of crawler.crawl(url, {
+          ...cmdOptions.crawl !== void 0 && { crawlInstruction: cmdOptions.crawl },
+          ...cmdOptions.extract !== void 0 && { extractInstruction: cmdOptions.extract },
+          maxPages,
+          ...cmdOptions.simple !== void 0 && { simple: cmdOptions.simple },
+          useHeadless: cmdOptions.headless ?? false
+        })) {
+          const contentToProcess = result.extracted ?? result.markdown;
+          const chunks = webChunker.chunk(contentToProcess, `${result.url}.md`);
+          const fileType = classifyWebContentType(result.url, result.title);
+          const urlHash = createHash("md5").update(result.url).digest("hex");
+          for (const chunk of chunks) {
+            const chunkId = chunks.length > 1 ? `${store.id}-${urlHash}-${String(chunk.chunkIndex)}` : `${store.id}-${urlHash}`;
+            const vector = await services.embeddings.embed(chunk.content);
+            docs.push({
+              id: createDocumentId(chunkId),
+              content: chunk.content,
+              vector,
+              metadata: {
+                type: chunks.length > 1 ? "chunk" : "web",
+                storeId: store.id,
+                url: result.url,
+                title: result.title,
+                extracted: result.extracted !== void 0,
+                depth: result.depth,
+                indexedAt: /* @__PURE__ */ new Date(),
+                fileType,
+                chunkIndex: chunk.chunkIndex,
+                totalChunks: chunk.totalChunks,
+                sectionHeader: chunk.sectionHeader
+              }
+            });
+            chunksCreated++;
+          }
+          pagesIndexed++;
         }
-      }
-      const result = await services.store.delete(s.id);
-      if (result.success) {
-        console.log(`Deleted store: ${s.name}`);
-      } else {
-        console.error(`Error: ${result.error.message}`);
-        process.exit(1);
-      }
-    } finally {
-      await destroyServices(services);
-    }
-  });
-  return store;
-}
-
-// src/cli/commands/search.ts
-import { Command as Command3 } from "commander";
-function createSearchCommand(getOptions) {
-  const search = new Command3("search").description("Search indexed documents using vector similarity + full-text matching").argument("<query>", "Search query").option("-s, --stores <stores>", "Limit search to specific stores (comma-separated IDs or names)").option("-m, --mode <mode>", "vector (embeddings only), fts (text only), hybrid (both, default)", "hybrid").option("-n, --limit <count>", "Maximum results to return (default: 10)", "10").option("-t, --threshold <score>", "Minimum score 0-1; omit low-relevance results").option("--include-content", "Show full document content, not just preview snippet").option("--detail <level>", "Context detail: minimal, contextual, full (default: minimal)", "minimal").action(async (query, options) => {
-    const globalOpts = getOptions();
-    const services = await createServices(globalOpts.config, globalOpts.dataDir);
-    try {
-      let storeIds = (await services.store.list()).map((s) => s.id);
-      if (options.stores !== void 0) {
-        const requestedStores = options.stores.split(",").map((s) => s.trim());
-        const resolvedStores = [];
-        for (const requested of requestedStores) {
-          const store = await services.store.getByIdOrName(requested);
-          if (store !== void 0) {
-            resolvedStores.push(store.id);
-          } else {
-            console.error(`Error: Store not found: ${requested}`);
-            process.exit(3);
+        if (docs.length > 0) {
+          if (spinner) {
+            spinner.text = "Indexing documents...";
           }
+          await services.lance.addDocuments(store.id, docs);
         }
-        storeIds = resolvedStores;
-      }
-      if (storeIds.length === 0) {
-        console.error("No stores to search. Create a store first.");
-        process.exit(1);
-      }
-      for (const storeId of storeIds) {
-        await services.lance.initialize(storeId);
-      }
-      const results = await services.search.search({
-        query,
-        stores: storeIds,
-        mode: options.mode ?? "hybrid",
-        limit: parseInt(options.limit ?? "10", 10),
-        threshold: options.threshold !== void 0 ? parseFloat(options.threshold) : void 0,
-        includeContent: options.includeContent,
-        detail: options.detail ?? "minimal"
-      });
-      if (globalOpts.format === "json") {
-        console.log(JSON.stringify(results, null, 2));
-      } else if (globalOpts.quiet === true) {
-        for (const r of results.results) {
-          const path = r.metadata.path ?? r.metadata.url ?? "unknown";
-          console.log(path);
+        const crawlResult = {
+          success: true,
+          store: store.name,
+          storeCreated,
+          url,
+          pagesCrawled: pagesIndexed,
+          chunksCreated,
+          mode: cmdOptions.simple === true ? "simple" : "intelligent",
+          hadCrawlInstruction: cmdOptions.crawl !== void 0,
+          hadExtractInstruction: cmdOptions.extract !== void 0
+        };
+        if (globalOpts.format === "json") {
+          console.log(JSON.stringify(crawlResult, null, 2));
+        } else if (spinner !== void 0) {
+          spinner.succeed(
+            `Crawled ${String(pagesIndexed)} pages, indexed ${String(chunksCreated)} chunks`
+          );
+        } else if (globalOpts.quiet !== true) {
+          console.log(
+            `Crawled ${String(pagesIndexed)} pages, indexed ${String(chunksCreated)} chunks`
+          );
         }
-      } else {
-        console.log(`
-Search: "${query}"`);
-        console.log(`Mode: ${results.mode} | Detail: ${String(options.detail)} | Stores: ${String(results.stores.length)} | Results: ${String(results.totalResults)} | Time: ${String(results.timeMs)}ms
-`);
-        if (results.results.length === 0) {
-          console.log("No results found.\n");
+      } catch (error) {
+        const message = `Crawl failed: ${error instanceof Error ? error.message : String(error)}`;
+        if (spinner) {
+          spinner.fail(message);
         } else {
-          for (let i = 0; i < results.results.length; i++) {
-            const r = results.results[i];
-            if (r === void 0) continue;
-            if (r.summary) {
-              console.log(`${String(i + 1)}. [${r.score.toFixed(2)}] ${r.summary.type}: ${r.summary.name}`);
-              console.log(`   ${r.summary.location}`);
-              console.log(`   ${r.summary.purpose}`);
-              if (r.context && options.detail !== "minimal") {
-                console.log(`   Imports: ${r.context.keyImports.slice(0, 3).join(", ")}`);
-                console.log(`   Related: ${r.context.relatedConcepts.slice(0, 3).join(", ")}`);
-              }
-              console.log();
-            } else {
-              const path = r.metadata.path ?? r.metadata.url ?? "unknown";
-              console.log(`${String(i + 1)}. [${r.score.toFixed(2)}] ${path}`);
-              const preview = r.highlight ?? r.content.slice(0, 150).replace(/\n/g, " ") + (r.content.length > 150 ? "..." : "");
-              console.log(`   ${preview}
-`);
-            }
-          }
+          console.error(`Error: ${message}`);
         }
+        exitCode = 6;
+      } finally {
+        await crawler.stop();
+        await destroyServices(services);
+      }
+      if (exitCode !== 0) {
+        process.exit(exitCode);
       }
-    } finally {
-      await destroyServices(services);
     }
-  });
-  return search;
+  );
 }
 
 // src/cli/commands/index-cmd.ts
-import { Command as Command4 } from "commander";
-import ora from "ora";
+import { Command as Command2 } from "commander";
+import ora2 from "ora";
 function createIndexCommand(getOptions) {
-  const index = new Command4("index").description("Scan store files, chunk text, generate embeddings, save to LanceDB").argument("<store>", "Store ID or name").option("--force", "Re-index all files even if unchanged").action(async (storeIdOrName, _options) => {
+  const index = new Command2("index").description("Scan store files, chunk text, generate embeddings, save to LanceDB").argument("<store>", "Store ID or name").option("--force", "Re-index all files even if unchanged").action(async (storeIdOrName, _options) => {
     const globalOpts = getOptions();
     const services = await createServices(globalOpts.config, globalOpts.dataDir);
+    let exitCode = 0;
     try {
-      const store = await services.store.getByIdOrName(storeIdOrName);
-      if (store === void 0) {
-        console.error(`Error: Store not found: ${storeIdOrName}`);
-        process.exit(3);
-      }
-      const isInteractive = process.stdout.isTTY && globalOpts.quiet !== true && globalOpts.format !== "json";
-      let spinner;
-      if (isInteractive) {
-        spinner = ora(`Indexing store: ${store.name}`).start();
-      } else if (globalOpts.quiet !== true && globalOpts.format !== "json") {
-        console.log(`Indexing store: ${store.name}`);
-      }
-      await services.lance.initialize(store.id);
-      const result = await services.index.indexStore(store, (event) => {
-        if (event.type === "progress") {
-          if (spinner) {
-            spinner.text = `Indexing: ${String(event.current)}/${String(event.total)} files - ${event.message}`;
-          }
+      indexLogic: {
+        const store = await services.store.getByIdOrName(storeIdOrName);
+        if (store === void 0) {
+          console.error(`Error: Store not found: ${storeIdOrName}`);
+          exitCode = 3;
+          break indexLogic;
         }
-      });
-      if (result.success) {
-        if (globalOpts.format === "json") {
-          console.log(JSON.stringify(result.data, null, 2));
+        const isInteractive = process.stdout.isTTY && globalOpts.quiet !== true && globalOpts.format !== "json";
+        let spinner;
+        if (isInteractive) {
+          spinner = ora2(`Indexing store: ${store.name}`).start();
+        } else if (globalOpts.quiet !== true && globalOpts.format !== "json") {
+          console.log(`Indexing store: ${store.name}`);
+        }
+        await services.lance.initialize(store.id);
+        const result = await services.index.indexStore(store, (event) => {
+          if (event.type === "progress") {
+            if (spinner) {
+              spinner.text = `Indexing: ${String(event.current)}/${String(event.total)} files - ${event.message}`;
+            }
+          }
+        });
+        if (result.success) {
+          if (globalOpts.format === "json") {
+            console.log(JSON.stringify(result.data, null, 2));
+          } else {
+            const message = `Indexed ${String(result.data.documentsIndexed)} documents, ${String(result.data.chunksCreated)} chunks in ${String(result.data.timeMs)}ms`;
+            if (spinner !== void 0) {
+              spinner.succeed(message);
+            } else if (globalOpts.quiet !== true) {
+              console.log(message);
+            }
+          }
         } else {
-          const message = `Indexed ${String(result.data.documentsIndexed)} documents, ${String(result.data.chunksCreated)} chunks in ${String(result.data.timeMs)}ms`;
+          const message = `Error: ${result.error.message}`;
           if (spinner !== void 0) {
-            spinner.succeed(message);
-          } else if (globalOpts.quiet !== true) {
-            console.log(message);
+            spinner.fail(message);
+          } else {
+            console.error(message);
           }
+          exitCode = 4;
+          break indexLogic;
         }
-      } else {
-        const message = `Error: ${result.error.message}`;
-        if (spinner !== void 0) {
-          spinner.fail(message);
-        } else {
-          console.error(message);
-        }
-        process.exit(4);
       }
     } finally {
       await destroyServices(services);
     }
+    if (exitCode !== 0) {
+      process.exit(exitCode);
+    }
   });
-  index.command("watch <store>").description("Watch store directory; re-index when files change").option("--debounce <ms>", "Wait N ms after last change before re-indexing (default: 1000)", "1000").action(async (storeIdOrName, options) => {
+  index.command("watch <store>").description("Watch store directory; re-index when files change").option(
+    "--debounce <ms>",
+    "Wait N ms after last change before re-indexing (default: 1000)",
+    "1000"
+  ).action(async (storeIdOrName, options) => {
     const globalOpts = getOptions();
     const services = await createServices(globalOpts.config, globalOpts.dataDir);
     const store = await services.store.getByIdOrName(storeIdOrName);
@@ -329,7 +255,7 @@ function createIndexCommand(getOptions) {
       console.error(`Error: File/repo store not found: ${storeIdOrName}`);
       process.exit(3);
     }
-    const { WatchService } = await import("./watch.service-YAIKKDCF.js");
+    const { WatchService } = await import("./watch.service-BJV3TI3F.js");
     const watchService = new WatchService(services.index, services.lance);
     if (globalOpts.quiet !== true) {
       console.log(`Watching ${store.name} for changes...`);
@@ -350,456 +276,29 @@ function createIndexCommand(getOptions) {
   return index;
 }
 
-// src/cli/commands/serve.ts
-import { Command as Command5 } from "commander";
-import { serve } from "@hono/node-server";
+// src/cli/commands/mcp.ts
+import { Command as Command3 } from "commander";
+function createMCPCommand(getOptions) {
+  const mcp = new Command3("mcp").description("Start MCP (Model Context Protocol) server for AI agent integration").action(async () => {
+    const opts = getOptions();
+    await runMCPServer({
+      dataDir: opts.dataDir,
+      config: opts.config
+    });
+  });
+  return mcp;
+}
 
-// src/server/app.ts
-import { Hono } from "hono";
-import { cors } from "hono/cors";
-import { z } from "zod";
-var CreateStoreBodySchema = z.object({
-  name: z.string().min(1, "Store name must be a non-empty string"),
-  type: z.enum(["file", "repo", "web"]),
-  path: z.string().min(1).optional(),
-  url: z.string().min(1).optional(),
-  description: z.string().optional(),
-  tags: z.array(z.string()).optional(),
-  branch: z.string().optional(),
-  depth: z.number().int().positive().optional()
-}).refine(
-  (data) => {
-    switch (data.type) {
-      case "file":
-        return data.path !== void 0;
-      case "web":
-        return data.url !== void 0;
-      case "repo":
-        return data.path !== void 0 || data.url !== void 0;
-    }
-  },
-  { message: "Missing required field: file stores need path, web stores need url, repo stores need path or url" }
-);
-var SearchBodySchema = z.object({
-  query: z.string().min(1, "Query must be a non-empty string"),
-  detail: z.enum(["minimal", "contextual", "full"]).optional(),
-  limit: z.number().int().positive().optional(),
-  stores: z.array(z.string()).optional()
-});
-function createApp(services) {
-  const app = new Hono();
-  app.use("*", cors());
-  app.get("/health", (c) => c.json({ status: "ok" }));
-  app.get("/api/stores", async (c) => {
-    const stores = await services.store.list();
-    return c.json(stores);
-  });
-  app.post("/api/stores", async (c) => {
-    const jsonData = await c.req.json();
-    const parseResult = CreateStoreBodySchema.safeParse(jsonData);
-    if (!parseResult.success) {
-      return c.json({ error: parseResult.error.issues[0]?.message ?? "Invalid request body" }, 400);
-    }
-    const result = await services.store.create(parseResult.data);
-    if (result.success) {
-      return c.json(result.data, 201);
-    }
-    return c.json({ error: result.error.message }, 400);
-  });
-  app.get("/api/stores/:id", async (c) => {
-    const store = await services.store.getByIdOrName(c.req.param("id"));
-    if (!store) return c.json({ error: "Not found" }, 404);
-    return c.json(store);
-  });
-  app.delete("/api/stores/:id", async (c) => {
-    const store = await services.store.getByIdOrName(c.req.param("id"));
-    if (!store) return c.json({ error: "Not found" }, 404);
-    const result = await services.store.delete(store.id);
-    if (result.success) return c.json({ deleted: true });
-    return c.json({ error: result.error.message }, 400);
-  });
-  app.post("/api/search", async (c) => {
-    const jsonData = await c.req.json();
-    const parseResult = SearchBodySchema.safeParse(jsonData);
-    if (!parseResult.success) {
-      return c.json({ error: parseResult.error.issues[0]?.message ?? "Invalid request body" }, 400);
-    }
-    const storeIds = (await services.store.list()).map((s) => s.id);
-    for (const id of storeIds) {
-      await services.lance.initialize(id);
-    }
-    const requestedStores = parseResult.data.stores !== void 0 ? parseResult.data.stores.map((s) => createStoreId(s)) : storeIds;
-    const query = {
-      query: parseResult.data.query,
-      detail: parseResult.data.detail ?? "minimal",
-      limit: parseResult.data.limit ?? 10,
-      stores: requestedStores
-    };
-    const results = await services.search.search(query);
-    return c.json(results);
-  });
-  app.post("/api/stores/:id/index", async (c) => {
-    const store = await services.store.getByIdOrName(c.req.param("id"));
-    if (!store) return c.json({ error: "Not found" }, 404);
-    await services.lance.initialize(store.id);
-    const result = await services.index.indexStore(store);
-    if (result.success) return c.json(result.data);
-    return c.json({ error: result.error.message }, 400);
-  });
-  return app;
-}
-
-// src/cli/commands/serve.ts
-function createServeCommand(getOptions) {
-  return new Command5("serve").description("Start HTTP API server for programmatic search access").option("-p, --port <port>", "Port to listen on (default: 3847)", "3847").option("--host <host>", "Bind address (default: 127.0.0.1, use 0.0.0.0 for all interfaces)", "127.0.0.1").action(async (options) => {
-    const globalOpts = getOptions();
-    const services = await createServices(globalOpts.config, globalOpts.dataDir);
-    const app = createApp(services);
-    const port = parseInt(options.port ?? "3847", 10);
-    const host = options.host ?? "127.0.0.1";
-    console.log(`Starting server on http://${host}:${String(port)}`);
-    serve({
-      fetch: app.fetch,
-      port,
-      hostname: host
-    });
-  });
-}
-
-// src/cli/commands/crawl.ts
-import { Command as Command6 } from "commander";
-import { createHash } from "crypto";
-import ora2 from "ora";
-function createCrawlCommand(getOptions) {
-  return new Command6("crawl").description("Crawl web pages with natural language control and index into store").argument("<url>", "URL to crawl").argument("<store>", "Target web store to add crawled content to").option("--crawl <instruction>", 'Natural language instruction for what to crawl (e.g., "all Getting Started pages")').option("--extract <instruction>", 'Natural language instruction for what to extract (e.g., "extract API references")').option("--simple", "Use simple BFS mode instead of intelligent crawling").option("--max-pages <number>", "Maximum number of pages to crawl", "50").option("--headless", "Use headless browser for JavaScript-rendered sites").action(async (url, storeIdOrName, cmdOptions) => {
-    const globalOpts = getOptions();
-    const services = await createServices(globalOpts.config, globalOpts.dataDir);
-    let store;
-    let storeCreated = false;
-    const existingStore = await services.store.getByIdOrName(storeIdOrName);
-    if (!existingStore) {
-      const result = await services.store.create({
-        name: storeIdOrName,
-        type: "web",
-        url
-      });
-      if (!result.success) {
-        await destroyServices(services);
-        throw new Error(`Failed to create store: ${result.error.message}`);
-      }
-      const createdStore = result.data;
-      if (createdStore.type !== "web") {
-        throw new Error("Unexpected store type after creation");
-      }
-      store = createdStore;
-      storeCreated = true;
-      if (globalOpts.quiet !== true && globalOpts.format !== "json") {
-        console.log(`Created web store: ${store.name}`);
-      }
-    } else if (existingStore.type !== "web") {
-      await destroyServices(services);
-      throw new Error(`Store "${storeIdOrName}" exists but is not a web store (type: ${existingStore.type})`);
-    } else {
-      store = existingStore;
-    }
-    const maxPages = cmdOptions.maxPages !== void 0 ? parseInt(cmdOptions.maxPages) : 50;
-    const isInteractive = process.stdout.isTTY && globalOpts.quiet !== true && globalOpts.format !== "json";
-    let spinner;
-    if (isInteractive) {
-      const mode = cmdOptions.simple === true ? "simple" : "intelligent";
-      spinner = ora2(`Crawling ${url} (${mode} mode)`).start();
-    } else if (globalOpts.quiet !== true && globalOpts.format !== "json") {
-      console.log(`Crawling ${url}`);
-    }
-    const crawler = new IntelligentCrawler();
-    const webChunker = ChunkingService.forContentType("web");
-    let pagesIndexed = 0;
-    let chunksCreated = 0;
-    let exitCode = 0;
-    crawler.on("progress", (progress) => {
-      if (spinner) {
-        if (progress.type === "strategy") {
-          spinner.text = progress.message !== void 0 ? progress.message : "Analyzing crawl strategy...";
-        } else if (progress.type === "page") {
-          const url2 = progress.currentUrl !== void 0 ? progress.currentUrl : "unknown";
-          spinner.text = `Crawling ${String(progress.pagesVisited + 1)}/${String(maxPages)} - ${url2}`;
-        } else if (progress.type === "extraction") {
-          const url2 = progress.currentUrl !== void 0 ? progress.currentUrl : "unknown";
-          spinner.text = `Extracting from ${url2}...`;
-        } else if (progress.type === "error" && progress.message !== void 0) {
-          spinner.warn(progress.message);
-        }
-      }
-    });
-    try {
-      await services.lance.initialize(store.id);
-      const docs = [];
-      for await (const result of crawler.crawl(url, {
-        ...cmdOptions.crawl !== void 0 && { crawlInstruction: cmdOptions.crawl },
-        ...cmdOptions.extract !== void 0 && { extractInstruction: cmdOptions.extract },
-        maxPages,
-        ...cmdOptions.simple !== void 0 && { simple: cmdOptions.simple },
-        useHeadless: cmdOptions.headless ?? false
-      })) {
-        const contentToProcess = result.extracted !== void 0 ? result.extracted : result.markdown;
-        const chunks = webChunker.chunk(contentToProcess, `${result.url}.md`);
-        const fileType = classifyWebContentType(result.url, result.title);
-        const urlHash = createHash("md5").update(result.url).digest("hex");
-        for (const chunk of chunks) {
-          const chunkId = chunks.length > 1 ? `${store.id}-${urlHash}-${String(chunk.chunkIndex)}` : `${store.id}-${urlHash}`;
-          const vector = await services.embeddings.embed(chunk.content);
-          docs.push({
-            id: createDocumentId(chunkId),
-            content: chunk.content,
-            vector,
-            metadata: {
-              type: chunks.length > 1 ? "chunk" : "web",
-              storeId: store.id,
-              url: result.url,
-              title: result.title,
-              extracted: result.extracted !== void 0,
-              depth: result.depth,
-              indexedAt: /* @__PURE__ */ new Date(),
-              fileType,
-              chunkIndex: chunk.chunkIndex,
-              totalChunks: chunk.totalChunks,
-              sectionHeader: chunk.sectionHeader
-            }
-          });
-          chunksCreated++;
-        }
-        pagesIndexed++;
-      }
-      if (docs.length > 0) {
-        if (spinner) {
-          spinner.text = "Indexing documents...";
-        }
-        await services.lance.addDocuments(store.id, docs);
-      }
-      const crawlResult = {
-        success: true,
-        store: store.name,
-        storeCreated,
-        url,
-        pagesCrawled: pagesIndexed,
-        chunksCreated,
-        mode: cmdOptions.simple === true ? "simple" : "intelligent",
-        hadCrawlInstruction: cmdOptions.crawl !== void 0,
-        hadExtractInstruction: cmdOptions.extract !== void 0
-      };
-      if (globalOpts.format === "json") {
-        console.log(JSON.stringify(crawlResult, null, 2));
-      } else if (spinner !== void 0) {
-        spinner.succeed(`Crawled ${String(pagesIndexed)} pages, indexed ${String(chunksCreated)} chunks`);
-      } else if (globalOpts.quiet !== true) {
-        console.log(`Crawled ${String(pagesIndexed)} pages, indexed ${String(chunksCreated)} chunks`);
-      }
-    } catch (error) {
-      const message = `Crawl failed: ${error instanceof Error ? error.message : String(error)}`;
-      if (spinner) {
-        spinner.fail(message);
-      } else {
-        console.error(`Error: ${message}`);
-      }
-      exitCode = 6;
-    } finally {
-      await crawler.stop();
-      await destroyServices(services);
-    }
-    if (exitCode !== 0) {
-      process.exit(exitCode);
-    }
-  });
-}
+// src/cli/commands/plugin-api.ts
+import { Command as Command4 } from "commander";
 
-// src/cli/commands/setup.ts
-import { Command as Command7 } from "commander";
-import { spawnSync } from "child_process";
-import { existsSync } from "fs";
-import { mkdir } from "fs/promises";
-import { join as join2 } from "path";
-import { homedir } from "os";
+// src/plugin/commands.ts
 import ora3 from "ora";
 
-// src/defaults/repos.ts
-var DEFAULT_REPOS = [
-  {
-    url: "git@github.com:ericbuess/claude-code-docs.git",
-    name: "claude-code-docs",
-    description: "Claude Code documentation",
-    tags: ["claude", "docs", "claude-code"]
-  },
-  {
-    url: "git@github.com:anthropics/claude-code.git",
-    name: "claude-code",
-    description: "Claude Code CLI tool source",
-    tags: ["claude", "cli", "anthropic"]
-  },
-  {
-    url: "git@github.com:anthropics/claude-agent-sdk-python.git",
-    name: "claude-agent-sdk-python",
-    description: "Claude Agent SDK for Python",
-    tags: ["claude", "sdk", "python", "agents"]
-  },
-  {
-    url: "git@github.com:anthropics/skills.git",
-    name: "claude-skills",
-    description: "Claude skills and capabilities",
-    tags: ["claude", "skills"]
-  },
-  {
-    url: "git@github.com:anthropics/claude-quickstarts.git",
-    name: "claude-quickstarts",
-    description: "Claude quickstart examples and tutorials",
-    tags: ["claude", "examples", "tutorials"]
-  },
-  {
-    url: "git@github.com:anthropics/claude-plugins-official.git",
-    name: "claude-plugins",
-    description: "Official Claude plugins",
-    tags: ["claude", "plugins"]
-  },
-  {
-    url: "git@github.com:anthropics/claude-agent-sdk-typescript.git",
-    name: "claude-agent-sdk-typescript",
-    description: "Claude Agent SDK for TypeScript",
-    tags: ["claude", "sdk", "typescript", "agents"]
-  },
-  {
-    url: "git@github.com:anthropics/claude-agent-sdk-demos.git",
-    name: "claude-agent-sdk-demos",
-    description: "Claude Agent SDK demo applications",
-    tags: ["claude", "sdk", "demos", "examples"]
-  }
-];
-
-// src/cli/commands/setup.ts
-var DEFAULT_REPOS_DIR = join2(homedir(), ".bluera", "bluera-knowledge", "repos");
-function createSetupCommand(getOptions) {
-  const setup = new Command7("setup").description("Quick-start with pre-configured Claude/Anthropic documentation repos");
-  setup.command("repos").description("Clone repos to ~/.bluera/bluera-knowledge/repos/, create stores, index all content").option("--repos-dir <path>", "Clone destination (default: ~/.bluera/bluera-knowledge/repos/)", DEFAULT_REPOS_DIR).option("--skip-clone", "Don't clone; assume repos already exist locally").option("--skip-index", "Clone and create stores but don't index yet").option("--only <names>", "Only process matching repos (comma-separated, partial match)").option("--list", "Print available repos without cloning/indexing").action(async (options) => {
-    const globalOpts = getOptions();
-    if (options.list === true) {
-      console.log("\nDefault repositories:\n");
-      for (const repo of DEFAULT_REPOS) {
-        console.log(`  ${repo.name}`);
-        console.log(`    URL: ${repo.url}`);
-        console.log(`    Description: ${repo.description}`);
-        console.log(`    Tags: ${repo.tags.join(", ")}`);
-        console.log("");
-      }
-      return;
-    }
-    const services = await createServices(globalOpts.config, globalOpts.dataDir);
-    try {
-      let repos = DEFAULT_REPOS;
-      if (options.only !== void 0 && options.only !== "") {
-        const onlyNames = options.only.split(",").map((n) => n.trim().toLowerCase());
-        repos = DEFAULT_REPOS.filter(
-          (r) => onlyNames.some((n) => r.name.toLowerCase().includes(n))
-        );
-        if (repos.length === 0) {
-          console.error(`No repos matched: ${options.only}`);
-          console.log("Available repos:", DEFAULT_REPOS.map((r) => r.name).join(", "));
-          process.exit(1);
-        }
-      }
-      console.log(`
-Setting up ${String(repos.length)} repositories...
-`);
-      await mkdir(options.reposDir, { recursive: true });
-      for (const repo of repos) {
-        const repoPath = join2(options.reposDir, repo.name);
-        const spinner = ora3(`Processing ${repo.name}`).start();
-        try {
-          if (options.skipClone !== true) {
-            if (existsSync(repoPath)) {
-              spinner.text = `${repo.name}: Already cloned, pulling latest...`;
-              const pullResult = spawnSync("git", ["pull", "--ff-only"], { cwd: repoPath, stdio: "pipe" });
-              if (pullResult.status !== 0) {
-                spinner.text = `${repo.name}: Pull skipped (local changes)`;
-              }
-            } else {
-              spinner.text = `${repo.name}: Cloning...`;
-              const cloneResult = spawnSync("git", ["clone", repo.url, repoPath], { stdio: "pipe" });
-              if (cloneResult.status !== 0) {
-                const errorMessage = cloneResult.stderr.length > 0 ? cloneResult.stderr.toString() : "Git clone failed";
-                throw new Error(errorMessage);
-              }
-            }
-          }
-          spinner.text = `${repo.name}: Creating store...`;
-          const existingStore = await services.store.getByIdOrName(repo.name);
-          let storeId;
-          if (existingStore) {
-            storeId = existingStore.id;
-            spinner.text = `${repo.name}: Store already exists`;
-          } else {
-            const result = await services.store.create({
-              name: repo.name,
-              type: "repo",
-              path: repoPath,
-              description: repo.description,
-              tags: repo.tags
-            });
-            if (!result.success) {
-              throw new Error(result.error instanceof Error ? result.error.message : String(result.error));
-            }
-            storeId = result.data.id;
-          }
-          if (options.skipIndex !== true) {
-            spinner.text = `${repo.name}: Indexing...`;
-            const store = await services.store.getByIdOrName(storeId);
-            if (store) {
-              await services.lance.initialize(store.id);
-              const indexResult = await services.index.indexStore(store, (event) => {
-                if (event.type === "progress") {
-                  spinner.text = `${repo.name}: Indexing ${String(event.current)}/${String(event.total)} files`;
-                }
-              });
-              if (indexResult.success) {
-                spinner.succeed(
-                  `${repo.name}: ${String(indexResult.data.documentsIndexed)} docs, ${String(indexResult.data.chunksCreated)} chunks`
-                );
-              } else {
-                throw new Error(indexResult.error instanceof Error ? indexResult.error.message : String(indexResult.error));
-              }
-            }
-          } else {
-            spinner.succeed(`${repo.name}: Ready (indexing skipped)`);
-          }
-        } catch (error) {
-          spinner.fail(`${repo.name}: ${error instanceof Error ? error.message : String(error)}`);
-        }
-      }
-      console.log('\nSetup complete! Use "bluera-knowledge search <query>" to search.\n');
-    } finally {
-      await destroyServices(services);
-    }
-  });
-  return setup;
-}
-
-// src/cli/commands/mcp.ts
-import { Command as Command8 } from "commander";
-function createMCPCommand(getOptions) {
-  const mcp = new Command8("mcp").description("Start MCP (Model Context Protocol) server for AI agent integration").action(async () => {
-    const opts = getOptions();
-    await runMCPServer({
-      dataDir: opts.dataDir,
-      config: opts.config
-    });
-  });
-  return mcp;
-}
-
-// src/cli/commands/plugin-api.ts
-import { Command as Command9 } from "commander";
-
 // src/analysis/dependency-usage-analyzer.ts
+import { existsSync } from "fs";
 import { readFile, readdir } from "fs/promises";
-import { existsSync as existsSync2 } from "fs";
-import { join as join3, extname } from "path";
+import { join, extname } from "path";
 var TEXT_EXTENSIONS = /* @__PURE__ */ new Set([
   ".ts",
   ".tsx",
@@ -861,25 +360,25 @@ var DependencyUsageAnalyzer = class {
             if (packageName !== null && declaredDeps.has(packageName)) {
               const dep = declaredDeps.get(packageName);
               if (dep !== void 0) {
-                this.incrementUsage(
-                  usageMap,
-                  packageName,
-                  filePath,
-                  dep.isDev,
-                  dep.language
-                );
+                this.incrementUsage(usageMap, packageName, filePath, dep.isDev, dep.language);
               }
             }
           }
           processedCount++;
           if (onProgress !== void 0 && processedCount % 10 === 0) {
-            onProgress(processedCount, files.length, `Analyzed ${String(processedCount)}/${String(files.length)} files`);
+            onProgress(
+              processedCount,
+              files.length,
+              `Analyzed ${String(processedCount)}/${String(files.length)} files`
+            );
           }
         } catch {
           skippedCount++;
         }
       }
-      const sortedUsages = Array.from(usageMap.values()).sort((a, b) => b.importCount - a.importCount);
+      const sortedUsages = Array.from(usageMap.values()).sort(
+        (a, b) => b.importCount - a.importCount
+      );
       return ok({
         usages: sortedUsages,
         totalFilesScanned: processedCount,
@@ -972,9 +471,18 @@ var DependencyUsageAnalyzer = class {
     try {
       const entries = await readdir(dir, { withFileTypes: true });
       for (const entry of entries) {
-        const fullPath = join3(dir, entry.name);
+        const fullPath = join(dir, entry.name);
         if (entry.isDirectory()) {
-          if (!["node_modules", ".git", "dist", "build", "coverage", "__pycache__", ".venv", "venv"].includes(entry.name)) {
+          if (![
+            "node_modules",
+            ".git",
+            "dist",
+            "build",
+            "coverage",
+            "__pycache__",
+            ".venv",
+            "venv"
+          ].includes(entry.name)) {
             files.push(...await this.scanDirectory(fullPath));
           }
         } else if (entry.isFile()) {
@@ -990,8 +498,8 @@ var DependencyUsageAnalyzer = class {
   }
   async readDeclaredDependencies(projectRoot) {
     const deps = /* @__PURE__ */ new Map();
-    const packageJsonPath = join3(projectRoot, "package.json");
-    if (existsSync2(packageJsonPath)) {
+    const packageJsonPath = join(projectRoot, "package.json");
+    if (existsSync(packageJsonPath)) {
       try {
         const content = await readFile(packageJsonPath, "utf-8");
         const parsed = JSON.parse(content);
@@ -1010,8 +518,8 @@ var DependencyUsageAnalyzer = class {
       } catch {
       }
     }
-    const reqPath = join3(projectRoot, "requirements.txt");
-    if (existsSync2(reqPath)) {
+    const reqPath = join(projectRoot, "requirements.txt");
+    if (existsSync(reqPath)) {
       try {
         const content = await readFile(reqPath, "utf-8");
         const lines = content.split("\n");
@@ -1019,7 +527,7 @@ var DependencyUsageAnalyzer = class {
           const trimmed = line.trim();
           if (trimmed === "" || trimmed.startsWith("#")) continue;
           const match = /^([a-zA-Z0-9_-]+)/.exec(trimmed);
-          if (match !== null && match[1] !== void 0) {
+          if (match?.[1] !== void 0) {
             const name = match[1].toLowerCase();
             deps.set(name, { name, isDev: false, language: "python" });
           }
@@ -1027,8 +535,8 @@ var DependencyUsageAnalyzer = class {
       } catch {
       }
     }
-    const pyprojectPath = join3(projectRoot, "pyproject.toml");
-    if (existsSync2(pyprojectPath)) {
+    const pyprojectPath = join(projectRoot, "pyproject.toml");
+    if (existsSync(pyprojectPath)) {
       try {
         const content = await readFile(pyprojectPath, "utf-8");
         const depMatches = content.matchAll(/"([a-zA-Z0-9_-]+)"/g);
@@ -1041,13 +549,13 @@ var DependencyUsageAnalyzer = class {
       } catch {
       }
     }
-    const cargoPath = join3(projectRoot, "Cargo.toml");
-    if (existsSync2(cargoPath)) {
+    const cargoPath = join(projectRoot, "Cargo.toml");
+    if (existsSync(cargoPath)) {
       try {
         const content = await readFile(cargoPath, "utf-8");
         const inDepsSection = /\[dependencies\]([\s\S]*?)(?=\n\[|$)/;
         const depsMatch = inDepsSection.exec(content);
-        if (depsMatch !== null && depsMatch[1] !== void 0) {
+        if (depsMatch?.[1] !== void 0) {
           const depsSection = depsMatch[1];
           const cratePattern = /^([a-zA-Z0-9_-]+)\s*=/gm;
           for (const match of depsSection.matchAll(cratePattern)) {
@@ -1058,7 +566,7 @@ var DependencyUsageAnalyzer = class {
         }
         const inDevDepsSection = /\[dev-dependencies\]([\s\S]*?)(?=\n\[|$)/;
         const devDepsMatch = inDevDepsSection.exec(content);
-        if (devDepsMatch !== null && devDepsMatch[1] !== void 0) {
+        if (devDepsMatch?.[1] !== void 0) {
           const devDepsSection = devDepsMatch[1];
           const cratePattern = /^([a-zA-Z0-9_-]+)\s*=/gm;
           for (const match of devDepsSection.matchAll(cratePattern)) {
@@ -1070,8 +578,8 @@ var DependencyUsageAnalyzer = class {
       } catch {
       }
     }
-    const goModPath = join3(projectRoot, "go.mod");
-    if (existsSync2(goModPath)) {
+    const goModPath = join(projectRoot, "go.mod");
+    if (existsSync(goModPath)) {
       try {
         const content = await readFile(goModPath, "utf-8");
         const requirePattern = /^\s*([a-zA-Z0-9._/-]+)\s+v[\d.]+/gm;
@@ -1257,7 +765,6 @@ var RepoUrlResolver = class {
 };
 
 // src/plugin/commands.ts
-import ora4 from "ora";
 async function handleAddRepo(args) {
   const services = await createServices(void 0, void 0, process.env["PWD"]);
   const storeName = args.name ?? extractRepoName(args.url);
@@ -1341,7 +848,7 @@ async function handleSuggest() {
   const services = await createServices(void 0, void 0, projectRoot);
   const analyzer = new DependencyUsageAnalyzer();
   const resolver = new RepoUrlResolver();
-  const spinner = ora4("Scanning source files...").start();
+  const spinner = ora3("Scanning source files...").start();
   const result = await analyzer.analyze(projectRoot, (current, total, message) => {
     spinner.text = `${message} (${String(current)}/${String(total)})`;
   });
@@ -1351,8 +858,10 @@ async function handleSuggest() {
     process.exit(1);
   }
   const { usages, totalFilesScanned, skippedFiles } = result.data;
-  console.log(`\u2714 Scanned ${String(totalFilesScanned)} files${skippedFiles > 0 ? ` (skipped ${String(skippedFiles)})` : ""}
-`);
+  console.log(
+    `\u2714 Scanned ${String(totalFilesScanned)} files${skippedFiles > 0 ? ` (skipped ${String(skippedFiles)})` : ""}
+`
+  );
   if (usages.length === 0) {
     console.log("No external dependencies found in this project.");
     console.log("\nMake sure you have a package.json or requirements.txt file.");
@@ -1369,23 +878,24 @@ async function handleSuggest() {
   console.log("Top dependencies by usage in this project:\n");
   topSuggestions.forEach((usage, i) => {
     console.log(`${String(i + 1)}. ${usage.packageName}`);
-    console.log(`   ${String(usage.importCount)} imports across ${String(usage.fileCount)} files
-`);
+    console.log(
+      `   ${String(usage.importCount)} imports across ${String(usage.fileCount)} files
+`
+    );
   });
   console.log("Searching for repository URLs...\n");
   for (const usage of topSuggestions) {
-    const repoResult = await resolver.findRepoUrl(
-      usage.packageName,
-      usage.language
-    );
+    const repoResult = await resolver.findRepoUrl(usage.packageName, usage.language);
     if (repoResult.url !== null) {
       console.log(`\u2714 ${usage.packageName}: ${repoResult.url}`);
       console.log(`  /bluera-knowledge:add-repo ${repoResult.url} --name=${usage.packageName}
 `);
     } else {
       console.log(`\u2717 ${usage.packageName}: Could not find repository URL`);
-      console.log(`  You can manually add it: /bluera-knowledge:add-repo <url> --name=${usage.packageName}
-`);
+      console.log(
+        `  You can manually add it: /bluera-knowledge:add-repo <url> --name=${usage.packageName}
+`
+      );
     }
   }
   console.log("Use the commands above to add repositories to your knowledge stores.");
@@ -1393,26 +903,627 @@ async function handleSuggest() {
 
 // src/cli/commands/plugin-api.ts
 function createAddRepoCommand(_getOptions) {
-  return new Command9("add-repo").description("Clone and index a library source repository").argument("<url>", "Git repository URL").option("--name <name>", "Store name (defaults to repo name)").option("--branch <branch>", "Git branch to clone").action(async (url, options) => {
+  return new Command4("add-repo").description("Clone and index a library source repository").argument("<url>", "Git repository URL").option("--name <name>", "Store name (defaults to repo name)").option("--branch <branch>", "Git branch to clone").action(async (url, options) => {
     await handleAddRepo({ url, ...options });
   });
 }
 function createAddFolderCommand(_getOptions) {
-  return new Command9("add-folder").description("Index a local folder of reference material").argument("<path>", "Folder path to index").option("--name <name>", "Store name (defaults to folder name)").action(async (path, options) => {
+  return new Command4("add-folder").description("Index a local folder of reference material").argument("<path>", "Folder path to index").option("--name <name>", "Store name (defaults to folder name)").action(async (path, options) => {
     await handleAddFolder({ path, ...options });
   });
 }
 function createStoresCommand(_getOptions) {
-  return new Command9("stores").description("List all indexed library stores").action(async () => {
+  return new Command4("stores").description("List all indexed library stores").action(async () => {
     await handleStores();
   });
 }
 function createSuggestCommand(_getOptions) {
-  return new Command9("suggest").description("Suggest important dependencies to add to knowledge stores").action(async () => {
+  return new Command4("suggest").description("Suggest important dependencies to add to knowledge stores").action(async () => {
     await handleSuggest();
   });
 }
 
+// src/cli/commands/search.ts
+import { Command as Command5 } from "commander";
+function createSearchCommand(getOptions) {
+  const search = new Command5("search").description("Search indexed documents using vector similarity + full-text matching").argument("<query>", "Search query").option(
+    "-s, --stores <stores>",
+    "Limit search to specific stores (comma-separated IDs or names)"
+  ).option(
+    "-m, --mode <mode>",
+    "vector (embeddings only), fts (text only), hybrid (both, default)",
+    "hybrid"
+  ).option("-n, --limit <count>", "Maximum results to return (default: 10)", "10").option("-t, --threshold <score>", "Minimum score 0-1; omit low-relevance results").option("--include-content", "Show full document content, not just preview snippet").option(
+    "--detail <level>",
+    "Context detail: minimal, contextual, full (default: minimal)",
+    "minimal"
+  ).action(
+    async (query, options) => {
+      const globalOpts = getOptions();
+      const services = await createServices(globalOpts.config, globalOpts.dataDir);
+      let exitCode = 0;
+      try {
+        let storeIds = (await services.store.list()).map((s) => s.id);
+        searchLogic: {
+          if (options.stores !== void 0) {
+            const requestedStores = options.stores.split(",").map((s) => s.trim());
+            const resolvedStores = [];
+            for (const requested of requestedStores) {
+              const store = await services.store.getByIdOrName(requested);
+              if (store !== void 0) {
+                resolvedStores.push(store.id);
+              } else {
+                console.error(`Error: Store not found: ${requested}`);
+                exitCode = 3;
+                break searchLogic;
+              }
+            }
+            storeIds = resolvedStores;
+          }
+          if (storeIds.length === 0) {
+            console.error("No stores to search. Create a store first.");
+            exitCode = 1;
+            break searchLogic;
+          }
+          for (const storeId of storeIds) {
+            await services.lance.initialize(storeId);
+          }
+          const results = await services.search.search({
+            query,
+            stores: storeIds,
+            mode: options.mode ?? "hybrid",
+            limit: parseInt(options.limit ?? "10", 10),
+            threshold: options.threshold !== void 0 ? parseFloat(options.threshold) : void 0,
+            includeContent: options.includeContent,
+            detail: options.detail ?? "minimal"
+          });
+          if (globalOpts.format === "json") {
+            console.log(JSON.stringify(results, null, 2));
+          } else if (globalOpts.quiet === true) {
+            for (const r of results.results) {
+              const path = r.metadata.path ?? r.metadata.url ?? "unknown";
+              console.log(path);
+            }
+          } else {
+            console.log(`
+Search: "${query}"`);
+            console.log(
+              `Mode: ${results.mode} | Detail: ${String(options.detail)} | Stores: ${String(results.stores.length)} | Results: ${String(results.totalResults)} | Time: ${String(results.timeMs)}ms
+`
+            );
+            if (results.results.length === 0) {
+              console.log("No results found.\n");
+            } else {
+              for (let i = 0; i < results.results.length; i++) {
+                const r = results.results[i];
+                if (r === void 0) continue;
+                if (r.summary) {
+                  console.log(
+                    `${String(i + 1)}. [${r.score.toFixed(2)}] ${r.summary.type}: ${r.summary.name}`
+                  );
+                  console.log(`   ${r.summary.location}`);
+                  console.log(`   ${r.summary.purpose}`);
+                  if (r.context && options.detail !== "minimal") {
+                    console.log(`   Imports: ${r.context.keyImports.slice(0, 3).join(", ")}`);
+                    console.log(
+                      `   Related: ${r.context.relatedConcepts.slice(0, 3).join(", ")}`
+                    );
+                  }
+                  console.log();
+                } else {
+                  const path = r.metadata.path ?? r.metadata.url ?? "unknown";
+                  console.log(`${String(i + 1)}. [${r.score.toFixed(2)}] ${path}`);
+                  const preview = r.highlight ?? r.content.slice(0, 150).replace(/\n/g, " ") + (r.content.length > 150 ? "..." : "");
+                  console.log(`   ${preview}
+`);
+                }
+              }
+            }
+          }
+        }
+      } finally {
+        await destroyServices(services);
+      }
+      if (exitCode !== 0) {
+        process.exit(exitCode);
+      }
+    }
+  );
+  return search;
+}
+
+// src/cli/commands/serve.ts
+import { serve } from "@hono/node-server";
+import { Command as Command6 } from "commander";
+
+// src/server/app.ts
+import { Hono } from "hono";
+import { cors } from "hono/cors";
+import { z } from "zod";
+var CreateStoreBodySchema = z.object({
+  name: z.string().min(1, "Store name must be a non-empty string"),
+  type: z.enum(["file", "repo", "web"]),
+  path: z.string().min(1).optional(),
+  url: z.string().min(1).optional(),
+  description: z.string().optional(),
+  tags: z.array(z.string()).optional(),
+  branch: z.string().optional(),
+  depth: z.number().int().positive().optional()
+}).refine(
+  (data) => {
+    switch (data.type) {
+      case "file":
+        return data.path !== void 0;
+      case "web":
+        return data.url !== void 0;
+      case "repo":
+        return data.path !== void 0 || data.url !== void 0;
+    }
+  },
+  {
+    message: "Missing required field: file stores need path, web stores need url, repo stores need path or url"
+  }
+);
+var SearchBodySchema = z.object({
+  query: z.string().min(1, "Query must be a non-empty string"),
+  detail: z.enum(["minimal", "contextual", "full"]).optional(),
+  limit: z.number().int().positive().optional(),
+  stores: z.array(z.string()).optional()
+});
+function createApp(services) {
+  const app = new Hono();
+  app.use("*", cors());
+  app.get("/health", (c) => c.json({ status: "ok" }));
+  app.get("/api/stores", async (c) => {
+    const stores = await services.store.list();
+    return c.json(stores);
+  });
+  app.post("/api/stores", async (c) => {
+    const jsonData = await c.req.json();
+    const parseResult = CreateStoreBodySchema.safeParse(jsonData);
+    if (!parseResult.success) {
+      return c.json({ error: parseResult.error.issues[0]?.message ?? "Invalid request body" }, 400);
+    }
+    const result = await services.store.create(parseResult.data);
+    if (result.success) {
+      return c.json(result.data, 201);
+    }
+    return c.json({ error: result.error.message }, 400);
+  });
+  app.get("/api/stores/:id", async (c) => {
+    const store = await services.store.getByIdOrName(c.req.param("id"));
+    if (!store) return c.json({ error: "Not found" }, 404);
+    return c.json(store);
+  });
+  app.delete("/api/stores/:id", async (c) => {
+    const store = await services.store.getByIdOrName(c.req.param("id"));
+    if (!store) return c.json({ error: "Not found" }, 404);
+    const result = await services.store.delete(store.id);
+    if (result.success) return c.json({ deleted: true });
+    return c.json({ error: result.error.message }, 400);
+  });
+  app.post("/api/search", async (c) => {
+    const jsonData = await c.req.json();
+    const parseResult = SearchBodySchema.safeParse(jsonData);
+    if (!parseResult.success) {
+      return c.json({ error: parseResult.error.issues[0]?.message ?? "Invalid request body" }, 400);
+    }
+    const storeIds = (await services.store.list()).map((s) => s.id);
+    for (const id of storeIds) {
+      await services.lance.initialize(id);
+    }
+    const requestedStores = parseResult.data.stores !== void 0 ? parseResult.data.stores.map((s) => createStoreId(s)) : storeIds;
+    const query = {
+      query: parseResult.data.query,
+      detail: parseResult.data.detail ?? "minimal",
+      limit: parseResult.data.limit ?? 10,
+      stores: requestedStores
+    };
+    const results = await services.search.search(query);
+    return c.json(results);
+  });
+  app.post("/api/stores/:id/index", async (c) => {
+    const store = await services.store.getByIdOrName(c.req.param("id"));
+    if (!store) return c.json({ error: "Not found" }, 404);
+    await services.lance.initialize(store.id);
+    const result = await services.index.indexStore(store);
+    if (result.success) return c.json(result.data);
+    return c.json({ error: result.error.message }, 400);
+  });
+  return app;
+}
+
+// src/cli/commands/serve.ts
+function createServeCommand(getOptions) {
+  return new Command6("serve").description("Start HTTP API server for programmatic search access").option("-p, --port <port>", "Port to listen on (default: 3847)", "3847").option(
+    "--host <host>",
+    "Bind address (default: 127.0.0.1, use 0.0.0.0 for all interfaces)",
+    "127.0.0.1"
+  ).action(async (options) => {
+    const globalOpts = getOptions();
+    const services = await createServices(globalOpts.config, globalOpts.dataDir);
+    const app = createApp(services);
+    const port = parseInt(options.port ?? "3847", 10);
+    const host = options.host ?? "127.0.0.1";
+    const shutdown = () => {
+      void (async () => {
+        await destroyServices(services);
+        process.exit(0);
+      })();
+    };
+    process.on("SIGINT", shutdown);
+    process.on("SIGTERM", shutdown);
+    console.log(`Starting server on http://${host}:${String(port)}`);
+    serve({
+      fetch: app.fetch,
+      port,
+      hostname: host
+    });
+  });
+}
+
+// src/cli/commands/setup.ts
+import { spawnSync } from "child_process";
+import { existsSync as existsSync2 } from "fs";
+import { mkdir } from "fs/promises";
+import { homedir } from "os";
+import { join as join2 } from "path";
+import { Command as Command7 } from "commander";
+import ora4 from "ora";
+
+// src/defaults/repos.ts
+var DEFAULT_REPOS = [
+  {
+    url: "git@github.com:ericbuess/claude-code-docs.git",
+    name: "claude-code-docs",
+    description: "Claude Code documentation",
+    tags: ["claude", "docs", "claude-code"]
+  },
+  {
+    url: "git@github.com:anthropics/claude-code.git",
+    name: "claude-code",
+    description: "Claude Code CLI tool source",
+    tags: ["claude", "cli", "anthropic"]
+  },
+  {
+    url: "git@github.com:anthropics/claude-agent-sdk-python.git",
+    name: "claude-agent-sdk-python",
+    description: "Claude Agent SDK for Python",
+    tags: ["claude", "sdk", "python", "agents"]
+  },
+  {
+    url: "git@github.com:anthropics/skills.git",
+    name: "claude-skills",
+    description: "Claude skills and capabilities",
+    tags: ["claude", "skills"]
+  },
+  {
+    url: "git@github.com:anthropics/claude-quickstarts.git",
+    name: "claude-quickstarts",
+    description: "Claude quickstart examples and tutorials",
+    tags: ["claude", "examples", "tutorials"]
+  },
+  {
+    url: "git@github.com:anthropics/claude-plugins-official.git",
+    name: "claude-plugins",
+    description: "Official Claude plugins",
+    tags: ["claude", "plugins"]
+  },
+  {
+    url: "git@github.com:anthropics/claude-agent-sdk-typescript.git",
+    name: "claude-agent-sdk-typescript",
+    description: "Claude Agent SDK for TypeScript",
+    tags: ["claude", "sdk", "typescript", "agents"]
+  },
+  {
+    url: "git@github.com:anthropics/claude-agent-sdk-demos.git",
+    name: "claude-agent-sdk-demos",
+    description: "Claude Agent SDK demo applications",
+    tags: ["claude", "sdk", "demos", "examples"]
+  }
+];
+
+// src/cli/commands/setup.ts
+var DEFAULT_REPOS_DIR = join2(homedir(), ".bluera", "bluera-knowledge", "repos");
+function createSetupCommand(getOptions) {
+  const setup = new Command7("setup").description(
+    "Quick-start with pre-configured Claude/Anthropic documentation repos"
+  );
+  setup.command("repos").description(
+    "Clone repos to ~/.bluera/bluera-knowledge/repos/, create stores, index all content"
+  ).option(
+    "--repos-dir <path>",
+    "Clone destination (default: ~/.bluera/bluera-knowledge/repos/)",
+    DEFAULT_REPOS_DIR
+  ).option("--skip-clone", "Don't clone; assume repos already exist locally").option("--skip-index", "Clone and create stores but don't index yet").option("--only <names>", "Only process matching repos (comma-separated, partial match)").option("--list", "Print available repos without cloning/indexing").action(
+    async (options) => {
+      const globalOpts = getOptions();
+      if (options.list === true) {
+        console.log("\nDefault repositories:\n");
+        for (const repo of DEFAULT_REPOS) {
+          console.log(`  ${repo.name}`);
+          console.log(`    URL: ${repo.url}`);
+          console.log(`    Description: ${repo.description}`);
+          console.log(`    Tags: ${repo.tags.join(", ")}`);
+          console.log("");
+        }
+        return;
+      }
+      const services = await createServices(globalOpts.config, globalOpts.dataDir);
+      try {
+        let repos = DEFAULT_REPOS;
+        if (options.only !== void 0 && options.only !== "") {
+          const onlyNames = options.only.split(",").map((n) => n.trim().toLowerCase());
+          repos = DEFAULT_REPOS.filter(
+            (r) => onlyNames.some((n) => r.name.toLowerCase().includes(n))
+          );
+          if (repos.length === 0) {
+            console.error(`No repos matched: ${options.only}`);
+            console.log("Available repos:", DEFAULT_REPOS.map((r) => r.name).join(", "));
+            process.exit(1);
+          }
+        }
+        console.log(`
+Setting up ${String(repos.length)} repositories...
+`);
+        await mkdir(options.reposDir, { recursive: true });
+        for (const repo of repos) {
+          const repoPath = join2(options.reposDir, repo.name);
+          const spinner = ora4(`Processing ${repo.name}`).start();
+          try {
+            if (options.skipClone !== true) {
+              if (existsSync2(repoPath)) {
+                spinner.text = `${repo.name}: Already cloned, pulling latest...`;
+                const pullResult = spawnSync("git", ["pull", "--ff-only"], {
+                  cwd: repoPath,
+                  stdio: "pipe"
+                });
+                if (pullResult.status !== 0) {
+                  spinner.text = `${repo.name}: Pull skipped (local changes)`;
+                }
+              } else {
+                spinner.text = `${repo.name}: Cloning...`;
+                const cloneResult = spawnSync("git", ["clone", repo.url, repoPath], {
+                  stdio: "pipe"
+                });
+                if (cloneResult.status !== 0) {
+                  const errorMessage = cloneResult.stderr.length > 0 ? cloneResult.stderr.toString() : "Git clone failed";
+                  throw new Error(errorMessage);
+                }
+              }
+            }
+            spinner.text = `${repo.name}: Creating store...`;
+            const existingStore = await services.store.getByIdOrName(repo.name);
+            let storeId;
+            if (existingStore) {
+              storeId = existingStore.id;
+              spinner.text = `${repo.name}: Store already exists`;
+            } else {
+              const result = await services.store.create({
+                name: repo.name,
+                type: "repo",
+                path: repoPath,
+                description: repo.description,
+                tags: repo.tags
+              });
+              if (!result.success) {
+                throw new Error(
+                  result.error instanceof Error ? result.error.message : String(result.error)
+                );
+              }
+              storeId = result.data.id;
+            }
+            if (options.skipIndex !== true) {
+              spinner.text = `${repo.name}: Indexing...`;
+              const store = await services.store.getByIdOrName(storeId);
+              if (store) {
+                await services.lance.initialize(store.id);
+                const indexResult = await services.index.indexStore(store, (event) => {
+                  if (event.type === "progress") {
+                    spinner.text = `${repo.name}: Indexing ${String(event.current)}/${String(event.total)} files`;
+                  }
+                });
+                if (indexResult.success) {
+                  spinner.succeed(
+                    `${repo.name}: ${String(indexResult.data.documentsIndexed)} docs, ${String(indexResult.data.chunksCreated)} chunks`
+                  );
+                } else {
+                  throw new Error(
+                    indexResult.error instanceof Error ? indexResult.error.message : String(indexResult.error)
+                  );
+                }
+              }
+            } else {
+              spinner.succeed(`${repo.name}: Ready (indexing skipped)`);
+            }
+          } catch (error) {
+            spinner.fail(
+              `${repo.name}: ${error instanceof Error ? error.message : String(error)}`
+            );
+          }
+        }
+        console.log('\nSetup complete! Use "bluera-knowledge search <query>" to search.\n');
+      } finally {
+        await destroyServices(services);
+      }
+    }
+  );
+  return setup;
+}
+
+// src/cli/commands/store.ts
+import { Command as Command8 } from "commander";
+function createStoreCommand(getOptions) {
+  const store = new Command8("store").description(
+    "Manage knowledge stores (collections of indexed documents)"
+  );
+  store.command("list").description("Show all stores with their type (file/repo/web) and ID").option("-t, --type <type>", "Filter by type: file, repo, or web").action(async (options) => {
+    const globalOpts = getOptions();
+    const services = await createServices(globalOpts.config, globalOpts.dataDir);
+    try {
+      const stores = await services.store.list(options.type);
+      if (globalOpts.format === "json") {
+        console.log(JSON.stringify(stores, null, 2));
+      } else if (globalOpts.quiet === true) {
+        for (const s of stores) {
+          console.log(s.name);
+        }
+      } else {
+        if (stores.length === 0) {
+          console.log("No stores found.");
+        } else {
+          console.log("\nStores:\n");
+          for (const s of stores) {
+            console.log(`  ${s.name} (${s.type}) - ${s.id}`);
+          }
+          console.log("");
+        }
+      }
+    } finally {
+      await destroyServices(services);
+    }
+  });
+  store.command("create <name>").description("Create a new store pointing to a local path or URL").requiredOption(
+    "-t, --type <type>",
+    "Store type: file (local dir), repo (git), web (crawled site)"
+  ).requiredOption("-s, --source <path>", "Local path for file/repo stores, URL for web stores").option("-d, --description <desc>", "Optional description for the store").option("--tags <tags>", "Comma-separated tags for filtering").action(
+    async (name, options) => {
+      const globalOpts = getOptions();
+      const services = await createServices(globalOpts.config, globalOpts.dataDir);
+      let exitCode = 0;
+      try {
+        const isUrl = options.source.startsWith("http://") || options.source.startsWith("https://");
+        const result = await services.store.create({
+          name,
+          type: options.type,
+          path: options.type === "file" || options.type === "repo" && !isUrl ? options.source : void 0,
+          url: options.type === "web" || options.type === "repo" && isUrl ? options.source : void 0,
+          description: options.description,
+          tags: options.tags?.split(",").map((t) => t.trim())
+        });
+        if (result.success) {
+          if (globalOpts.format === "json") {
+            console.log(JSON.stringify(result.data, null, 2));
+          } else {
+            console.log(`
+Created store: ${result.data.name} (${result.data.id})
+`);
+          }
+        } else {
+          console.error(`Error: ${result.error.message}`);
+          exitCode = 1;
+        }
+      } finally {
+        await destroyServices(services);
+      }
+      if (exitCode !== 0) {
+        process.exit(exitCode);
+      }
+    }
+  );
+  store.command("info <store>").description("Show store details: ID, type, path/URL, timestamps").action(async (storeIdOrName) => {
+    const globalOpts = getOptions();
+    const services = await createServices(globalOpts.config, globalOpts.dataDir);
+    try {
+      const s = await services.store.getByIdOrName(storeIdOrName);
+      if (s === void 0) {
+        console.error(`Error: Store not found: ${storeIdOrName}`);
+        process.exit(3);
+      }
+      if (globalOpts.format === "json") {
+        console.log(JSON.stringify(s, null, 2));
+      } else {
+        console.log(`
+Store: ${s.name}`);
+        console.log(`  ID: ${s.id}`);
+        console.log(`  Type: ${s.type}`);
+        if ("path" in s) console.log(`  Path: ${s.path}`);
+        if ("url" in s && s.url !== void 0) console.log(`  URL: ${s.url}`);
+        if (s.description !== void 0) console.log(`  Description: ${s.description}`);
+        console.log(`  Created: ${s.createdAt.toISOString()}`);
+        console.log(`  Updated: ${s.updatedAt.toISOString()}`);
+        console.log("");
+      }
+    } finally {
+      await destroyServices(services);
+    }
+  });
+  store.command("delete <store>").description("Remove store and its indexed documents from LanceDB").option("-f, --force", "Delete without confirmation prompt").option("-y, --yes", "Alias for --force").action(async (storeIdOrName, options) => {
+    const globalOpts = getOptions();
+    const services = await createServices(globalOpts.config, globalOpts.dataDir);
+    try {
+      const s = await services.store.getByIdOrName(storeIdOrName);
+      if (s === void 0) {
+        console.error(`Error: Store not found: ${storeIdOrName}`);
+        process.exit(3);
+      }
+      const skipConfirmation = options.force === true || options.yes === true;
+      if (!skipConfirmation) {
+        if (!process.stdin.isTTY) {
+          console.error(
+            "Error: Use --force or -y to delete without confirmation in non-interactive mode"
+          );
+          process.exit(1);
+        }
+        const readline = await import("readline");
+        const rl = readline.createInterface({
+          input: process.stdin,
+          output: process.stdout
+        });
+        const answer = await new Promise((resolve) => {
+          rl.question(`Delete store "${s.name}"? [y/N] `, resolve);
+        });
+        rl.close();
+        if (answer.toLowerCase() !== "y" && answer.toLowerCase() !== "yes") {
+          console.log("Cancelled.");
+          process.exit(0);
+        }
+      }
+      const result = await services.store.delete(s.id);
+      if (result.success) {
+        console.log(`Deleted store: ${s.name}`);
+      } else {
+        console.error(`Error: ${result.error.message}`);
+        process.exit(1);
+      }
+    } finally {
+      await destroyServices(services);
+    }
+  });
+  return store;
+}
+
+// src/cli/program.ts
+import { readFileSync } from "fs";
+import { dirname, join as join3 } from "path";
+import { fileURLToPath } from "url";
+import { Command as Command9 } from "commander";
+function getVersion() {
+  const __filename2 = fileURLToPath(import.meta.url);
+  const __dirname2 = dirname(__filename2);
+  const content = readFileSync(join3(__dirname2, "../package.json"), "utf-8");
+  const pkg = JSON.parse(content);
+  return pkg.version;
+}
+var version = getVersion();
+function createProgram() {
+  const program2 = new Command9();
+  program2.name("bluera-knowledge").description("CLI tool for managing knowledge stores with semantic search").version(version);
+  program2.option("-c, --config <path>", "Path to config file").option("-d, --data-dir <path>", "Data directory").option("-p, --project-root <path>", "Project root directory (for resolving relative paths)").option("-f, --format <format>", "Output format: json | table | plain", "table").option("-q, --quiet", "Suppress non-essential output").option("-v, --verbose", "Enable verbose logging");
+  return program2;
+}
+function getGlobalOptions(program2) {
+  const opts = program2.opts();
+  return {
+    config: opts.config,
+    dataDir: opts.dataDir,
+    projectRoot: opts.projectRoot,
+    format: opts.format,
+    quiet: opts.quiet,
+    verbose: opts.verbose
+  };
+}
+
 // src/index.ts
 var DEFAULT_DATA_DIR = join4(homedir2(), ".bluera", "bluera-knowledge", "data");
 var DEFAULT_CONFIG = join4(homedir2(), ".bluera", "bluera-knowledge", "config.json");
@@ -1425,7 +1536,7 @@ function formatCommandHelp(cmd, indent = "") {
     const req = a.required;
     return req ? `<${a.name()}>` : `[${a.name()}]`;
   }).join(" ");
-  lines.push(`${indent}${name}${args ? " " + args : ""}`);
+  lines.push(`${indent}${name}${args ? ` ${args}` : ""}`);
   if (desc) {
     lines.push(`${indent}  ${desc}`);
   }
@@ -1436,7 +1547,7 @@ function formatCommandHelp(cmd, indent = "") {
   const subcommands = cmd.commands.filter((c) => c.name() !== "help");
   for (const sub of subcommands) {
     lines.push("");
-    lines.push(...formatCommandHelp(sub, indent + "  "));
+    lines.push(...formatCommandHelp(sub, `${indent}  `));
   }
   return lines;
 }
@@ -1447,7 +1558,9 @@ function printFullHelp(program2) {
   console.log(`  config      ${DEFAULT_CONFIG}`);
   console.log(`  repos       ${DEFAULT_REPOS_DIR2}`);
   console.log("\nGlobal options:");
-  const globalOpts = program2.options.filter((o) => o.flags !== "-h, --help" && o.flags !== "-V, --version");
+  const globalOpts = program2.options.filter(
+    (o) => o.flags !== "-h, --help" && o.flags !== "-V, --version"
+  );
   for (const opt of globalOpts) {
     console.log(`  ${opt.flags.padEnd(28)} ${opt.description}`);
   }