brainbank 0.7.0 → 0.8.0

package/dist/cli.js

@@ -1,314 +1,392 @@
 #!/usr/bin/env node
 import {
-  BrainBank
-} from "./chunk-DI3H6JVZ.js";
-import "./chunk-B77KABWH.js";
+  SUPPORTED_EXTENSIONS,
+  args,
+  c,
+  createBrain,
+  findDocsPlugin,
+  getConfig,
+  getFlag,
+  hasFlag,
+  isIgnoredDir,
+  isIgnoredFile,
+  loadConfig,
+  printResults,
+  registerConfigCollections,
+  stripFlags
+} from "./chunk-JRVYSTMP.js";
 import {
-  code
-} from "./chunk-FGL32LUJ.js";
-import {
-  git
-} from "./chunk-JRSKWF6K.js";
-import {
-  docs
-} from "./chunk-VQ27YUHH.js";
-import "./chunk-YOLKSYWK.js";
-import "./chunk-U2Q2XGPZ.js";
+  DEFAULT_PORT,
+  isServerRunning,
+  removePid
+} from "./chunk-OLDHLOMT.js";
+import "./chunk-E3J37GDA.js";
+import "./chunk-7T2ZCZQA.js";
 import {
   __name
 } from "./chunk-7QVYU63E.js";
 
-// src/cli/utils.ts
-var c = {
-  green: /* @__PURE__ */ __name((s) => `\x1B[32m${s}\x1B[0m`, "green"),
-  red: /* @__PURE__ */ __name((s) => `\x1B[31m${s}\x1B[0m`, "red"),
-  yellow: /* @__PURE__ */ __name((s) => `\x1B[33m${s}\x1B[0m`, "yellow"),
-  cyan: /* @__PURE__ */ __name((s) => `\x1B[36m${s}\x1B[0m`, "cyan"),
-  dim: /* @__PURE__ */ __name((s) => `\x1B[2m${s}\x1B[0m`, "dim"),
-  bold: /* @__PURE__ */ __name((s) => `\x1B[1m${s}\x1B[0m`, "bold"),
-  magenta: /* @__PURE__ */ __name((s) => `\x1B[35m${s}\x1B[0m`, "magenta")
-};
-var args = process.argv.slice(2);
-function getFlag(name) {
-  const idx = args.indexOf(`--${name}`);
-  return idx >= 0 ? args[idx + 1] : void 0;
-}
-__name(getFlag, "getFlag");
-function hasFlag(name) {
-  return args.includes(`--${name}`);
-}
-__name(hasFlag, "hasFlag");
-var VALUE_FLAGS = /* @__PURE__ */ new Set([
-  "repo",
-  "depth",
-  "collection",
-  "pattern",
-  "context",
-  "name",
-  "keep",
-  "reranker",
-  "only",
-  "docs",
-  "ignore",
-  "meta",
-  "k",
-  "mode",
-  "limit"
-]);
-function stripFlags(argv) {
-  const result = [];
-  for (let i = 0; i < argv.length; i++) {
-    if (argv[i].startsWith("--")) {
-      const name = argv[i].slice(2);
-      if (VALUE_FLAGS.has(name)) i++;
-      continue;
-    }
-    result.push(argv[i]);
-  }
-  return result;
-}
-__name(stripFlags, "stripFlags");
-function printResults(results) {
-  if (results.length === 0) {
-    console.log(c.yellow("  No results found."));
-    return;
-  }
-  for (const r of results) {
-    const score = Math.round(r.score * 100);
-    if (r.type === "code") {
-      const m = r.metadata;
-      console.log(
-        `${c.green(`[CODE ${score}%]`)} ${c.bold(r.filePath)} \u2014 ${m.name || m.chunkType} ${c.dim(`L${m.startLine}-${m.endLine}`)}`
-      );
-      console.log(c.dim(r.content.split("\n").slice(0, 5).join("\n")));
-      console.log("");
-    } else if (r.type === "commit") {
-      const m = r.metadata;
-      console.log(
-        `${c.cyan(`[COMMIT ${score}%]`)} ${c.bold(m.shortHash)} ${r.content} ${c.dim(`(${m.author})`)}`
-      );
-      if (m.files?.length) console.log(c.dim(`  Files: ${m.files.slice(0, 4).join(", ")}`));
-      console.log("");
-    } else if (r.type === "document") {
-      const ctx = r.context ? ` \u2014 ${c.dim(r.context)}` : "";
-      console.log(
-        `${c.magenta(`[DOC ${score}%]`)} ${c.bold(r.filePath)} [${r.metadata.collection}]${ctx}`
-      );
-      console.log(c.dim(r.content.split("\n").slice(0, 4).join("\n")));
-      console.log("");
-    }
-  }
-}
-__name(printResults, "printResults");
-
-// src/cli/commands/index-cmd.ts
+// src/cli/commands/index.ts
+import * as fs2 from "fs";
 import * as path2 from "path";
 
-// src/cli/factory.ts
-import * as path from "path";
+// src/cli/commands/scan.ts
 import * as fs from "fs";
-var CONFIG_NAMES = ["config.json", "config.ts", "config.js", "config.mjs"];
-var INDEXER_EXTENSIONS = [".ts", ".js", ".mjs"];
-var NOT_LOADED = /* @__PURE__ */ Symbol("not-loaded");
-var _configCache = NOT_LOADED;
-var _folderPluginsCache = NOT_LOADED;
-async function loadConfig() {
-  if (_configCache !== NOT_LOADED) return _configCache;
-  const repoPath = getFlag("repo") ?? ".";
-  const brainbankDir = path.resolve(repoPath, ".brainbank");
-  for (const name of CONFIG_NAMES) {
-    const configPath = path.join(brainbankDir, name);
-    if (!fs.existsSync(configPath)) continue;
+import * as path from "path";
+import { execSync } from "child_process";
+function scanRepo(repoPath) {
+  const resolved = path.resolve(repoPath);
+  const gitSubdirs = scanGitSubdirs(resolved);
+  return {
+    repoPath: resolved,
+    modules: scanModules(resolved, gitSubdirs),
+    config: scanConfig(resolved),
+    db: scanDb(resolved),
+    gitSubdirs
+  };
+}
+__name(scanRepo, "scanRepo");
+function scanModules(repoPath, gitSubdirs) {
+  return [
+    scanCodeModule(repoPath),
+    scanGitModule(repoPath, gitSubdirs),
+    scanDocsModule(repoPath)
+  ];
+}
+__name(scanModules, "scanModules");
+function scanCodeModule(repoPath) {
+  const byLanguage = /* @__PURE__ */ new Map();
+  let total = 0;
+  function walk(dir) {
+    let entries;
     try {
-      if (name === "config.json") {
-        const raw = fs.readFileSync(configPath, "utf-8");
-        _configCache = JSON.parse(raw);
-      } else {
-        const mod = await import(configPath);
-        _configCache = mod.default ?? mod;
+      entries = fs.readdirSync(dir, { withFileTypes: true });
+    } catch {
+      return;
+    }
+    for (const entry of entries) {
+      const fullPath = path.join(dir, entry.name);
+      const isDir = entry.isDirectory() || entry.isSymbolicLink() && (() => {
+        try {
+          return fs.statSync(fullPath).isDirectory();
+        } catch {
+          return false;
+        }
+      })();
+      if (isDir) {
+        if (isIgnoredDir(entry.name)) continue;
+        walk(fullPath);
+      } else if (entry.isFile()) {
+        if (isIgnoredFile(entry.name)) continue;
+        const ext = path.extname(entry.name).toLowerCase();
+        const lang = SUPPORTED_EXTENSIONS[ext];
+        if (!lang) continue;
+        byLanguage.set(lang, (byLanguage.get(lang) ?? 0) + 1);
+        total++;
       }
-      return _configCache;
-    } catch (err) {
-      console.error(c.red(`Error loading .brainbank/${name}: ${err.message}`));
-      process.exit(1);
     }
   }
-  _configCache = null;
-  return null;
+  __name(walk, "walk");
+  walk(repoPath);
+  if (total === 0) {
+    return { name: "code", available: false, summary: "no supported source files found", icon: "\u{1F4C1}", checked: false, disabled: "nothing to index" };
+  }
+  const langCount = byLanguage.size;
+  const sorted = [...byLanguage.entries()].sort((a, b) => b[1] - a[1]);
+  const maxShow = 7;
+  const shown = sorted.slice(0, maxShow);
+  const remaining = sorted.length - maxShow;
+  const details = [];
+  for (let i = 0; i < shown.length; i++) {
+    const [lang, count] = shown[i];
+    const isLast = i === shown.length - 1 && remaining <= 0;
+    const prefix = isLast ? "\u2514\u2500\u2500" : "\u251C\u2500\u2500";
+    details.push(`${prefix} ${lang.padEnd(14)} ${count} files`);
+  }
+  if (remaining > 0) {
+    details.push(`\u2514\u2500\u2500 ...and ${remaining} more`);
+  }
+  return {
+    name: "code",
+    available: true,
+    summary: `${total} files (${langCount} language${langCount > 1 ? "s" : ""})`,
+    icon: "\u{1F4C1}",
+    checked: true,
+    details
+  };
 }
-__name(loadConfig, "loadConfig");
-async function getConfig() {
-  return loadConfig();
+__name(scanCodeModule, "scanCodeModule");
+function scanGitModule(repoPath, gitSubdirs) {
+  const stats = scanGitStats(repoPath, gitSubdirs);
+  if (!stats) {
+    return { name: "git", available: false, summary: "no .git directory found", icon: "\u{1F4DC}", checked: false, disabled: "not a git repo" };
+  }
+  const details = [];
+  if (stats.lastMessage) {
+    details.push(`Last: ${stats.lastMessage} (${stats.lastDate})`);
+  }
+  return {
+    name: "git",
+    available: true,
+    summary: `${stats.commitCount.toLocaleString()} commits`,
+    icon: "\u{1F4DC}",
+    checked: true,
+    details
+  };
 }
-__name(getConfig, "getConfig");
-async function resolveEmbeddingKey(key) {
-  const { resolveEmbedding } = await import("./resolve-CUJWY6HP.js");
-  return resolveEmbedding(key);
+__name(scanGitModule, "scanGitModule");
+function scanDocsModule(repoPath) {
+  const collections = scanDocsCollections(repoPath);
+  if (collections.length === 0) {
+    return { name: "docs", available: false, summary: "no documents found", icon: "\u{1F4C4}", checked: false, disabled: "no .md/.mdx files" };
+  }
+  const totalFiles = collections.reduce((s, d) => s + d.fileCount, 0);
+  const details = collections.map((d, i) => {
+    const isLast = i === collections.length - 1;
+    const prefix = isLast ? "\u2514\u2500\u2500" : "\u251C\u2500\u2500";
+    return `${prefix} ${d.name.padEnd(10)} \u2192 ${d.path} (${d.fileCount} files)`;
+  });
+  return {
+    name: "docs",
+    available: true,
+    summary: `${collections.length} collection${collections.length > 1 ? "s" : ""} (${totalFiles} files)`,
+    icon: "\u{1F4C4}",
+    checked: true,
+    details
+  };
 }
-__name(resolveEmbeddingKey, "resolveEmbeddingKey");
-async function discoverFolderPlugins() {
-  if (_folderPluginsCache !== NOT_LOADED) return _folderPluginsCache;
-  const repoPath = getFlag("repo") ?? ".";
-  const indexersDir = path.resolve(repoPath, ".brainbank", "indexers");
-  if (!fs.existsSync(indexersDir)) {
-    _folderPluginsCache = [];
-    return [];
+__name(scanDocsModule, "scanDocsModule");
+function scanGitStats(repoPath, gitSubdirs) {
+  if (fs.existsSync(path.join(repoPath, ".git"))) {
+    return gitStats(repoPath);
   }
-  const files = fs.readdirSync(indexersDir).filter((f) => INDEXER_EXTENSIONS.some((ext) => f.endsWith(ext))).sort();
-  const indexers = [];
-  for (const file of files) {
-    const filePath = path.join(indexersDir, file);
-    try {
-      const mod = await import(filePath);
-      const indexer = mod.default ?? mod;
-      if (indexer && typeof indexer === "object" && indexer.name) {
-        indexers.push(indexer);
-      } else {
-        console.error(c.yellow(`\u26A0 ${file}: must export a default Plugin with a 'name' property, skipping`));
+  if (gitSubdirs.length === 0) return null;
+  let totalCommits = 0;
+  let latestMessage = "";
+  let latestDate = "";
+  for (const sub of gitSubdirs) {
+    const stats = gitStats(path.join(repoPath, sub.name));
+    if (stats) {
+      totalCommits += stats.commitCount;
+      if (!latestMessage) {
+        latestMessage = stats.lastMessage;
+        latestDate = stats.lastDate;
       }
-    } catch (err) {
-      console.error(c.red(`Error loading indexer ${file}: ${err.message}`));
     }
   }
-  _folderPluginsCache = indexers;
-  return indexers;
+  return totalCommits > 0 ? { commitCount: totalCommits, lastMessage: latestMessage, lastDate: latestDate } : null;
 }
-__name(discoverFolderPlugins, "discoverFolderPlugins");
-function detectGitSubdirs(parentPath) {
+__name(scanGitStats, "scanGitStats");
+function gitStats(dir) {
   try {
-    const entries = fs.readdirSync(parentPath, { withFileTypes: true });
-    return entries.filter(
-      (e) => e.isDirectory() && !e.name.startsWith(".") && !e.name.startsWith("node_modules") && fs.existsSync(path.join(parentPath, e.name, ".git"))
-    ).map((e) => ({ name: e.name, path: path.join(parentPath, e.name) }));
+    const count = parseInt(execSync("git rev-list --count HEAD", { cwd: dir, encoding: "utf-8" }).trim(), 10);
+    const log = execSync('git log -1 --format="%s|%ar"', { cwd: dir, encoding: "utf-8" }).trim();
+    const [lastMessage, lastDate] = log.split("|");
+    return { commitCount: count, lastMessage: lastMessage ?? "", lastDate: lastDate ?? "" };
   } catch {
-    return [];
+    return null;
   }
 }
-__name(detectGitSubdirs, "detectGitSubdirs");
-async function createBrain(repoPath) {
-  const rp = repoPath ?? getFlag("repo") ?? ".";
-  const config = await loadConfig();
-  const folderIndexers = await discoverFolderPlugins();
-  const brainOpts = { repoPath: rp, ...config?.brainbank ?? {} };
-  if (config?.maxFileSize) brainOpts.maxFileSize = config.maxFileSize;
-  await setupProviders(brainOpts, config);
-  const brain = new BrainBank(brainOpts);
-  const builtins = config?.plugins ?? config?.builtins ?? ["code", "git", "docs"];
-  await registerBuiltins(brain, rp, builtins, config);
-  for (const indexer of folderIndexers) brain.use(indexer);
-  if (config?.indexers) {
-    for (const indexer of config.indexers) brain.use(indexer);
-  }
-  return brain;
-}
-__name(createBrain, "createBrain");
-async function setupProviders(brainOpts, config) {
-  const rerankerFlag = getFlag("reranker") ?? config?.reranker;
-  if (rerankerFlag === "qwen3") {
-    const { Qwen3Reranker } = await import("./qwen3-reranker-3MHEENT5.js");
-    brainOpts.reranker = new Qwen3Reranker();
-  }
-  const embFlag = getFlag("embedding") ?? config?.embedding;
-  if (embFlag) {
-    const provider = await resolveEmbeddingKey(embFlag);
-    brainOpts.embeddingProvider = provider;
-    brainOpts.embeddingDims = provider.dims;
-  }
-}
-__name(setupProviders, "setupProviders");
-async function registerBuiltins(brain, rp, builtins, config) {
-  const resolvedRp = path.resolve(rp);
-  const hasRootGit = fs.existsSync(path.join(resolvedRp, ".git"));
-  const gitSubdirs = !hasRootGit ? detectGitSubdirs(resolvedRp) : [];
-  const codeEmb = config?.code?.embedding ? await resolveEmbeddingKey(config.code.embedding) : void 0;
-  const gitEmb = config?.git?.embedding ? await resolveEmbeddingKey(config.git.embedding) : void 0;
-  const docsEmb = config?.docs?.embedding ? await resolveEmbeddingKey(config.docs.embedding) : void 0;
-  if (gitSubdirs.length > 0 && (builtins.includes("code") || builtins.includes("git"))) {
-    console.log(c.cyan(`  Multi-repo: found ${gitSubdirs.length} git repos: ${gitSubdirs.map((d) => d.name).join(", ")}`));
-    for (const sub of gitSubdirs) {
-      if (builtins.includes("code")) {
-        brain.use(code({
-          repoPath: sub.path,
-          name: `code:${sub.name}`,
-          embeddingProvider: codeEmb,
-          maxFileSize: config?.code?.maxFileSize
-        }));
+__name(gitStats, "gitStats");
+function scanDocsCollections(repoPath) {
+  const results = [];
+  const seen = /* @__PURE__ */ new Set();
+  const configPath = path.join(repoPath, ".brainbank", "config.json");
+  try {
+    if (fs.existsSync(configPath)) {
+      const config = JSON.parse(fs.readFileSync(configPath, "utf-8"));
+      const docsCfg = config?.docs;
+      const collections = docsCfg?.collections;
+      if (collections) {
+        for (const coll of collections) {
+          const absPath = path.resolve(repoPath, coll.path);
+          results.push({ name: coll.name, path: coll.path, fileCount: countDocs(absPath) });
+          seen.add(absPath);
+        }
       }
-      if (builtins.includes("git")) {
-        brain.use(git({
-          repoPath: sub.path,
-          name: `git:${sub.name}`,
-          embeddingProvider: gitEmb,
-          depth: config?.git?.depth,
-          maxDiffBytes: config?.git?.maxDiffBytes
-        }));
+    }
+  } catch {
+  }
+  const rootDocs = countDocsShallow(repoPath);
+  if (rootDocs > 0) {
+    results.push({ name: "(root)", path: ".", fileCount: rootDocs });
+  }
+  try {
+    for (const entry of fs.readdirSync(repoPath, { withFileTypes: true })) {
+      if (!entry.isDirectory()) continue;
+      if (isIgnoredDir(entry.name)) continue;
+      if (entry.name.startsWith(".")) continue;
+      const dirPath = path.join(repoPath, entry.name);
+      if (seen.has(dirPath)) continue;
+      const count = countDocs(dirPath);
+      if (count > 0) {
+        results.push({ name: entry.name, path: `./${entry.name}`, fileCount: count });
       }
     }
-  } else {
-    if (builtins.includes("code")) {
-      brain.use(code({
-        repoPath: rp,
-        embeddingProvider: codeEmb,
-        maxFileSize: config?.code?.maxFileSize
-      }));
-    }
-    if (builtins.includes("git")) {
-      brain.use(git({
-        embeddingProvider: gitEmb,
-        depth: config?.git?.depth,
-        maxDiffBytes: config?.git?.maxDiffBytes
-      }));
-    }
-  }
-  if (builtins.includes("docs")) {
-    brain.use(docs({ embeddingProvider: docsEmb }));
-  }
-}
-__name(registerBuiltins, "registerBuiltins");
-async function registerConfigCollections(brain, config) {
-  const collections = config?.docs?.collections;
-  if (!collections?.length) return;
-  for (const coll of collections) {
-    const absPath = path.resolve(coll.path);
-    try {
-      await brain.addCollection({
-        name: coll.name,
-        path: absPath,
-        pattern: coll.pattern ?? "**/*.md",
-        ignore: coll.ignore,
-        context: coll.context
-      });
-    } catch {
+  } catch {
+  }
+  return results;
+}
+__name(scanDocsCollections, "scanDocsCollections");
+function countDocs(dir) {
+  let count = 0;
+  try {
+    for (const e of fs.readdirSync(dir, { withFileTypes: true })) {
+      const ePath = path.join(dir, e.name);
+      const isDir = e.isDirectory() || e.isSymbolicLink() && (() => {
+        try {
+          return fs.statSync(ePath).isDirectory();
+        } catch {
+          return false;
+        }
+      })();
+      if (isDir) {
+        if (isIgnoredDir(e.name)) continue;
+        count += countDocs(ePath);
+      } else if ((e.isFile() || e.isSymbolicLink()) && /\.mdx?$/i.test(e.name)) {
+        count++;
+      }
+    }
+  } catch {
+  }
+  return count;
+}
+__name(countDocs, "countDocs");
+function countDocsShallow(dir) {
+  let count = 0;
+  try {
+    for (const e of fs.readdirSync(dir, { withFileTypes: true })) {
+      if (e.isFile() && /\.mdx?$/i.test(e.name)) count++;
     }
+  } catch {
+  }
+  return count;
+}
+__name(countDocsShallow, "countDocsShallow");
+function scanConfig(repoPath) {
+  const configPath = path.join(repoPath, ".brainbank", "config.json");
+  if (!fs.existsSync(configPath)) return { exists: false };
+  try {
+    const config = JSON.parse(fs.readFileSync(configPath, "utf-8"));
+    const codeCfg = config?.code;
+    return {
+      exists: true,
+      ignore: codeCfg?.ignore,
+      plugins: config?.plugins
+    };
+  } catch {
+    return { exists: false };
   }
 }
-__name(registerConfigCollections, "registerConfigCollections");
+__name(scanConfig, "scanConfig");
+function scanDb(repoPath) {
+  const dbPath = path.join(repoPath, ".brainbank", "data", "brainbank.db");
+  if (!fs.existsSync(dbPath)) return { exists: false, sizeMB: 0 };
+  try {
+    const stat = fs.statSync(dbPath);
+    return {
+      exists: true,
+      sizeMB: Math.round(stat.size / 1024 / 1024 * 10) / 10,
+      lastModified: stat.mtime
+    };
+  } catch {
+    return { exists: false, sizeMB: 0 };
+  }
+}
+__name(scanDb, "scanDb");
+function scanGitSubdirs(repoPath) {
+  if (fs.existsSync(path.join(repoPath, ".git"))) return [];
+  try {
+    let subdirs = fs.readdirSync(repoPath, { withFileTypes: true }).filter((e) => {
+      if (e.name.startsWith(".")) return false;
+      const isDir = e.isDirectory() || e.isSymbolicLink() && (() => {
+        try {
+          return fs.statSync(path.join(repoPath, e.name)).isDirectory();
+        } catch {
+          return false;
+        }
+      })();
+      return isDir;
+    }).filter((e) => fs.existsSync(path.join(repoPath, e.name, ".git"))).map((e) => ({ name: e.name }));
+    const configRepos = readReposFromConfig(repoPath);
+    if (configRepos) {
+      subdirs = subdirs.filter((s) => configRepos.includes(s.name));
+    }
+    return subdirs;
+  } catch {
+    return [];
+  }
+}
+__name(scanGitSubdirs, "scanGitSubdirs");
+function readReposFromConfig(repoPath) {
+  const configPath = path.join(repoPath, ".brainbank", "config.json");
+  try {
+    if (!fs.existsSync(configPath)) return null;
+    const config = JSON.parse(fs.readFileSync(configPath, "utf-8"));
+    const repos = config.repos;
+    if (Array.isArray(repos) && repos.every((r) => typeof r === "string")) {
+      return repos;
+    }
+    return null;
+  } catch {
+    return null;
+  }
+}
+__name(readReposFromConfig, "readReposFromConfig");
 
-// src/cli/commands/index-cmd.ts
+// src/cli/commands/index.ts
 async function cmdIndex() {
-  const repoPath = args[1] || ".";
+  const positional = stripFlags(args);
+  const repoPath = positional[1] || ".";
   const force = hasFlag("force");
   const depth = parseInt(getFlag("depth") || "500", 10);
   const onlyRaw = getFlag("only");
   const docsPath = getFlag("docs");
-  const modules = onlyRaw ? onlyRaw.split(",").map((s) => s.trim()) : void 0;
-  if (docsPath && modules && !modules.includes("docs")) {
+  const skipPrompt = hasFlag("yes") || hasFlag("y");
+  const scan = scanRepo(repoPath);
+  printScanTree(scan, depth);
+  let modules;
+  if (onlyRaw) {
+    modules = onlyRaw.split(",").map((s) => s.trim());
+  } else if (scan.config.plugins && scan.config.plugins.length > 0) {
+    modules = scan.config.plugins;
+    console.log(c.dim(`
+  Using config: plugins = [${modules.join(", ")}]
+`));
+  } else if (skipPrompt) {
+    modules = buildDefaultModules(scan);
+  } else {
+    modules = await promptModules(scan);
+    if (modules.length === 0) {
+      console.log(c.dim("\n  Nothing selected. Exiting.\n"));
+      return;
+    }
+    console.clear();
+    console.log(c.bold("\n\u2501\u2501\u2501 BrainBank \u2501\u2501\u2501\n"));
+    console.log("  Selected modules:");
+    for (const m of modules) {
+      console.log(`    ${c.green("\u2713")} ${m}`);
+    }
+    console.log("");
+  }
+  if (docsPath && !modules.includes("docs")) {
     modules.push("docs");
   }
-  console.log(c.bold("\n\u2501\u2501\u2501 BrainBank Index \u2501\u2501\u2501"));
-  console.log(c.dim(`  Repo: ${repoPath}`));
-  console.log(c.dim(`  Force: ${force}`));
-  console.log(c.dim(`  Git depth: ${depth}`));
-  if (modules) console.log(c.dim(`  Modules: ${modules.join(", ")}`));
-  if (docsPath) console.log(c.dim(`  Docs path: ${docsPath}`));
+  if (!scan.config.exists && !skipPrompt) {
+    await saveConfig(scan.repoPath, modules);
+  }
+  console.log(c.bold(`
+\u2501\u2501\u2501 Indexing: ${modules.join(", ")} \u2501\u2501\u2501`));
   const brain = await createBrain(repoPath);
-  const config = await getConfig();
-  await registerConfigCollections(brain, config);
+  await brain.initialize();
+  const config = await getConfig(repoPath);
+  await registerConfigCollections(brain, repoPath, config);
   if (docsPath) {
     const absDocsPath = path2.resolve(docsPath);
     const collName = path2.basename(absDocsPath);
     try {
-      await brain.addCollection({
+      const docsPlugin = findDocsPlugin(brain);
+      await docsPlugin?.addCollection({
         name: collName,
         path: absDocsPath,
         pattern: "**/*.md",
@@ -322,33 +400,163 @@ async function cmdIndex() {
   const result = await brain.index({
     modules,
     forceReindex: force,
-    gitDepth: depth,
+    pluginOptions: { depth },
     onProgress: /* @__PURE__ */ __name((stage, msg) => {
       process.stdout.write(`\r  ${c.cyan(stage.toUpperCase())} ${msg}                    `);
     }, "onProgress")
   });
   console.log("\n");
-  if (result.code) {
-    console.log(`  ${c.green("Code")}: ${result.code.indexed} indexed, ${result.code.skipped} skipped, ${result.code.chunks ?? 0} chunks`);
-  }
-  if (result.git) {
-    console.log(`  ${c.green("Git")}:  ${result.git.indexed} indexed, ${result.git.skipped} skipped`);
-  }
-  if (result.docs) {
-    for (const [name, stat] of Object.entries(result.docs)) {
-      console.log(`  ${c.green("Docs")}: [${name}] ${stat.indexed} indexed, ${stat.skipped} skipped, ${stat.chunks} chunks`);
+  for (const [name, value] of Object.entries(result)) {
+    if (!value) continue;
+    const v = value;
+    if (typeof v.indexed === "number") {
+      const parts = [`${v.indexed} indexed`, `${v.skipped ?? 0} skipped`];
+      if (typeof v.chunks === "number") parts.push(`${v.chunks} chunks`);
+      if (typeof v.removed === "number" && v.removed > 0) parts.push(`${v.removed} removed`);
+      console.log(`  ${c.green(name)}: ${parts.join(", ")}`);
+    } else {
+      console.log(`  ${c.green(name)}: done`);
     }
   }
   const stats = brain.stats();
   console.log(`
   ${c.bold("Totals")}:`);
-  if (stats.code) console.log(`    Code chunks:  ${stats.code.chunks}`);
-  if (stats.git) console.log(`    Git commits:  ${stats.git.commits}`);
-  if (stats.git) console.log(`    Co-edit pairs: ${stats.git.coEdits}`);
-  if (stats.documents) console.log(`    Documents:    ${stats.documents.documents}`);
+  for (const [name, s] of Object.entries(stats)) {
+    if (!s || typeof s !== "object") continue;
+    const entries = Object.entries(s).map(([k, v]) => `${k}: ${v}`).join(", ");
+    console.log(`    ${name}: ${entries}`);
+  }
   brain.close();
 }
 __name(cmdIndex, "cmdIndex");
+function printScanTree(scan, depth) {
+  console.clear();
+  console.log(c.bold("\n\u2501\u2501\u2501 BrainBank Scan \u2501\u2501\u2501"));
+  console.log(c.dim(`  Repo: ${scan.repoPath}`));
+  if (scan.gitSubdirs.length > 0) {
+    console.log(c.cyan(`
+  \u{1F500} Multi-repo \u2014 ${scan.gitSubdirs.length} git repos detected`));
+    for (const sub of scan.gitSubdirs) {
+      console.log(c.dim(`     \u2514\u2500\u2500 ${sub.name}`));
+    }
+  }
+  for (const mod of scan.modules) {
+    console.log("");
+    if (mod.available) {
+      const extra = mod.name === "git" ? ` (depth: ${depth})` : "";
+      console.log(`  ${mod.icon} ${c.bold(capitalizeFirst(mod.name))} \u2014 ${mod.summary}${extra}`);
+      if (mod.details) {
+        for (const d of mod.details) {
+          console.log(c.dim(`     ${d}`));
+        }
+      }
+    } else {
+      console.log(`  ${mod.icon} ${c.dim(`${capitalizeFirst(mod.name)} \u2014 ${mod.summary}`)}`);
+    }
+  }
+  if (scan.config.ignore?.length) {
+    console.log(c.dim(`     Ignore: ${scan.config.ignore.join(", ")}`));
+  }
+  console.log("");
+  if (scan.config.exists) {
+    console.log(`  \u2699\uFE0F  ${c.dim("Config:")} .brainbank/config.json ${c.green("\u2713")}`);
+  }
+  if (scan.db?.exists) {
+    const ago = scan.db.lastModified ? timeSince(scan.db.lastModified) : "";
+    console.log(`  \u{1F4BE} ${c.dim("DB:")} ${scan.db.sizeMB} MB${ago ? `, last indexed ${ago}` : ""}`);
+  } else {
+    console.log(`  \u{1F4BE} ${c.dim("DB: new (first index)")}`);
+  }
+  console.log("");
+}
+__name(printScanTree, "printScanTree");
+function buildDefaultModules(scan) {
+  return scan.modules.filter((m) => m.available && m.checked).map((m) => m.name);
+}
+__name(buildDefaultModules, "buildDefaultModules");
+async function promptModules(scan) {
+  const { checkbox } = await import("@inquirer/prompts");
+  console.log(c.dim("  \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n"));
+  const choices = scan.modules.map((m) => ({
+    name: `${capitalizeFirst(m.name).padEnd(6)} \u2014 ${m.summary}`,
+    value: m.name,
+    checked: m.checked && m.available,
+    disabled: m.available ? void 0 : m.disabled
+  }));
+  return checkbox({
+    message: "Select modules to index:\n",
+    choices
+  });
+}
+__name(promptModules, "promptModules");
+function timeSince(date) {
+  const seconds = Math.floor((Date.now() - date.getTime()) / 1e3);
+  if (seconds < 60) return "just now";
+  const minutes = Math.floor(seconds / 60);
+  if (minutes < 60) return `${minutes}m ago`;
+  const hours = Math.floor(minutes / 60);
+  if (hours < 24) return `${hours}h ago`;
+  const days = Math.floor(hours / 24);
+  return `${days}d ago`;
+}
+__name(timeSince, "timeSince");
+function capitalizeFirst(s) {
+  return s.charAt(0).toUpperCase() + s.slice(1);
+}
+__name(capitalizeFirst, "capitalizeFirst");
+async function saveConfig(repoPath, modules) {
+  const { select } = await import("@inquirer/prompts");
+  const envEmbedding = process.env.BRAINBANK_EMBEDDING;
+  const embedding = await select({
+    message: "Embedding provider:",
+    choices: [
+      {
+        name: "perplexity-context  \u2014 best accuracy (recommended)",
+        value: "perplexity-context"
+      },
+      {
+        name: "perplexity          \u2014 fast, high quality",
+        value: "perplexity"
+      },
+      {
+        name: "openai              \u2014 text-embedding-3-small",
+        value: "openai"
+      },
+      {
+        name: "local               \u2014 offline, no API key needed",
+        value: "local"
+      }
+    ],
+    default: envEmbedding ?? "perplexity-context"
+  });
+  const pruner = await select({
+    message: "Noise pruner:",
+    choices: [
+      {
+        name: "none   \u2014 no pruning (default)",
+        value: "none"
+      },
+      {
+        name: "haiku  \u2014 AI-powered noise filter (Claude Haiku)",
+        value: "haiku"
+      }
+    ],
+    default: "none"
+  });
+  const configDir = path2.join(repoPath, ".brainbank");
+  const configPath = path2.join(configDir, "config.json");
+  const config = {
+    plugins: modules,
+    embedding
+  };
+  if (pruner !== "none") {
+    config.pruner = pruner;
+  }
+  fs2.mkdirSync(configDir, { recursive: true });
+  fs2.writeFileSync(configPath, JSON.stringify(config, null, 2) + "\n");
+  console.log(c.green(`  \u2713 Saved ${path2.relative(process.cwd(), configPath)}`));
+}
+__name(saveConfig, "saveConfig");
 
 // src/cli/commands/collection.ts
 async function cmdCollection() {
@@ -365,7 +573,12 @@ async function cmdCollection() {
       process.exit(1);
     }
     const brain = await createBrain();
-    await brain.addCollection({
+    const docsPlugin = findDocsPlugin(brain);
+    if (!docsPlugin) {
+      console.log(c.red("Docs plugin not loaded. Install @brainbank/docs."));
+      process.exit(1);
+    }
+    await docsPlugin.addCollection({
       name,
       path: path3,
       pattern,
@@ -380,7 +593,13 @@ async function cmdCollection() {
   if (sub === "list") {
     const brain = await createBrain();
     await brain.initialize();
-    const collections = brain.listCollections();
+    const docsPlugin = findDocsPlugin(brain);
+    if (!docsPlugin) {
+      console.log(c.yellow("  Docs plugin not loaded."));
+      brain.close();
+      return;
+    }
+    const collections = docsPlugin.listCollections();
     if (collections.length === 0) {
       console.log(c.yellow("  No collections registered."));
     } else {
@@ -401,7 +620,12 @@ async function cmdCollection() {
       process.exit(1);
     }
     const brain = await createBrain();
-    await brain.removeCollection(name);
+    const docsPlugin = findDocsPlugin(brain);
+    if (!docsPlugin) {
+      console.log(c.red("Docs plugin not loaded."));
+      process.exit(1);
+    }
+    await docsPlugin.removeCollection(name);
     console.log(c.green(`\u2713 Collection '${name}' removed.`));
     brain.close();
     return;
@@ -544,10 +768,16 @@ async function cmdDocs() {
   opts.onProgress = (col, file, cur, total) => {
     process.stdout.write(`\r  ${c.cyan(col)} [${cur}/${total}] ${file}                    `);
   };
-  const results = await brain.indexDocs(opts);
+  const docsPlugin = findDocsPlugin(brain);
+  if (!docsPlugin) {
+    console.log(c.red("  Docs plugin not loaded. Install @brainbank/docs."));
+    process.exit(1);
+  }
+  const results = await docsPlugin.indexDocs(opts);
   console.log("\n");
   for (const [name, stat] of Object.entries(results)) {
-    console.log(`  ${c.green(name)}: ${stat.indexed} indexed, ${stat.skipped} skipped, ${stat.chunks} chunks`);
+    const removedStr = stat.removed > 0 ? `, ${c.red(String(stat.removed) + " removed")}` : "";
+    console.log(`  ${c.green(name)}: ${stat.indexed} indexed, ${stat.skipped} skipped${removedStr}, ${stat.chunks} chunks`);
   }
   brain.close();
 }
@@ -564,7 +794,12 @@ async function cmdDocSearch() {
   console.log(c.bold(`
 \u2501\u2501\u2501 BrainBank Doc Search: "${query}" \u2501\u2501\u2501
 `));
-  const results = await brain.searchDocs(query, { collection: collection ?? void 0, k });
+  const docsPlugin = findDocsPlugin(brain);
+  if (!docsPlugin) {
+    console.log(c.red("Docs plugin not loaded. Install @brainbank/docs."));
+    process.exit(1);
+  }
+  const results = await docsPlugin.search(query, { collection: collection ?? void 0, k });
   if (results.length === 0) {
     console.log(c.yellow("  No results found."));
     brain.close();
@@ -573,7 +808,7 @@ async function cmdDocSearch() {
   for (const r of results) {
     const score = Math.round(r.score * 100);
     const ctx = r.context ? ` \u2014 ${c.dim(r.context)}` : "";
-    console.log(`${c.magenta(`[DOC ${score}%]`)} ${c.bold(r.filePath)} [${r.metadata.collection}]${ctx}`);
+    console.log(`${c.magenta(`[DOC ${score}%]`)} ${c.bold(r.filePath)} [${r.type === "document" ? r.metadata.collection ?? "" : ""}]${ctx}`);
     const preview = r.content.split("\n").slice(0, 4).join("\n");
     console.log(c.dim(preview));
     console.log("");
@@ -583,56 +818,244 @@ async function cmdDocSearch() {
 __name(cmdDocSearch, "cmdDocSearch");
 
 // src/cli/commands/search.ts
+function parseSourceFlags() {
+  const NON_SOURCE_FLAGS = /* @__PURE__ */ new Set([
+    "repo",
+    "depth",
+    "collection",
+    "pattern",
+    "context",
+    "name",
+    "keep",
+    "reranker",
+    "pruner",
+    "only",
+    "docs-path",
+    "mode",
+    "limit",
+    "ignore",
+    "meta",
+    "k",
+    "yes",
+    "y",
+    "force",
+    "verbose"
+  ]);
+  const sources = {};
+  const positional = [];
+  for (let i = 0; i < args.length; i++) {
+    if (args[i].startsWith("--")) {
+      const name = args[i].slice(2);
+      if (name === "yes" || name === "force" || name === "verbose") continue;
+      const next = args[i + 1];
+      if (next !== void 0 && /^\d+$/.test(next) && !NON_SOURCE_FLAGS.has(name)) {
+        sources[name] = parseInt(next, 10);
+        i++;
+        continue;
+      }
+      if (NON_SOURCE_FLAGS.has(name) && next !== void 0 && !next.startsWith("--")) {
+        i++;
+      }
+      continue;
+    }
+    positional.push(args[i]);
+  }
+  const query = positional.slice(1).join(" ");
+  return { sources, query };
+}
+__name(parseSourceFlags, "parseSourceFlags");
+function printFilterInfo(sources) {
+  const entries = Object.entries(sources);
+  if (entries.length === 0) return;
+  const parts = entries.map(([k, v]) => `${k}=${v}`);
+  console.log(c.dim(`  Sources: ${parts.join(", ")}`));
+}
+__name(printFilterInfo, "printFilterInfo");
+function buildSearchOptions(sources) {
+  return Object.keys(sources).length > 0 ? { sources, source: "cli" } : { sources: {}, source: "cli" };
+}
+__name(buildSearchOptions, "buildSearchOptions");
 async function cmdSearch() {
-  const query = stripFlags(args).slice(1).join(" ");
+  const { sources, query } = parseSourceFlags();
   if (!query) {
-    console.log(c.red("Usage: brainbank search <query>"));
+    console.log(c.red("Usage: brainbank search <query> [--code <n>] [--git <n>] [--<source> <n>]"));
     process.exit(1);
   }
   const brain = await createBrain();
   console.log(c.bold(`
 \u2501\u2501\u2501 BrainBank Search: "${query}" \u2501\u2501\u2501
 `));
-  const results = await brain.search(query);
+  printFilterInfo(sources);
+  const opts = buildSearchOptions(sources);
+  const results = await brain.search(query, opts);
   printResults(results);
   brain.close();
 }
 __name(cmdSearch, "cmdSearch");
 async function cmdHybridSearch() {
-  const query = stripFlags(args).slice(1).join(" ");
+  const { sources, query } = parseSourceFlags();
   if (!query) {
-    console.log(c.red("Usage: brainbank hsearch <query>"));
+    console.log(c.red("Usage: brainbank hsearch <query> [--code <n>] [--git <n>] [--docs <n>] [--<source> <n>]"));
     process.exit(1);
   }
   const brain = await createBrain();
   console.log(c.bold(`
 \u2501\u2501\u2501 BrainBank Hybrid Search: "${query}" \u2501\u2501\u2501`));
-  console.log(c.dim(`  Mode: vector + BM25 \u2192 Reciprocal Rank Fusion
-`));
-  const results = await brain.hybridSearch(query);
+  console.log(c.dim(`  Mode: vector + BM25 \u2192 Reciprocal Rank Fusion`));
+  printFilterInfo(sources);
+  console.log("");
+  const opts = buildSearchOptions(sources);
+  const results = await brain.hybridSearch(query, opts);
   printResults(results);
   brain.close();
 }
 __name(cmdHybridSearch, "cmdHybridSearch");
 async function cmdKeywordSearch() {
-  const query = stripFlags(args).slice(1).join(" ");
+  const { sources, query } = parseSourceFlags();
   if (!query) {
-    console.log(c.red("Usage: brainbank ksearch <query>"));
+    console.log(c.red("Usage: brainbank ksearch <query> [--code <n>] [--git <n>] [--<source> <n>]"));
     process.exit(1);
   }
   const brain = await createBrain();
   await brain.initialize();
   console.log(c.bold(`
 \u2501\u2501\u2501 BrainBank Keyword Search: "${query}" \u2501\u2501\u2501`));
-  console.log(c.dim(`  Mode: BM25 full-text (instant)
-`));
-  const results = await brain.searchBM25(query);
+  console.log(c.dim(`  Mode: BM25 full-text (instant)`));
+  printFilterInfo(sources);
+  console.log("");
+  const opts = buildSearchOptions(sources);
+  const results = await brain.searchBM25(query, opts);
   printResults(results);
   brain.close();
 }
 __name(cmdKeywordSearch, "cmdKeywordSearch");
 
+// src/cli/server-client.ts
+import * as http from "http";
+async function tryServerContext(options) {
+  const info = isServerRunning();
+  if (!info) return null;
+  try {
+    const body = JSON.stringify({
+      task: options.task,
+      repo: options.repo,
+      sources: options.sources,
+      pathPrefix: options.pathPrefix,
+      affectedFiles: options.affectedFiles
+    });
+    const response = await httpPost(info.port, "/context", body);
+    const data = JSON.parse(response);
+    if (data.error) return null;
+    return data.context ?? null;
+  } catch {
+    return null;
+  }
+}
+__name(tryServerContext, "tryServerContext");
+async function serverHealth() {
+  const info = isServerRunning();
+  if (!info) return null;
+  try {
+    const response = await httpGet(info.port, "/health");
+    return JSON.parse(response);
+  } catch {
+    return null;
+  }
+}
+__name(serverHealth, "serverHealth");
+function httpPost(port, path3, body) {
+  return new Promise((resolve3, reject) => {
+    const req = http.request({
+      hostname: "127.0.0.1",
+      port,
+      path: path3,
+      method: "POST",
+      headers: {
+        "Content-Type": "application/json",
+        "Content-Length": Buffer.byteLength(body)
+      },
+      timeout: 12e4
+      // 2 minutes — context queries can be slow on first load
+    }, (res) => {
+      const chunks = [];
+      res.on("data", (chunk) => chunks.push(chunk));
+      res.on("end", () => resolve3(Buffer.concat(chunks).toString("utf8")));
+    });
+    req.on("error", reject);
+    req.on("timeout", () => {
+      req.destroy();
+      reject(new Error("Request timed out"));
+    });
+    req.write(body);
+    req.end();
+  });
+}
+__name(httpPost, "httpPost");
+function httpGet(port, path3) {
+  return new Promise((resolve3, reject) => {
+    const req = http.request({
+      hostname: "127.0.0.1",
+      port,
+      path: path3,
+      method: "GET",
+      timeout: 5e3
+    }, (res) => {
+      const chunks = [];
+      res.on("data", (chunk) => chunks.push(chunk));
+      res.on("end", () => resolve3(Buffer.concat(chunks).toString("utf8")));
+    });
+    req.on("error", reject);
+    req.on("timeout", () => {
+      req.destroy();
+      reject(new Error("Request timed out"));
+    });
+    req.end();
+  });
+}
+__name(httpGet, "httpGet");
+
 // src/cli/commands/context.ts
+function parseContextFlags() {
+  const NON_SOURCE = /* @__PURE__ */ new Set([
+    "repo",
+    "depth",
+    "collection",
+    "pattern",
+    "context",
+    "name",
+    "keep",
+    "reranker",
+    "pruner",
+    "only",
+    "docs-path",
+    "mode",
+    "limit",
+    "ignore",
+    "meta",
+    "k",
+    "yes",
+    "y",
+    "force",
+    "verbose",
+    "path"
+  ]);
+  const sources = {};
+  for (let i = 0; i < args.length; i++) {
+    if (!args[i].startsWith("--")) continue;
+    const name = args[i].slice(2);
+    if (name.startsWith("no-")) {
+      sources[name.slice(3)] = 0;
+      continue;
+    }
+    const next = args[i + 1];
+    if (next !== void 0 && /^\d+$/.test(next) && !NON_SOURCE.has(name)) {
+      sources[name] = parseInt(next, 10);
+      i++;
+    }
+  }
+  return sources;
+}
+__name(parseContextFlags, "parseContextFlags");
 async function cmdContext() {
   const pos = stripFlags(args);
   const sub = pos[1];
@@ -646,7 +1069,12 @@ async function cmdContext() {
     }
     const brain2 = await createBrain();
     await brain2.initialize();
-    brain2.addContext(collection, path3, desc);
+    const docsPlugin = findDocsPlugin(brain2);
+    if (!docsPlugin) {
+      console.log(c.red("Docs plugin not loaded."));
+      process.exit(1);
+    }
+    docsPlugin.addContext(collection, path3, desc);
     console.log(c.green(`\u2713 Context added: ${collection}:${path3} \u2192 "${desc}"`));
     brain2.close();
     return;
@@ -654,7 +1082,13 @@ async function cmdContext() {
   if (sub === "list") {
     const brain2 = await createBrain();
     await brain2.initialize();
-    const contexts = brain2.listContexts();
+    const docsPlugin = findDocsPlugin(brain2);
+    if (!docsPlugin) {
+      console.log(c.yellow("  Docs plugin not loaded."));
+      brain2.close();
+      return;
+    }
+    const contexts = docsPlugin.listContexts();
     if (contexts.length === 0) {
       console.log(c.yellow("  No contexts configured."));
     } else {
@@ -673,14 +1107,126 @@ async function cmdContext() {
     console.log(c.dim("       brainbank context list"));
     process.exit(1);
   }
+  const sources = parseContextFlags();
+  const pathPrefix = getFlag("path");
+  const repo = getFlag("repo");
+  const fields = parseFieldFlags();
+  const serverResult = await tryServerContext({
+    task,
+    repo: repo ?? process.cwd(),
+    sources: Object.keys(sources).length > 0 ? sources : void 0,
+    pathPrefix
+  });
+  if (serverResult !== null) {
+    console.log(serverResult);
+    return;
+  }
   const brain = await createBrain();
-  const context = await brain.getContext(task);
+  const context = await brain.getContext(task, {
+    sources: Object.keys(sources).length > 0 ? sources : void 0,
+    pathPrefix,
+    source: "cli",
+    fields: Object.keys(fields).length > 0 ? fields : void 0
+  });
   console.log(context);
   brain.close();
 }
 __name(cmdContext, "cmdContext");
+function parseFieldFlags() {
+  const FIELD_BOOLEANS = /* @__PURE__ */ new Set(["lines", "symbols", "compact", "expander"]);
+  const FIELD_NEGATABLE = /* @__PURE__ */ new Set(["callTree", "imports"]);
+  const fields = {};
+  for (let i = 0; i < args.length; i++) {
+    if (!args[i].startsWith("--")) continue;
+    const raw = args[i].slice(2);
+    if (raw.startsWith("no-")) {
+      const name = raw.slice(3);
+      if (FIELD_NEGATABLE.has(name)) {
+        fields[name] = false;
+      }
+      continue;
+    }
+    const dotIdx = raw.indexOf(".");
+    if (dotIdx > 0) {
+      const fieldName = raw.slice(0, dotIdx);
+      const rest = raw.slice(dotIdx + 1);
+      const eqIdx = rest.indexOf("=");
+      if (eqIdx > 0) {
+        const key = rest.slice(0, eqIdx);
+        const val = parseInt(rest.slice(eqIdx + 1), 10);
+        if (!isNaN(val)) {
+          fields[fieldName] = { [key]: val };
+        }
+      }
+      continue;
+    }
+    if (FIELD_BOOLEANS.has(raw)) {
+      fields[raw] = true;
+    }
+  }
+  return fields;
+}
+__name(parseFieldFlags, "parseFieldFlags");
+
+// src/cli/commands/files.ts
+async function cmdFiles() {
+  const patterns = [];
+  const showLines = args.includes("--lines");
+  for (let i = 1; i < args.length; i++) {
+    if (args[i].startsWith("--")) {
+      if (args[i] === "--repo") {
+        i++;
+      }
+      continue;
+    }
+    patterns.push(args[i]);
+  }
+  if (patterns.length === 0) {
+    console.log(c.red("Usage: brainbank files <path|glob> [...paths] [--lines]"));
+    console.log(c.dim("  Exact:     brainbank files src/auth/login.ts"));
+    console.log(c.dim("  Directory: brainbank files src/graph/"));
+    console.log(c.dim('  Glob:      brainbank files "src/**/*.service.ts"'));
+    console.log(c.dim("  Fuzzy:     brainbank files plugin.ts"));
+    console.log(c.dim("  Lines:     brainbank files src/plugin.ts --lines"));
+    process.exit(1);
+  }
+  const brain = await createBrain();
+  await brain.initialize();
+  const results = brain.resolveFiles(patterns);
+  if (results.length === 0) {
+    console.log(c.yellow("No matching files found in the index."));
+    console.log(c.dim("Run `brainbank index` first to index your codebase."));
+    brain.close();
+    return;
+  }
+  for (const r of results) {
+    const meta = r.metadata;
+    const startLine = meta.startLine ?? 1;
+    console.log(c.bold(`
+\u2500\u2500 ${r.filePath} \u2500\u2500
+`));
+    if (showLines) {
+      const codeLines = r.content.split("\n");
+      const pad = String(startLine + codeLines.length - 1).length;
+      for (let i = 0; i < codeLines.length; i++) {
+        const lineNum = c.dim(`${String(startLine + i).padStart(pad)}|`);
+        console.log(`${lineNum} ${codeLines[i]}`);
+      }
+    } else {
+      console.log(r.content);
+    }
+  }
+  console.log(c.dim(`
+${results.length} file(s) resolved.`));
+  brain.close();
+}
+__name(cmdFiles, "cmdFiles");
 
-// src/cli/commands/system.ts
+// src/cli/commands/stats.ts
+function formatStatKey(key) {
+  return key.replace(/([a-z])([A-Z])/g, "$1 $2").replace(/_/g, " ").replace(/\b\w/g, (c2) => c2.toUpperCase()).padEnd(16);
+}
+__name(formatStatKey, "formatStatKey");
 async function cmdStats() {
   const brain = await createBrain();
   await brain.initialize();
@@ -688,27 +1234,12 @@ async function cmdStats() {
   console.log(c.bold("\n\u2501\u2501\u2501 BrainBank Stats \u2501\u2501\u2501\n"));
   console.log(`  ${c.cyan("Plugins")}: ${brain.plugins.join(", ")}
 `);
-  if (s.code) {
-    console.log(`  ${c.cyan("Code")}`);
-    console.log(`    Files indexed:  ${s.code.files}`);
-    console.log(`    Code chunks:    ${s.code.chunks}`);
-    console.log(`    HNSW vectors:   ${s.code.hnswSize}`);
-    console.log("");
-  }
-  if (s.git) {
-    console.log(`  ${c.cyan("Git History")}`);
-    console.log(`    Commits:        ${s.git.commits}`);
-    console.log(`    Files tracked:  ${s.git.filesTracked}`);
-    console.log(`    Co-edit pairs:  ${s.git.coEdits}`);
-    console.log(`    HNSW vectors:   ${s.git.hnswSize}`);
-    console.log("");
-  }
-  if (s.documents) {
-    console.log(`  ${c.cyan("Documents")}`);
-    console.log(`    Collections:    ${s.documents.collections}`);
-    console.log(`    Documents:      ${s.documents.documents}`);
-    console.log(`    Chunks:         ${s.documents.chunks}`);
-    console.log(`    HNSW vectors:   ${s.documents.hnswSize}`);
+  for (const [name, pluginStats] of Object.entries(s)) {
+    if (!pluginStats) continue;
+    console.log(`  ${c.cyan(name)}`);
+    for (const [key, value] of Object.entries(pluginStats)) {
+      console.log(`    ${formatStatKey(key)}${value}`);
+    }
     console.log("");
   }
   const kvNames = brain.listCollectionNames();
@@ -723,6 +1254,8 @@ async function cmdStats() {
   brain.close();
 }
 __name(cmdStats, "cmdStats");
+
+// src/cli/commands/reembed.ts
 async function cmdReembed() {
   const brain = await createBrain();
   await brain.initialize();
@@ -735,29 +1268,37 @@ async function cmdReembed() {
     }, "onProgress")
   });
   console.log("\n");
-  if (result.code > 0) console.log(`  ${c.green("\u2713")} Code:    ${result.code} vectors`);
-  if (result.git > 0) console.log(`  ${c.green("\u2713")} Git:     ${result.git} vectors`);
-  if (result.docs > 0) console.log(`  ${c.green("\u2713")} Docs:    ${result.docs} vectors`);
-  if (result.kv > 0) console.log(`  ${c.green("\u2713")} KV:      ${result.kv} vectors`);
-  if (result.notes > 0) console.log(`  ${c.green("\u2713")} Notes:   ${result.notes} vectors`);
-  if (result.memory > 0) console.log(`  ${c.green("\u2713")} Memory:  ${result.memory} vectors`);
+  for (const [name, count] of Object.entries(result.counts)) {
+    if (count > 0) {
+      const label = name.charAt(0).toUpperCase() + name.slice(1);
+      console.log(`  ${c.green("\u2713")} ${label.padEnd(8)} ${count} vectors`);
+    }
+  }
   console.log(`
   ${c.bold("Total")}: ${result.total} vectors regenerated
 `);
   brain.close();
 }
 __name(cmdReembed, "cmdReembed");
+
+// src/cli/commands/watch.ts
 async function cmdWatch() {
   const brain = await createBrain();
   await brain.initialize();
+  const config = await loadConfig(brain.config.repoPath);
+  const codeIgnore = config?.code?.ignore ?? [];
   console.log(c.bold("\n\u2501\u2501\u2501 BrainBank Watch \u2501\u2501\u2501\n"));
   console.log(c.dim(`  Watching ${brain.config.repoPath} for changes...`));
+  if (codeIgnore.length > 0) {
+    console.log(c.dim(`  Ignoring: ${codeIgnore.join(", ")}`));
+  }
   console.log(c.dim("  Press Ctrl+C to stop.\n"));
   const watcher = brain.watch({
     debounceMs: 2e3,
-    onIndex: /* @__PURE__ */ __name((file, indexer) => {
+    ignore: codeIgnore,
+    onIndex: /* @__PURE__ */ __name((sourceId, pluginName) => {
       const ts = (/* @__PURE__ */ new Date()).toLocaleTimeString();
-      console.log(`  ${c.dim(ts)} ${c.green("\u2713")} ${c.cyan(indexer)}: ${file}`);
+      console.log(`  ${c.dim(ts)} ${c.green("\u2713")} ${c.cyan(pluginName)}: ${sourceId}`);
     }, "onIndex"),
     onError: /* @__PURE__ */ __name((err) => {
       console.error(`  ${c.red("\u2717")} ${err.message}`);
@@ -773,14 +1314,141 @@ async function cmdWatch() {
   });
 }
 __name(cmdWatch, "cmdWatch");
-async function cmdServe() {
-  await import("@brainbank/mcp");
+
+// src/cli/commands/mcp.ts
+async function cmdMcp() {
+  try {
+    await import("@brainbank/mcp");
+  } catch {
+    console.error(c.red("Error: @brainbank/mcp is not installed."));
+    console.error(c.dim("  Install: npm i @brainbank/mcp"));
+    process.exit(1);
+  }
 }
-__name(cmdServe, "cmdServe");
+__name(cmdMcp, "cmdMcp");
+
+// src/cli/commands/daemon.ts
+async function cmdDaemon() {
+  const pos = stripFlags(args);
+  const sub = pos[1];
+  if (sub === "stop") return stopDaemon();
+  if (sub === "restart") {
+    stopDaemon();
+    return forkDaemon();
+  }
+  if (sub === "start") return forkDaemon();
+  return startForeground();
+}
+__name(cmdDaemon, "cmdDaemon");
+async function startForeground() {
+  const port = parseInt(getFlag("port") ?? String(DEFAULT_PORT), 10);
+  const { HttpServer } = await import("./http-server-GIRELCCL.js");
+  const server = new HttpServer({
+    port,
+    factory: /* @__PURE__ */ __name(async (repoPath) => {
+      const brain = await createBrain(repoPath);
+      await brain.initialize();
+      return brain;
+    }, "factory"),
+    onError: /* @__PURE__ */ __name((repo, err) => {
+      const msg = err instanceof Error ? err.message : String(err);
+      console.error(c.red(`  Pool error [${repo}]: ${msg}`));
+    }, "onError"),
+    onLog: /* @__PURE__ */ __name((msg) => console.log(c.dim(`  ${msg}`)), "onLog")
+  });
+  console.log(c.bold("\n\u2501\u2501\u2501 BrainBank HTTP Daemon \u2501\u2501\u2501\n"));
+  await server.start();
+  console.log(c.dim(`  Port: ${port}`));
+  console.log(c.dim("  Press Ctrl+C to stop.\n"));
+  const shutdown = /* @__PURE__ */ __name(() => {
+    console.log(c.dim("\n  Shutting down..."));
+    server.close();
+    process.exit(0);
+  }, "shutdown");
+  process.on("SIGINT", shutdown);
+  process.on("SIGTERM", shutdown);
+  await new Promise(() => {
+  });
+}
+__name(startForeground, "startForeground");
+async function forkDaemon() {
+  const port = parseInt(getFlag("port") ?? String(DEFAULT_PORT), 10);
+  const { fork } = await import("child_process");
+  const existing = isServerRunning();
+  if (existing) {
+    console.log(c.yellow(`  Daemon already running (PID ${existing.pid}, port ${existing.port})`));
+    return;
+  }
+  const child = fork(process.argv[1], ["daemon", "--port", String(port)], {
+    detached: true,
+    stdio: "ignore"
+  });
+  child.unref();
+  console.log(c.green(`  \u2713 Daemon started (PID ${child.pid}, port ${port})`));
+  console.log(c.dim("  Stop with: brainbank daemon stop"));
+}
+__name(forkDaemon, "forkDaemon");
+function stopDaemon() {
+  const info = isServerRunning();
+  if (!info) {
+    console.log(c.yellow("  No daemon running."));
+    return;
+  }
+  try {
+    process.kill(info.pid, "SIGTERM");
+    removePid();
+    console.log(c.green(`  \u2713 Daemon stopped (PID ${info.pid})`));
+  } catch {
+    removePid();
+    console.log(c.yellow(`  PID ${info.pid} not found. Cleaned up stale PID file.`));
+  }
+}
+__name(stopDaemon, "stopDaemon");
+
+// src/cli/commands/status.ts
+function formatUptime(seconds) {
+  if (seconds < 60) return `${seconds}s`;
+  const minutes = Math.floor(seconds / 60);
+  if (minutes < 60) return `${minutes}m`;
+  const hours = Math.floor(minutes / 60);
+  const remainMinutes = minutes % 60;
+  return remainMinutes > 0 ? `${hours}h ${remainMinutes}m` : `${hours}h`;
+}
+__name(formatUptime, "formatUptime");
+async function cmdStatus() {
+  const info = isServerRunning();
+  if (!info) {
+    console.log(`
+  ${c.dim("HTTP Server:")} ${c.yellow("stopped")}
+`);
+    console.log(c.dim("  Start with: brainbank daemon"));
+    console.log("");
+    return;
+  }
+  const health = await serverHealth();
+  if (health) {
+    const uptime = formatUptime(health.uptime);
+    console.log(`
+  ${c.dim("HTTP Server:")} ${c.green("running")}`);
+    console.log(`  ${c.dim("PID:")}         ${health.pid}`);
+    console.log(`  ${c.dim("Port:")}        ${health.port}`);
+    console.log(`  ${c.dim("Uptime:")}      ${uptime}`);
+    console.log(`  ${c.dim("Workspaces:")}  ${health.workspaces}`);
+    console.log("");
+  } else {
+    console.log(`
+  ${c.dim("HTTP Server:")} ${c.yellow("stale")} (PID ${info.pid} not responding)`);
+    console.log(c.dim("  The PID file may be stale. Restart with: brainbank daemon"));
+    console.log("");
+  }
+}
+__name(cmdStatus, "cmdStatus");
+
+// src/cli/commands/help.ts
 function showHelp() {
   console.log(c.bold("\n\u2501\u2501\u2501 BrainBank \u2014 Semantic Knowledge Bank \u2501\u2501\u2501\n"));
   console.log(c.bold("Indexing:"));
-  console.log(`  ${c.cyan("index")} [path]                      Index code + git history`);
+  console.log(`  ${c.cyan("index")} ${c.dim("(i)")} [path]                  Index code + git history`);
   console.log(`  ${c.cyan("collection add")} <path> --name      Add a document collection`);
   console.log(`  ${c.cyan("collection list")}                    List collections`);
   console.log(`  ${c.cyan("collection remove")} <name>           Remove a collection`);
@@ -791,11 +1459,13 @@ function showHelp() {
   console.log(`  ${c.cyan("hsearch")} <query>                    Hybrid search (${c.bold("best quality")})`);
   console.log(`  ${c.cyan("ksearch")} <query>                    Keyword search (BM25, instant)`);
   console.log(`  ${c.cyan("dsearch")} <query>                    Document search`);
+  console.log(c.dim("    All search commands accept --<source> <n> to filter by source"));
   console.log("");
   console.log(c.bold("Context:"));
   console.log(`  ${c.cyan("context")} <task>                     Get formatted context for a task`);
   console.log(`  ${c.cyan("context add")} <col> <path> <desc>    Add context metadata`);
   console.log(`  ${c.cyan("context list")}                       List all context metadata`);
+  console.log(`  ${c.cyan("files")} <path|glob> [...] [--lines]  View full indexed files directly`);
   console.log("");
   console.log(c.bold("KV Store:"));
   console.log(`  ${c.cyan("kv add")} <coll> <content>            Add item to a collection`);
@@ -808,7 +1478,12 @@ function showHelp() {
   console.log(`  ${c.cyan("stats")}                              Show index statistics`);
   console.log(`  ${c.cyan("reembed")}                            Re-embed all vectors`);
   console.log(`  ${c.cyan("watch")}                              Watch files, auto-re-index`);
-  console.log(`  ${c.cyan("serve")}                              Start MCP server (stdio)`);
+  console.log(`  ${c.cyan("mcp")}                                Start MCP server (stdio)`);
+  console.log(`  ${c.cyan("daemon")}                             Start HTTP daemon (foreground)`);
+  console.log(`  ${c.cyan("daemon start")}                       Start HTTP daemon (background)`);
+  console.log(`  ${c.cyan("daemon stop")}                        Stop background daemon`);
+  console.log(`  ${c.cyan("daemon restart")}                     Restart background daemon`);
+  console.log(`  ${c.cyan("status")}                             Show daemon status`);
   console.log("");
   console.log(c.bold("Options:"));
   console.log(`  ${c.dim("--repo <path>")}           Repository path (default: .)`);
@@ -817,16 +1492,26 @@ function showHelp() {
   console.log(`  ${c.dim("--collection <name>")}     Filter by collection`);
   console.log(`  ${c.dim("--pattern <glob>")}        Collection glob (default: **/*.md)`);
   console.log(`  ${c.dim("--context <desc>")}        Context description`);
+  console.log(`  ${c.dim("--<source> <n>")}          Source filter: max results from <source> (0 = skip)`);
+  console.log(`  ${c.dim("--path <dir>")}            Filter context results to files under this path prefix`);
+  console.log(`  ${c.dim("--ignore <globs>")}        Ignore glob patterns for code indexing (comma-separated)`);
+  console.log(`  ${c.dim("--yes / -y")}              Skip interactive prompt (auto-select all available)`);
   console.log(`  ${c.dim("--reranker <name>")}       Reranker to use (qwen3)`);
+  console.log(`  ${c.dim("--port <n>")}              HTTP daemon port (default: 8181)`);
   console.log("");
   console.log(c.bold("Examples:"));
   console.log(c.dim("  brainbank index ."));
+  console.log(c.dim('  brainbank index . --ignore "sdk/**,vendor/**"'));
   console.log(c.dim('  brainbank kv add errors "Fixed null pointer in api.ts"'));
   console.log(c.dim('  brainbank kv search errors "null pointer"'));
   console.log(c.dim("  brainbank kv list"));
   console.log(c.dim('  brainbank hsearch "authentication middleware"'));
-  console.log(c.dim('  brainbank context "add rate limiting to the API"'));
-  console.log(c.dim("  brainbank serve"));
+  console.log(c.dim('  brainbank hsearch "auth" --code 0 --git 10           # git only'));
+  console.log(c.dim('  brainbank search "handler" --git 0                   # code only'));
+  console.log(c.dim('  brainbank hsearch "api" --docs 10 --code 0 --git 0   # docs only'));
+  console.log(c.dim('  brainbank context "auth flow" | pbcopy               # \u2192 clipboard'));
+  console.log(c.dim("  brainbank daemon start                               # background HTTP"));
+  console.log(c.dim("  brainbank mcp                                        # MCP stdio"));
 }
 __name(showHelp, "showHelp");
 
@@ -834,6 +1519,7 @@ __name(showHelp, "showHelp");
 var command = args[0];
 async function main() {
   switch (command) {
+    case "i":
     case "index":
       return cmdIndex();
     case "collection":
@@ -852,14 +1538,23 @@ async function main() {
       return cmdKeywordSearch();
     case "context":
       return cmdContext();
+    case "files":
+      return cmdFiles();
     case "stats":
       return cmdStats();
     case "reembed":
       return cmdReembed();
     case "watch":
       return cmdWatch();
+    case "mcp":
+      return cmdMcp();
     case "serve":
-      return cmdServe();
+      return cmdMcp();
+    // backward compat
+    case "daemon":
+      return cmdDaemon();
+    case "status":
+      return cmdStatus();
     case "help":
     case "--help":
     case "-h":