brainbank 0.9.5 → 0.9.6

package/README.md

@@ -88,7 +88,7 @@ Extensions that connect BrainBank to external tools and workflows.
 
 | Package | Description | Install |
 |---------|-------------|----------|
-| [`@brainbank/mcp`](packages/mcp/) | MCP server for Antigravity, Claude, Cursor | `npm i @brainbank/mcp` |
+| [`@brainbank/mcp`](packages/mcp/) | MCP server for Antigravity, Claude, Cursor (read-only, 2 tools) | `npm i @brainbank/mcp` |
 
 ---
 
@@ -105,7 +105,7 @@ Extensions that connect BrainBank to external tools and workflows.
 | **[Configuration](docs/config.md)** | `.brainbank/config.json`, env vars |
 | **[Embeddings, Reranker & Pruner](docs/embeddings.md)** | Providers, benchmarks, per-plugin overrides, LLM noise filter |
 | **[Multi-Repo](docs/multi-repo.md)** | Index multiple repositories into one DB |
-| **[MCP Server](docs/mcp.md)** | AI tool integration (stdio) |
+| **[MCP Server](docs/mcp.md)** | AI tool integration (stdio), `mcp:export` setup |
 | **[Indexing](docs/indexing.md)** | Code graph, incremental indexing, re-embedding |
 | **[Migrations](docs/migrations.md)** | Plugin schema migrations, built-in schemas |
 | **[Architecture](docs/architecture.md)** | System internals, data flows, design patterns |

package/dist/cli.js

@@ -44,7 +44,7 @@ var TARGETS = {
     label: "Gemini Antigravity"
   }
 };
-function buildBrainbankMcpBlock(config, repoPath) {
+function buildBrainbankMcpBlock(config) {
   const nodeBin = process.execPath;
   const globalCliJs = path.join(path.dirname(nodeBin), "..", "lib", "node_modules", "brainbank", "dist", "cli.js");
   const localCliJs = path.resolve(__dirname, "..", "..", "dist", "cli.js");
@@ -57,7 +57,6 @@ function buildBrainbankMcpBlock(config, repoPath) {
   if (perplexityKey) env.PERPLEXITY_API_KEY = perplexityKey;
   if (anthropicKey) env.ANTHROPIC_API_KEY = anthropicKey;
   if (openaiKey) env.OPENAI_API_KEY = openaiKey;
-  env.BRAINBANK_REPO = path.resolve(repoPath);
   const block = {
     command: nodeBin,
     args: ["--disable-warning=ExperimentalWarning", resolvedCliJs, "mcp"]
@@ -104,7 +103,7 @@ async function autoExportMcp(repoPath) {
   if (!fs.existsSync(antigravityDir)) return;
   if (hasBrainbankMcpEntry(target.configPath)) return;
   const config = await getConfig(repoPath);
-  const block = buildBrainbankMcpBlock(config, repoPath);
+  const block = buildBrainbankMcpBlock(config);
   mergeAndWrite(target.configPath, block);
   console.log(`  ${c.green("\u2713")} Exported MCP config to ${c.dim(path.relative(process.env.HOME ?? "", target.configPath))}`);
 }
@@ -170,7 +169,7 @@ __name(replaceGeminiSection, "replaceGeminiSection");
 async function cmdMcpExport() {
   const targetName = args[1] || getFlag("target") || "antigravity";
   const repoPath = getFlag("repo") || ".";
-  const { confirm } = await import("@inquirer/prompts");
+  const force = args.includes("--force") || args.includes("-f");
   const target = TARGETS[targetName];
   if (!target) {
     console.error(c.red(`Unknown export target: ${targetName}`));
@@ -178,18 +177,19 @@ async function cmdMcpExport() {
     process.exit(1);
   }
   const config = await getConfig(repoPath);
-  const block = buildBrainbankMcpBlock(config, repoPath);
+  const block = buildBrainbankMcpBlock(config);
   console.log(c.bold(`
 \u2501\u2501\u2501 MCP Export: ${target.label} \u2501\u2501\u2501
 `));
   const mcpExists = hasBrainbankMcpEntry(target.configPath);
   let writeMcp = true;
-  if (mcpExists) {
+  if (mcpExists && !force) {
     console.log(`  ${c.yellow("\u25CF")} MCP config already has brainbank entry`);
     const cliPath = block.args.find((a) => !a.startsWith("--")) ?? block.args[0];
     console.log(`  ${c.dim("  New:")} ${block.command} ${cliPath}`);
     const envKeys = block.env ? Object.keys(block.env) : [];
     if (envKeys.length > 0) console.log(`  ${c.dim("  Keys:")} ${envKeys.join(", ")}`);
+    const { confirm } = await import("@inquirer/prompts");
     writeMcp = await confirm({ message: "Override existing brainbank MCP entry?", default: true });
   }
   if (writeMcp) {
@@ -200,22 +200,34 @@ async function cmdMcpExport() {
   }
   const geminiHasSection = hasGeminiSection(GLOBAL_GEMINI);
   if (geminiHasSection) {
-    console.log(`  ${c.yellow("\u25CF")} ~/.gemini/GEMINI.md already has BrainBank section`);
-    const override = await confirm({ message: "Override existing BrainBank section?", default: false });
-    if (override) {
+    if (force) {
       replaceGeminiSection(GLOBAL_GEMINI);
       console.log(`  ${c.green("\u2713")} Replaced BrainBank section in ${c.dim("~/.gemini/GEMINI.md")}`);
     } else {
-      console.log(`  ${c.dim("GEMINI.md \u2014 skipped")}`);
+      console.log(`  ${c.yellow("\u25CF")} ~/.gemini/GEMINI.md already has BrainBank section`);
+      const { confirm } = await import("@inquirer/prompts");
+      const override = await confirm({ message: "Override existing BrainBank section?", default: false });
+      if (override) {
+        replaceGeminiSection(GLOBAL_GEMINI);
+        console.log(`  ${c.green("\u2713")} Replaced BrainBank section in ${c.dim("~/.gemini/GEMINI.md")}`);
+      } else {
+        console.log(`  ${c.dim("GEMINI.md \u2014 skipped")}`);
+      }
     }
   } else {
-    const addGemini = await confirm({
-      message: "Add BrainBank instructions to ~/.gemini/GEMINI.md? (teaches AI tools how to use BrainBank)",
-      default: true
-    });
-    if (addGemini) {
+    if (force) {
       appendGeminiSection(GLOBAL_GEMINI);
       console.log(`  ${c.green("\u2713")} Added BrainBank section to ${c.dim("~/.gemini/GEMINI.md")}`);
+    } else {
+      const { confirm } = await import("@inquirer/prompts");
+      const addGemini = await confirm({
+        message: "Add BrainBank instructions to ~/.gemini/GEMINI.md? (teaches AI tools how to use BrainBank)",
+        default: true
+      });
+      if (addGemini) {
+        appendGeminiSection(GLOBAL_GEMINI);
+        console.log(`  ${c.green("\u2713")} Added BrainBank section to ${c.dim("~/.gemini/GEMINI.md")}`);
+      }
     }
   }
   console.log(`

package/dist/cli.js.map

@@ -1 +1 @@
-{"version":3,"sources":["../src/cli/commands/index.ts","../src/cli/commands/mcp-export.ts","../src/cli/commands/scan.ts","../src/cli/commands/collection.ts","../src/cli/commands/kv.ts","../src/cli/commands/docs.ts","../src/cli/commands/search.ts","../src/cli/server-client.ts","../src/cli/commands/context.ts","../src/cli/commands/files.ts","../src/cli/commands/stats.ts","../src/cli/commands/reembed.ts","../src/cli/commands/watch.ts","../src/cli/commands/mcp.ts","../src/cli/commands/daemon.ts","../src/cli/commands/status.ts","../src/cli/commands/help.ts","../src/cli/index.ts"],"sourcesContent":["/**\n * brainbank index [path] — Interactive scan → select → index\n *\n * Scans the repo first, shows a summary tree, and prompts the user\n * with checkboxes to select which modules to index. Use --yes to skip.\n */\n\nimport type { ScanResult, ScanModule } from './scan.ts';\n\nimport * as fs from 'node:fs';\nimport * as path from 'node:path';\nimport { c, args, getFlag, hasFlag, stripFlags } from '@/cli/utils.ts';\nimport { createBrain, getConfig, registerConfigCollections } from '@/cli/factory/index.ts';\nimport { findDocsPlugin } from '@/cli/utils.ts';\nimport { autoExportMcp } from './mcp-export.ts';\nimport { scanRepo } from './scan.ts';\n\nexport async function cmdIndex(): Promise<void> {\n    const positional = stripFlags(args);\n    const repoPath = positional[1] || '.';\n    const force = hasFlag('force');\n    const depth = parseInt(getFlag('depth') || '500', 10);\n    const onlyRaw = getFlag('only');\n    const docsPath = getFlag('docs');\n    const skipPrompt = hasFlag('yes') || hasFlag('y');\n\n\n    const scan = scanRepo(repoPath);\n    printScanTree(scan, depth);\n\n\n    let modules: string[];\n\n    if (onlyRaw) {\n        // --only flag: explicit module selection\n        modules = onlyRaw.split(',').map(s => s.trim());\n    } else if (scan.config.plugins && scan.config.plugins.length > 0) {\n        // Config exists with plugins field — use it as source of truth\n        modules = scan.config.plugins;\n        console.log(c.dim(`\\n  Using config: plugins = [${modules.join(', ')}]\\n`));\n    } else if (skipPrompt) {\n        modules = buildDefaultModules(scan);\n    } else {\n        modules = await promptModules(scan);\n        if (modules.length === 0) {\n            console.log(c.dim('\\n  Nothing selected. Exiting.\\n'));\n            return;\n        }\n\n        // Clean screen and show selection summary\n        console.clear();\n        console.log(c.bold('\\n━━━ BrainBank ━━━\\n'));\n        console.log('  Selected modules:');\n        for (const m of modules) {\n            console.log(`    ${c.green('✓')} ${m}`);\n        }\n        console.log('');\n    }\n\n    // If --docs is passed, auto-include 'docs' in modules\n    if (docsPath && !modules.includes('docs')) {\n        modules.push('docs');\n    }\n\n    // Auto-generate config.json if it doesn't exist yet\n    if (!scan.config.exists && !skipPrompt) {\n        await saveConfig(scan.repoPath, modules);\n    }\n\n\n    console.log(c.bold(`\\n━━━ Indexing: ${modules.join(', ')} ━━━`));\n\n    const brain = await createBrain(repoPath);\n    await brain.initialize();\n\n    const config = await getConfig(repoPath);\n    await registerConfigCollections(brain, repoPath, config);\n\n    if (docsPath) {\n        const absDocsPath = path.resolve(docsPath);\n        const collName = path.basename(absDocsPath);\n        try {\n            const docsPlugin = findDocsPlugin(brain);\n            await docsPlugin?.addCollection({\n                name: collName,\n                path: absDocsPath,\n                pattern: '**/*.md',\n                ignore: ['deprecated/**', 'node_modules/**'],\n            });\n            console.log(c.dim(`  Registered docs collection: ${collName}`));\n        } catch {\n            console.log(c.yellow(`  Warning: docs module not loaded, skipping --docs`));\n        }\n    }\n\n    const result = await brain.index({\n        modules,\n        forceReindex: force,\n        pluginOptions: { depth },\n        onProgress: (stage, msg) => {\n            process.stdout.write(`\\r  ${c.cyan(stage.toUpperCase())} ${msg}                    `);\n        },\n    });\n\n    console.log('\\n');\n    for (const [name, value] of Object.entries(result)) {\n        if (!value) continue;\n        const v = value as Record<string, unknown>;\n        if (typeof v.indexed === 'number') {\n            const parts = [`${v.indexed} indexed`, `${v.skipped ?? 0} skipped`];\n            if (typeof v.chunks === 'number') parts.push(`${v.chunks} chunks`);\n            if (typeof v.removed === 'number' && v.removed > 0) parts.push(`${v.removed} removed`);\n            console.log(`  ${c.green(name)}: ${parts.join(', ')}`);\n        } else {\n            console.log(`  ${c.green(name)}: done`);\n        }\n    }\n\n    const stats = brain.stats();\n    console.log(`\\n  ${c.bold('Totals')}:`);\n    for (const [name, s] of Object.entries(stats)) {\n        if (!s || typeof s !== 'object') continue;\n        const entries = Object.entries(s as Record<string, unknown>)\n            .map(([k, v]) => `${k}: ${v}`)\n            .join(', ');\n        console.log(`    ${name}: ${entries}`);\n    }\n\n    brain.close();\n\n    // Auto-export MCP config to Antigravity if detected and not already configured\n    await autoExportMcp(repoPath);\n}\n\n\nfunction printScanTree(scan: ScanResult, depth: number): void {\n    console.clear();\n    console.log(c.bold('\\n━━━ BrainBank Scan ━━━'));\n    console.log(c.dim(`  Repo: ${scan.repoPath}`));\n\n    // Multi-repo detection\n    if (scan.gitSubdirs.length > 0) {\n        console.log(c.cyan(`\\n  🔀 Multi-repo — ${scan.gitSubdirs.length} git repos detected`));\n        for (const sub of scan.gitSubdirs) {\n            console.log(c.dim(`     └── ${sub.name}`));\n        }\n    }\n\n    // Dynamic module display\n    for (const mod of scan.modules) {\n        console.log('');\n        if (mod.available) {\n            const extra = mod.name === 'git' ? ` (depth: ${depth})` : '';\n            console.log(`  ${mod.icon} ${c.bold(capitalizeFirst(mod.name))} — ${mod.summary}${extra}`);\n            if (mod.details) {\n                for (const d of mod.details) {\n                    console.log(c.dim(`     ${d}`));\n                }\n            }\n        } else {\n            console.log(`  ${mod.icon} ${c.dim(`${capitalizeFirst(mod.name)} — ${mod.summary}`)}`);\n        }\n    }\n\n    // Config ignore\n    if (scan.config.ignore?.length) {\n        console.log(c.dim(`     Ignore: ${scan.config.ignore.join(', ')}`));\n    }\n\n    // Config & DB\n    console.log('');\n    if (scan.config.exists) {\n        console.log(`  ⚙️  ${c.dim('Config:')} .brainbank/config.json ${c.green('✓')}`);\n    }\n    if (scan.db?.exists) {\n        const ago = scan.db.lastModified ? timeSince(scan.db.lastModified) : '';\n        console.log(`  💾 ${c.dim('DB:')} ${scan.db.sizeMB} MB${ago ? `, last indexed ${ago}` : ''}`);\n    } else {\n        console.log(`  💾 ${c.dim('DB: new (first index)')}`);\n    }\n    console.log('');\n}\n\n\n/** Build the default list of available modules based on scan. */\nfunction buildDefaultModules(scan: ScanResult): string[] {\n    return scan.modules.filter(m => m.available && m.checked).map(m => m.name);\n}\n\n/** Interactive checkbox prompt via @inquirer/prompts. */\nasync function promptModules(scan: ScanResult): Promise<string[]> {\n    const { checkbox } = await import('@inquirer/prompts');\n    console.log(c.dim('  ─────────────────────────────────────────\\n'));\n\n    const choices = scan.modules.map((m: ScanModule) => ({\n        name: `${capitalizeFirst(m.name).padEnd(6)} — ${m.summary}`,\n        value: m.name,\n        checked: m.checked && m.available,\n        disabled: m.available ? undefined : m.disabled,\n    }));\n\n    return checkbox<string>({\n        message: 'Select modules to index:\\n',\n        choices,\n    });\n}\n\n\nfunction timeSince(date: Date): string {\n    const seconds = Math.floor((Date.now() - date.getTime()) / 1000);\n    if (seconds < 60) return 'just now';\n    const minutes = Math.floor(seconds / 60);\n    if (minutes < 60) return `${minutes}m ago`;\n    const hours = Math.floor(minutes / 60);\n    if (hours < 24) return `${hours}h ago`;\n    const days = Math.floor(hours / 24);\n    return `${days}d ago`;\n}\n\n/** Capitalize first letter. */\nfunction capitalizeFirst(s: string): string {\n    return s.charAt(0).toUpperCase() + s.slice(1);\n}\n\n/** Generate .brainbank/config.json from the selected modules. */\nasync function saveConfig(repoPath: string, modules: string[]): Promise<void> {\n    const { select, confirm } = await import('@inquirer/prompts');\n\n    // Embedding provider selection\n    const envEmbedding = process.env.BRAINBANK_EMBEDDING;\n    const embedding = await select<string>({\n        message: 'Embedding provider:',\n        choices: [\n            {\n                name: 'perplexity-context  — best accuracy (recommended)',\n                value: 'perplexity-context',\n            },\n            {\n                name: 'perplexity          — fast, high quality',\n                value: 'perplexity',\n            },\n            {\n                name: 'openai              — text-embedding-3-small',\n                value: 'openai',\n            },\n            {\n                name: 'local               — offline, no API key needed',\n                value: 'local',\n            },\n        ],\n        default: envEmbedding ?? 'perplexity-context',\n    });\n\n    // Pruner selection\n    const pruner = await select<string>({\n        message: 'Noise pruner:',\n        choices: [\n            {\n                name: 'haiku  — AI-powered noise filter (recommended)',\n                value: 'haiku',\n            },\n            {\n                name: 'none   — no pruning',\n                value: 'none',\n            },\n        ],\n        default: 'haiku',\n    });\n\n    const configDir = path.join(repoPath, '.brainbank');\n    const configPath = path.join(configDir, 'config.json');\n\n    const config: Record<string, unknown> = {\n        plugins: modules,\n        embedding,\n    };\n\n    if (pruner !== 'none') {\n        config.pruner = pruner;\n    }\n\n    // Key management: detect available keys and offer to save\n    const detectedKeys: Record<string, string> = {};\n    const needsPerplexity = embedding.startsWith('perplexity');\n    const needsAnthropic = pruner === 'haiku';\n    const needsOpenai = embedding === 'openai';\n\n    if (needsPerplexity && process.env.PERPLEXITY_API_KEY) {\n        detectedKeys.perplexity = process.env.PERPLEXITY_API_KEY;\n    }\n    if (needsAnthropic && process.env.ANTHROPIC_API_KEY) {\n        detectedKeys.anthropic = process.env.ANTHROPIC_API_KEY;\n    }\n    if (needsOpenai && process.env.OPENAI_API_KEY) {\n        detectedKeys.openai = process.env.OPENAI_API_KEY;\n    }\n\n    if (Object.keys(detectedKeys).length > 0) {\n        const keyNames = Object.keys(detectedKeys).join(', ');\n        const saveKeys = await confirm({\n            message: `Save API keys (${keyNames}) to config.json? (portable, no env vars needed)`,\n            default: true,\n        });\n        if (saveKeys) {\n            config.keys = detectedKeys;\n        }\n    }\n\n    fs.mkdirSync(configDir, { recursive: true });\n    fs.writeFileSync(configPath, JSON.stringify(config, null, 2) + '\\n');\n    console.log(c.green(`  ✓ Saved ${path.relative(process.cwd(), configPath)}`));\n}\n\n","/**\n * brainbank mcp:export [target] — Export MCP server config for AI IDEs.\n *\n * Generates the MCP server config block for brainbank and merges it into\n * the target IDE's config file. Currently supports: antigravity.\n *\n * Detects: node path, cli.js path, API keys from config or env vars.\n */\n\nimport type { ProjectConfig } from '@/cli/factory/config-loader.ts';\n\nimport * as fs from 'node:fs';\nimport * as path from 'node:path';\nimport { fileURLToPath } from 'node:url';\nimport { c, args, getFlag } from '@/cli/utils.ts';\nimport { getConfig } from '@/cli/factory/index.ts';\n\nconst __filename = fileURLToPath(import.meta.url);\nconst __dirname = path.dirname(__filename);\n\n/** Supported export targets and their config file paths. */\nconst TARGETS: Record<string, { configPath: string; label: string }> = {\n    antigravity: {\n        configPath: path.join(process.env.HOME ?? '~', '.gemini', 'antigravity', 'mcp_config.json'),\n        label: 'Gemini Antigravity',\n    },\n};\n\ninterface McpServerConfig {\n    command: string;\n    args: string[];\n    env?: Record<string, string>;\n    cwd?: string;\n}\n\ninterface McpConfig {\n    mcpServers: Record<string, McpServerConfig>;\n}\n\n/**\n * Build the brainbank MCP server config block.\n * Resolves node binary, dist/cli.js path, and API keys.\n */\nfunction buildBrainbankMcpBlock(config: ProjectConfig | null, repoPath: string): McpServerConfig {\n    const nodeBin = process.execPath;\n\n    // Resolve dist/cli.js from the global install location (node_prefix/lib/node_modules/brainbank/dist/cli.js)\n    const globalCliJs = path.join(path.dirname(nodeBin), '..', 'lib', 'node_modules', 'brainbank', 'dist', 'cli.js');\n    // Fallback: relative to this file (dev / npm link)\n    const localCliJs = path.resolve(__dirname, '..', '..', 'dist', 'cli.js');\n    const resolvedCliJs = fs.existsSync(globalCliJs) ? globalCliJs : localCliJs;\n\n    const env: Record<string, string> = {};\n\n    // Resolve API keys: config.keys > env vars\n    const keys = config?.keys;\n    const perplexityKey = keys?.perplexity ?? process.env.PERPLEXITY_API_KEY;\n    const anthropicKey = keys?.anthropic ?? process.env.ANTHROPIC_API_KEY;\n    const openaiKey = keys?.openai ?? process.env.OPENAI_API_KEY;\n\n    if (perplexityKey) env.PERPLEXITY_API_KEY = perplexityKey;\n    if (anthropicKey) env.ANTHROPIC_API_KEY = anthropicKey;\n    if (openaiKey) env.OPENAI_API_KEY = openaiKey;\n\n    // Inject repo path so the MCP server knows where the index lives\n    env.BRAINBANK_REPO = path.resolve(repoPath);\n\n    const block: McpServerConfig = {\n        command: nodeBin,\n        args: ['--disable-warning=ExperimentalWarning', resolvedCliJs, 'mcp'],\n    };\n\n    if (Object.keys(env).length > 0) {\n        block.env = env;\n    }\n\n    return block;\n}\n\n/**\n * Load existing MCP config, merge brainbank entry, and write back.\n * Preserves all other server entries.\n */\nfunction mergeAndWrite(targetPath: string, block: McpServerConfig): { created: boolean } {\n    let existing: McpConfig = { mcpServers: {} };\n    const created = !fs.existsSync(targetPath);\n\n    if (!created) {\n        try {\n            const raw = fs.readFileSync(targetPath, 'utf-8');\n            existing = JSON.parse(raw) as McpConfig;\n            if (!existing.mcpServers) existing.mcpServers = {};\n        } catch {\n            // Corrupt or empty file — start fresh\n            existing = { mcpServers: {} };\n        }\n    }\n\n    existing.mcpServers.brainbank = block;\n\n    fs.mkdirSync(path.dirname(targetPath), { recursive: true });\n    fs.writeFileSync(targetPath, JSON.stringify(existing, null, 2) + '\\n');\n\n    return { created };\n}\n\n/** Check if an MCP config already has a brainbank entry. */\nexport function hasBrainbankMcpEntry(targetPath: string): boolean {\n    if (!fs.existsSync(targetPath)) return false;\n    try {\n        const raw = fs.readFileSync(targetPath, 'utf-8');\n        const config = JSON.parse(raw) as McpConfig;\n        return !!config.mcpServers?.brainbank;\n    } catch {\n        return false;\n    }\n}\n\n/** Auto-export: called after index when Antigravity is detected. */\nexport async function autoExportMcp(repoPath: string): Promise<void> {\n    const target = TARGETS.antigravity;\n    if (!target) return;\n\n    // Only auto-export if Antigravity dir exists\n    const antigravityDir = path.dirname(target.configPath);\n    if (!fs.existsSync(antigravityDir)) return;\n\n    // Only auto-export if brainbank isn't already configured\n    if (hasBrainbankMcpEntry(target.configPath)) return;\n\n    const config = await getConfig(repoPath);\n    const block = buildBrainbankMcpBlock(config, repoPath);\n    mergeAndWrite(target.configPath, block);\n    console.log(`  ${c.green('✓')} Exported MCP config to ${c.dim(path.relative(process.env.HOME ?? '', target.configPath))}`);\n}\n\n// ── GEMINI.md BrainBank Section ──────────────────────────────\n\nconst BRAINBANK_SECTION_MARKER = '<!-- brainbank:start -->';\nconst BRAINBANK_SECTION_END = '<!-- brainbank:end -->';\n\n/** Global GEMINI.md path — ~/.gemini/GEMINI.md (shared across all projects). */\nconst GLOBAL_GEMINI = path.join(process.env.HOME ?? '~', '.gemini', 'GEMINI.md');\n\nfunction buildGeminiSection(): string {\n    return `${BRAINBANK_SECTION_MARKER}\n\n## BrainBank — Code Intelligence\n\nWhen \\`brainbank_context\\` and \\`brainbank_files\\` MCP tools are available, **always use them instead of \\`grep_search\\` or \\`list_dir\\`**.\n\n**\\`brainbank_context\\`** — semantic search. \\`repo\\` is **required** (the project root where \\`brainbank index\\` was run). Use \\`path:\\` to scope within it, \\`compact: false\\`, \\`sources: { code: 25, docs: 0, git: 0 }\\`.\n\n**\\`brainbank_files\\`** — read full indexed files (\\`lines: true\\` always). Only works with files tracked by the index — for \\`.env\\`, \\`docker-compose.yml\\`, etc. use \\`view_file\\`.\n\n**Sources rule:** Default to code-only (\\`docs: 0\\`). Only add \\`docs\\` when the user explicitly asks about documentation. Never mix code and docs in the same query — fire separate queries.\n\n### Output handling (critical)\n\nBrainBank may return results **inline** or save them to an **output file**:\n\n- **Inline:** read and proceed normally.\n- **File result** (saved to \\`output.txt\\`): show the path as a clickable link, ask user to paste, then **STOP and WAIT**:\n\n  📋 Output: [output.txt](file:///path/to/output.txt) — _\"Could you paste the context output here?\"_\n\n  Do **NOT** read the file yourself. Wait for the paste before proceeding.\n\n${BRAINBANK_SECTION_END}\n`;\n}\n\n/** Check if GEMINI.md already has the brainbank section. */\nfunction hasGeminiSection(geminiPath: string): boolean {\n    if (!fs.existsSync(geminiPath)) return false;\n    const content = fs.readFileSync(geminiPath, 'utf-8');\n    return content.includes(BRAINBANK_SECTION_MARKER);\n}\n\n/** Append BrainBank section to GEMINI.md (creates if doesn't exist). */\nfunction appendGeminiSection(geminiPath: string): void {\n    const section = buildGeminiSection();\n    if (fs.existsSync(geminiPath)) {\n        fs.appendFileSync(geminiPath, section);\n    } else {\n        fs.writeFileSync(geminiPath, `# GEMINI.md\\n${section}`);\n    }\n}\n\n/** Replace BrainBank section between markers in GEMINI.md. */\nfunction replaceGeminiSection(geminiPath: string): void {\n    const content = fs.readFileSync(geminiPath, 'utf-8');\n    const startIdx = content.indexOf(BRAINBANK_SECTION_MARKER);\n    const endIdx = content.indexOf(BRAINBANK_SECTION_END);\n    if (startIdx === -1 || endIdx === -1) return;\n\n    const before = content.slice(0, startIdx);\n    const after = content.slice(endIdx + BRAINBANK_SECTION_END.length);\n    const section = buildGeminiSection();\n    fs.writeFileSync(geminiPath, before + section + after);\n}\n\n/** CLI command: brainbank mcp:export [target] */\nexport async function cmdMcpExport(): Promise<void> {\n    const targetName = args[1] || getFlag('target') || 'antigravity';\n    const repoPath = getFlag('repo') || '.';\n    const { confirm } = await import('@inquirer/prompts');\n\n    const target = TARGETS[targetName];\n    if (!target) {\n        console.error(c.red(`Unknown export target: ${targetName}`));\n        console.error(c.dim(`  Available: ${Object.keys(TARGETS).join(', ')}`));\n        process.exit(1);\n    }\n\n    const config = await getConfig(repoPath);\n    const block = buildBrainbankMcpBlock(config, repoPath);\n\n    console.log(c.bold(`\\n━━━ MCP Export: ${target.label} ━━━\\n`));\n\n    // ── MCP Config ────────────────────────────────────────────\n    const mcpExists = hasBrainbankMcpEntry(target.configPath);\n    let writeMcp = true;\n\n    if (mcpExists) {\n        console.log(`  ${c.yellow('●')} MCP config already has brainbank entry`);\n        const cliPath = block.args.find(a => !a.startsWith('--')) ?? block.args[0];\n        console.log(`  ${c.dim('  New:')} ${block.command} ${cliPath}`);\n        const envKeys = block.env ? Object.keys(block.env) : [];\n        if (envKeys.length > 0) console.log(`  ${c.dim('  Keys:')} ${envKeys.join(', ')}`);\n        writeMcp = await confirm({ message: 'Override existing brainbank MCP entry?', default: true });\n    }\n\n    if (writeMcp) {\n        const { created } = mergeAndWrite(target.configPath, block);\n        console.log(`  ${c.green('✓')} ${created ? 'Created' : 'Updated'} ${c.dim(target.configPath)}`);\n    } else {\n        console.log(`  ${c.dim('MCP config — skipped')}`);\n    }\n\n    // ── Global GEMINI.md (~/.gemini/GEMINI.md) ────────────────\n    const geminiHasSection = hasGeminiSection(GLOBAL_GEMINI);\n\n    if (geminiHasSection) {\n        console.log(`  ${c.yellow('●')} ~/.gemini/GEMINI.md already has BrainBank section`);\n        const override = await confirm({ message: 'Override existing BrainBank section?', default: false });\n        if (override) {\n            replaceGeminiSection(GLOBAL_GEMINI);\n            console.log(`  ${c.green('✓')} Replaced BrainBank section in ${c.dim('~/.gemini/GEMINI.md')}`);\n        } else {\n            console.log(`  ${c.dim('GEMINI.md — skipped')}`);\n        }\n    } else {\n        const addGemini = await confirm({\n            message: 'Add BrainBank instructions to ~/.gemini/GEMINI.md? (teaches AI tools how to use BrainBank)',\n            default: true,\n        });\n        if (addGemini) {\n            appendGeminiSection(GLOBAL_GEMINI);\n            console.log(`  ${c.green('✓')} Added BrainBank section to ${c.dim('~/.gemini/GEMINI.md')}`);\n        }\n    }\n\n    console.log(`\\n  ${c.dim('Restart your IDE to apply changes.')}\\n`);\n}\n","/**\n * brainbank scan — Lightweight repo scanner for the interactive index flow.\n *\n * Scans the filesystem WITHOUT initializing BrainBank. Returns a ScanResult\n * describing what's available to index via dynamic ScanModule descriptors.\n */\n\nimport * as fs from 'node:fs';\nimport * as path from 'node:path';\nimport { execSync } from 'node:child_process';\nimport { SUPPORTED_EXTENSIONS, isIgnoredDir, isIgnoredFile } from '@/lib/languages.ts';\n\n\n/** A single scannable module (plugin). */\nexport interface ScanModule {\n    /** Plugin name (e.g. 'code', 'git', 'docs'). */\n    name: string;\n    /** Whether there's content available to index. */\n    available: boolean;\n    /** Human-readable summary (e.g. '1243 files (5 languages)'). */\n    summary: string;\n    /** Emoji icon for display. */\n    icon: string;\n    /** Whether checked by default in the prompt. */\n    checked: boolean;\n    /** Reason this module is disabled (shown in prompt). */\n    disabled?: string;\n    /** Detail lines for the scan tree (e.g. per-language breakdown). */\n    details?: string[];\n}\n\nexport interface ScanResult {\n    repoPath: string;\n    modules: ScanModule[];\n    config: { exists: boolean; ignore?: string[]; plugins?: string[] };\n    db: { exists: boolean; sizeMB: number; lastModified?: Date } | null;\n    gitSubdirs: { name: string }[];\n}\n\n\n/** Scan a repo path and return what's available to index. */\nexport function scanRepo(repoPath: string): ScanResult {\n    const resolved = path.resolve(repoPath);\n    const gitSubdirs = scanGitSubdirs(resolved);\n\n    return {\n        repoPath: resolved,\n        modules: scanModules(resolved, gitSubdirs),\n        config: scanConfig(resolved),\n        db: scanDb(resolved),\n        gitSubdirs,\n    };\n}\n\n/** Produce ScanModule descriptors for known plugin types. */\nfunction scanModules(repoPath: string, gitSubdirs: { name: string }[]): ScanModule[] {\n    return [\n        scanCodeModule(repoPath),\n        scanGitModule(repoPath, gitSubdirs),\n        scanDocsModule(repoPath),\n    ];\n}\n\n\n/** Scan for indexable code files. */\nfunction scanCodeModule(repoPath: string): ScanModule {\n    const byLanguage = new Map<string, number>();\n    let total = 0;\n\n    function walk(dir: string): void {\n        let entries: fs.Dirent[];\n        try { entries = fs.readdirSync(dir, { withFileTypes: true }); }\n        catch { return; }\n\n        for (const entry of entries) {\n            const fullPath = path.join(dir, entry.name);\n            const isDir = entry.isDirectory() || (entry.isSymbolicLink() && (() => { try { return fs.statSync(fullPath).isDirectory(); } catch { return false; } })());\n            if (isDir) {\n                if (isIgnoredDir(entry.name)) continue;\n                walk(fullPath);\n            } else if (entry.isFile()) {\n                if (isIgnoredFile(entry.name)) continue;\n                const ext = path.extname(entry.name).toLowerCase();\n                const lang = SUPPORTED_EXTENSIONS[ext];\n                if (!lang) continue;\n                byLanguage.set(lang, (byLanguage.get(lang) ?? 0) + 1);\n                total++;\n            }\n        }\n    }\n\n    walk(repoPath);\n\n    if (total === 0) {\n        return { name: 'code', available: false, summary: 'no supported source files found', icon: '📁', checked: false, disabled: 'nothing to index' };\n    }\n\n    const langCount = byLanguage.size;\n    const sorted = [...byLanguage.entries()].sort((a, b) => b[1] - a[1]);\n    const maxShow = 7;\n    const shown = sorted.slice(0, maxShow);\n    const remaining = sorted.length - maxShow;\n\n    const details: string[] = [];\n    for (let i = 0; i < shown.length; i++) {\n        const [lang, count] = shown[i];\n        const isLast = i === shown.length - 1 && remaining <= 0;\n        const prefix = isLast ? '└──' : '├──';\n        details.push(`${prefix} ${lang.padEnd(14)} ${count} files`);\n    }\n    if (remaining > 0) {\n        details.push(`└── ...and ${remaining} more`);\n    }\n\n    return {\n        name: 'code',\n        available: true,\n        summary: `${total} files (${langCount} language${langCount > 1 ? 's' : ''})`,\n        icon: '📁',\n        checked: true,\n        details,\n    };\n}\n\n/** Scan for git history. */\nfunction scanGitModule(repoPath: string, gitSubdirs: { name: string }[]): ScanModule {\n    const stats = scanGitStats(repoPath, gitSubdirs);\n\n    if (!stats) {\n        return { name: 'git', available: false, summary: 'no .git directory found', icon: '📜', checked: false, disabled: 'not a git repo' };\n    }\n\n    const details: string[] = [];\n    if (stats.lastMessage) {\n        details.push(`Last: ${stats.lastMessage} (${stats.lastDate})`);\n    }\n\n    return {\n        name: 'git',\n        available: true,\n        summary: `${stats.commitCount.toLocaleString()} commits`,\n        icon: '📜',\n        checked: true,\n        details,\n    };\n}\n\n/** Scan for document collections. */\nfunction scanDocsModule(repoPath: string): ScanModule {\n    const collections = scanDocsCollections(repoPath);\n\n    if (collections.length === 0) {\n        return { name: 'docs', available: false, summary: 'no documents found', icon: '📄', checked: false, disabled: 'no .md/.mdx files' };\n    }\n\n    const totalFiles = collections.reduce((s, d) => s + d.fileCount, 0);\n    const details = collections.map((d, i) => {\n        const isLast = i === collections.length - 1;\n        const prefix = isLast ? '└──' : '├──';\n        return `${prefix} ${d.name.padEnd(10)} → ${d.path} (${d.fileCount} files)`;\n    });\n\n    return {\n        name: 'docs',\n        available: true,\n        summary: `${collections.length} collection${collections.length > 1 ? 's' : ''} (${totalFiles} files)`,\n        icon: '📄',\n        checked: true,\n        details,\n    };\n}\n\n\n/** Get git stats. Supports single repo and multi-repo aggregation. */\nfunction scanGitStats(repoPath: string, gitSubdirs: { name: string }[]): { commitCount: number; lastMessage: string; lastDate: string } | null {\n    if (fs.existsSync(path.join(repoPath, '.git'))) {\n        return gitStats(repoPath);\n    }\n\n    if (gitSubdirs.length === 0) return null;\n\n    let totalCommits = 0;\n    let latestMessage = '';\n    let latestDate = '';\n\n    for (const sub of gitSubdirs) {\n        const stats = gitStats(path.join(repoPath, sub.name));\n        if (stats) {\n            totalCommits += stats.commitCount;\n            if (!latestMessage) {\n                latestMessage = stats.lastMessage;\n                latestDate = stats.lastDate;\n            }\n        }\n    }\n\n    return totalCommits > 0\n        ? { commitCount: totalCommits, lastMessage: latestMessage, lastDate: latestDate }\n        : null;\n}\n\n/** Get git stats for a single directory. */\nfunction gitStats(dir: string): { commitCount: number; lastMessage: string; lastDate: string } | null {\n    try {\n        const count = parseInt(execSync('git rev-list --count HEAD', { cwd: dir, encoding: 'utf-8' }).trim(), 10);\n        const log = execSync('git log -1 --format=\"%s|%ar\"', { cwd: dir, encoding: 'utf-8' }).trim();\n        const [lastMessage, lastDate] = log.split('|');\n        return { commitCount: count, lastMessage: lastMessage ?? '', lastDate: lastDate ?? '' };\n    } catch {\n        return null;\n    }\n}\n\n/** Scan for document collections (config + auto-detect). */\nfunction scanDocsCollections(repoPath: string): { name: string; path: string; fileCount: number }[] {\n    const results: { name: string; path: string; fileCount: number }[] = [];\n    const seen = new Set<string>();\n\n    // 1. Read explicit collections from config.json\n    const configPath = path.join(repoPath, '.brainbank', 'config.json');\n    try {\n        if (fs.existsSync(configPath)) {\n            const config = JSON.parse(fs.readFileSync(configPath, 'utf-8')) as Record<string, unknown>;\n            const docsCfg = config?.docs as Record<string, unknown> | undefined;\n            const collections = docsCfg?.collections as { name: string; path: string }[] | undefined;\n            if (collections) {\n                for (const coll of collections) {\n                    const absPath = path.resolve(repoPath, coll.path);\n                    results.push({ name: coll.name, path: coll.path, fileCount: countDocs(absPath) });\n                    seen.add(absPath);\n                }\n            }\n        }\n    } catch {}\n\n    // 2. Auto-detect .md/.mdx in the repo root and top-level dirs\n    const rootDocs = countDocsShallow(repoPath);\n    if (rootDocs > 0) {\n        results.push({ name: '(root)', path: '.', fileCount: rootDocs });\n    }\n\n    try {\n        for (const entry of fs.readdirSync(repoPath, { withFileTypes: true })) {\n            if (!entry.isDirectory()) continue;\n            if (isIgnoredDir(entry.name)) continue;\n            if (entry.name.startsWith('.')) continue;\n\n            const dirPath = path.join(repoPath, entry.name);\n            if (seen.has(dirPath)) continue;\n\n            const count = countDocs(dirPath);\n            if (count > 0) {\n                results.push({ name: entry.name, path: `./${entry.name}`, fileCount: count });\n            }\n        }\n    } catch {}\n\n    return results;\n}\n\n/** Count .md/.mdx files recursively in a directory. */\nfunction countDocs(dir: string): number {\n    let count = 0;\n    try {\n        for (const e of fs.readdirSync(dir, { withFileTypes: true })) {\n            const ePath = path.join(dir, e.name);\n            const isDir = e.isDirectory() || (e.isSymbolicLink() && (() => { try { return fs.statSync(ePath).isDirectory(); } catch { return false; } })());\n            if (isDir) {\n                if (isIgnoredDir(e.name)) continue;\n                count += countDocs(ePath);\n            } else if ((e.isFile() || e.isSymbolicLink()) && /\\.mdx?$/i.test(e.name)) {\n                count++;\n            }\n        }\n    } catch {}\n    return count;\n}\n\n/** Count .md/.mdx files in a directory (non-recursive, root level only). */\nfunction countDocsShallow(dir: string): number {\n    let count = 0;\n    try {\n        for (const e of fs.readdirSync(dir, { withFileTypes: true })) {\n            if (e.isFile() && /\\.mdx?$/i.test(e.name)) count++;\n        }\n    } catch {}\n    return count;\n}\n\n/** Check if config.json exists and read key fields. */\nfunction scanConfig(repoPath: string): ScanResult['config'] {\n    const configPath = path.join(repoPath, '.brainbank', 'config.json');\n    if (!fs.existsSync(configPath)) return { exists: false };\n\n    try {\n        const config = JSON.parse(fs.readFileSync(configPath, 'utf-8')) as Record<string, unknown>;\n        const codeCfg = config?.code as Record<string, unknown> | undefined;\n        return {\n            exists: true,\n            ignore: codeCfg?.ignore as string[] | undefined,\n            plugins: config?.plugins as string[] | undefined,\n        };\n    } catch {\n        return { exists: false };\n    }\n}\n\n/** Check DB existence and size. */\nfunction scanDb(repoPath: string): ScanResult['db'] {\n    const dbPath = path.join(repoPath, '.brainbank', 'data', 'brainbank.db');\n    if (!fs.existsSync(dbPath)) return { exists: false, sizeMB: 0 };\n\n    try {\n        const stat = fs.statSync(dbPath);\n        return {\n            exists: true,\n            sizeMB: Math.round(stat.size / 1024 / 1024 * 10) / 10,\n            lastModified: stat.mtime,\n        };\n    } catch {\n        return { exists: false, sizeMB: 0 };\n    }\n}\n\n/** Detect subdirectories with their own .git (mono-repo). Respects `repos` whitelist from config. */\nfunction scanGitSubdirs(repoPath: string): ScanResult['gitSubdirs'] {\n    if (fs.existsSync(path.join(repoPath, '.git'))) return [];\n\n    try {\n        let subdirs = fs.readdirSync(repoPath, { withFileTypes: true })\n            .filter(e => {\n                if (e.name.startsWith('.')) return false;\n                const isDir = e.isDirectory() || (e.isSymbolicLink() && (() => { try { return fs.statSync(path.join(repoPath, e.name)).isDirectory(); } catch { return false; } })());\n                return isDir;\n            })\n            .filter(e => fs.existsSync(path.join(repoPath, e.name, '.git')))\n            .map(e => ({ name: e.name }));\n\n        // Apply repos whitelist from config if present\n        const configRepos = readReposFromConfig(repoPath);\n        if (configRepos) {\n            subdirs = subdirs.filter(s => configRepos.includes(s.name));\n        }\n\n        return subdirs;\n    } catch {\n        return [];\n    }\n}\n\n/** Read the `repos` whitelist from .brainbank/config.json. Returns null if not set. */\nfunction readReposFromConfig(repoPath: string): string[] | null {\n    const configPath = path.join(repoPath, '.brainbank', 'config.json');\n    try {\n        if (!fs.existsSync(configPath)) return null;\n        const config = JSON.parse(fs.readFileSync(configPath, 'utf-8')) as Record<string, unknown>;\n        const repos = config.repos;\n        if (Array.isArray(repos) && repos.every(r => typeof r === 'string')) {\n            return repos as string[];\n        }\n        return null;\n    } catch {\n        return null;\n    }\n}\n","/**\n * brainbank collection add|list|remove — Document collection management\n */\n\nimport { c, args, getFlag, stripFlags, findDocsPlugin } from '@/cli/utils.ts';\nimport { createBrain } from '@/cli/factory/index.ts';\n\nexport async function cmdCollection(): Promise<void> {\n    const pos = stripFlags(args);\n    const sub = pos[1];\n\n    if (sub === 'add') {\n        const path = pos[2];\n        const name = getFlag('name');\n        const pattern = getFlag('pattern') ?? '**/*.md';\n        const context = getFlag('context');\n        const ignoreRaw = getFlag('ignore');\n\n        if (!path || !name) {\n            console.log(c.red('Usage: brainbank collection add <path> --name <name> [--pattern \"**/*.md\"] [--ignore \"glob\"] [--context \"description\"]'));\n            process.exit(1);\n        }\n\n        const brain = await createBrain();\n        const docsPlugin = findDocsPlugin(brain);\n        if (!docsPlugin) { console.log(c.red('Docs plugin not loaded. Install @brainbank/docs.')); process.exit(1); }\n        await docsPlugin.addCollection({\n            name,\n            path,\n            pattern,\n            ignore: ignoreRaw ? ignoreRaw.split(',') : [],\n            context: context ?? undefined,\n        });\n        console.log(c.green(`✓ Collection '${name}' added: ${path} (${pattern})`));\n        if (context) console.log(c.dim(`  Context: ${context}`));\n        brain.close();\n        return;\n    }\n\n    if (sub === 'list') {\n        const brain = await createBrain();\n        await brain.initialize();\n        const docsPlugin = findDocsPlugin(brain);\n        if (!docsPlugin) { console.log(c.yellow('  Docs plugin not loaded.')); brain.close(); return; }\n        const collections = docsPlugin.listCollections();\n        if (collections.length === 0) {\n            console.log(c.yellow('  No collections registered.'));\n        } else {\n            console.log(c.bold('\\n━━━ Collections ━━━\\n'));\n            for (const col of collections) {\n                console.log(`  ${c.cyan(col.name)} ${c.dim('→')} ${col.path}`);\n                console.log(`    Pattern: ${col.pattern ?? '**/*.md'}`);\n                if (col.context) console.log(`    Context: ${c.dim(col.context)}`);\n            }\n        }\n        brain.close();\n        return;\n    }\n\n    if (sub === 'remove') {\n        const name = pos[2];\n        if (!name) {\n            console.log(c.red('Usage: brainbank collection remove <name>'));\n            process.exit(1);\n        }\n        const brain = await createBrain();\n        const docsPlugin = findDocsPlugin(brain);\n        if (!docsPlugin) { console.log(c.red('Docs plugin not loaded.')); process.exit(1); }\n        await docsPlugin.removeCollection(name);\n        console.log(c.green(`✓ Collection '${name}' removed.`));\n        brain.close();\n        return;\n    }\n\n    console.log(c.red('Usage: brainbank collection <add|list|remove>'));\n    process.exit(1);\n}\n","/**\n * brainbank kv add|search|list|trim|clear — Dynamic KV collection management\n */\n\nimport { c, args, getFlag, stripFlags } from '@/cli/utils.ts';\nimport { createBrain } from '@/cli/factory/index.ts';\n\nexport async function cmdKv(): Promise<void> {\n    const pos = stripFlags(args);\n    const sub = pos[1];\n\n    if (sub === 'add') {\n        const collName = pos[2];\n        const content = pos.slice(3).join(' ');\n        const metaRaw = getFlag('meta');\n\n        if (!collName || !content) {\n            console.log(c.red(\"Usage: brainbank kv add <collection> <content> [--meta '{\\\"key\\\":\\\"val\\\"}']\"));\n            process.exit(1);\n        }\n\n        const brain = await createBrain();\n        await brain.initialize();\n        const coll = brain.collection(collName);\n        const meta = metaRaw ? JSON.parse(metaRaw) : {};\n        const id = await coll.add(content, meta);\n        console.log(c.green(`✓ Added item #${id} to '${collName}'`));\n        brain.close();\n        return;\n    }\n\n    if (sub === 'search') {\n        const collName = pos[2];\n        const query = pos.slice(3).join(' ');\n        const k = parseInt(getFlag('k') || '5', 10);\n        const mode = (getFlag('mode') || 'hybrid') as 'hybrid' | 'vector' | 'keyword';\n\n        if (!collName || !query) {\n            console.log(c.red('Usage: brainbank kv search <collection> <query> [--k 5] [--mode hybrid|keyword|vector]'));\n            process.exit(1);\n        }\n\n        const brain = await createBrain();\n        await brain.initialize();\n        const coll = brain.collection(collName);\n        const results = await coll.search(query, { k, mode });\n\n        if (results.length === 0) {\n            console.log(c.yellow('  No results found.'));\n        } else {\n            console.log(c.bold(`\\n━━━ ${collName}: \"${query}\" ━━━\\n`));\n            for (const r of results) {\n                const score = Math.round((r.score ?? 0) * 100);\n                console.log(`  ${c.cyan(`[${score}%]`)} ${r.content}`);\n                if (Object.keys(r.metadata).length > 0) {\n                    console.log(`    ${c.dim(JSON.stringify(r.metadata))}`);\n                }\n            }\n        }\n        brain.close();\n        return;\n    }\n\n    if (sub === 'list') {\n        const collName = pos[2];\n        const limit = parseInt(getFlag('limit') || '20', 10);\n\n        if (!collName) {\n            const brain = await createBrain();\n            await brain.initialize();\n            const names = brain.listCollectionNames();\n            if (names.length === 0) {\n                console.log(c.yellow('  No KV collections found.'));\n            } else {\n                console.log(c.bold('\\n━━━ KV Collections ━━━\\n'));\n                for (const n of names) {\n                    const coll = brain.collection(n);\n                    console.log(`  ${c.cyan(n)} — ${coll.count()} items`);\n                }\n            }\n            brain.close();\n            return;\n        }\n\n        const brain = await createBrain();\n        await brain.initialize();\n        const coll = brain.collection(collName);\n        const items = coll.list({ limit });\n        if (items.length === 0) {\n            console.log(c.yellow(`  Collection '${collName}' is empty.`));\n        } else {\n            console.log(c.bold(`\\n━━━ ${collName} (${coll.count()} items) ━━━\\n`));\n            for (const item of items) {\n                const age = Math.round((Date.now() / 1000 - item.createdAt) / 60);\n                console.log(`  #${item.id} ${c.dim(`(${age}m ago)`)} ${item.content.slice(0, 80)}`);\n            }\n        }\n        brain.close();\n        return;\n    }\n\n    if (sub === 'trim') {\n        const collName = pos[2];\n        const keep = parseInt(getFlag('keep') || '0', 10);\n\n        if (!collName || keep <= 0) {\n            console.log(c.red('Usage: brainbank kv trim <collection> --keep <n>'));\n            process.exit(1);\n        }\n\n        const brain = await createBrain();\n        await brain.initialize();\n        const coll = brain.collection(collName);\n        const result = await coll.trim({ keep });\n        console.log(c.green(`✓ Trimmed ${result.removed} items from '${collName}' (kept ${keep})`));\n        brain.close();\n        return;\n    }\n\n    if (sub === 'clear') {\n        const collName = pos[2];\n        if (!collName) {\n            console.log(c.red('Usage: brainbank kv clear <collection>'));\n            process.exit(1);\n        }\n\n        const brain = await createBrain();\n        await brain.initialize();\n        const coll = brain.collection(collName);\n        const before = coll.count();\n        coll.clear();\n        console.log(c.green(`✓ Cleared ${before} items from '${collName}'`));\n        brain.close();\n        return;\n    }\n\n    console.log(c.red('Usage: brainbank kv <add|search|list|trim|clear>'));\n    process.exit(1);\n}\n\n","/**\n * brainbank docs — Index document collections\n * brainbank dsearch — Search documents only\n */\n\nimport { c, args, getFlag, stripFlags, findDocsPlugin } from '@/cli/utils.ts';\nimport { createBrain } from '@/cli/factory/index.ts';\n\nexport async function cmdDocs(): Promise<void> {\n    const collection = getFlag('collection');\n    const brain = await createBrain();\n\n    console.log(c.bold('\\n━━━ BrainBank Docs Index ━━━\\n'));\n\n    const opts: { collections?: string[]; onProgress?: (collection: string, file: string, current: number, total: number) => void } = {};\n    if (collection) opts.collections = [collection];\n    opts.onProgress = (col: string, file: string, cur: number, total: number) => {\n        process.stdout.write(`\\r  ${c.cyan(col)} [${cur}/${total}] ${file}                    `);\n    };\n\n    const docsPlugin = findDocsPlugin(brain);\n    if (!docsPlugin) { console.log(c.red('  Docs plugin not loaded. Install @brainbank/docs.')); process.exit(1); }\n\n    const results = await docsPlugin.indexDocs(opts);\n\n    console.log('\\n');\n    for (const [name, stat] of Object.entries(results) as [string, { indexed: number; skipped: number; removed: number; chunks: number }][]) {\n        const removedStr = stat.removed > 0 ? `, ${c.red(String(stat.removed) + ' removed')}` : '';\n        console.log(`  ${c.green(name)}: ${stat.indexed} indexed, ${stat.skipped} skipped${removedStr}, ${stat.chunks} chunks`);\n    }\n\n    brain.close();\n}\n\nexport async function cmdDocSearch(): Promise<void> {\n    const query = stripFlags(args).slice(1).join(' ');\n    if (!query) {\n        console.log(c.red('Usage: brainbank dsearch <query>'));\n        process.exit(1);\n    }\n\n    const brain = await createBrain();\n    const collection = getFlag('collection');\n    const k = parseInt(getFlag('k') || '8', 10);\n\n    console.log(c.bold(`\\n━━━ BrainBank Doc Search: \"${query}\" ━━━\\n`));\n\n    const docsPlugin = findDocsPlugin(brain);\n    if (!docsPlugin) {\n        console.log(c.red('Docs plugin not loaded. Install @brainbank/docs.'));\n        process.exit(1);\n    }\n    const results = await docsPlugin.search(query, { collection: collection ?? undefined, k });\n\n    if (results.length === 0) {\n        console.log(c.yellow('  No results found.'));\n        brain.close();\n        return;\n    }\n\n    for (const r of results) {\n        const score = Math.round(r.score * 100);\n        const ctx = r.context ? ` — ${c.dim(r.context)}` : '';\n        console.log(`${c.magenta(`[DOC ${score}%]`)} ${c.bold(r.filePath!)} [${r.type === 'document' ? r.metadata.collection ?? '' : ''}]${ctx}`);\n        const preview = r.content.split('\\n').slice(0, 4).join('\\n');\n        console.log(c.dim(preview));\n        console.log('');\n    }\n\n    brain.close();\n}\n","/**\n * brainbank search  — Semantic search (vector)\n * brainbank hsearch — Hybrid search (vector + BM25)\n * brainbank ksearch — Keyword search (BM25)\n *\n * Source filtering:\n *   --code 10             Max code results\n *   --git 0               Skip git results\n *   --docs 5              Max document results\n *   --notes 10            Custom plugin results\n *   --slack_messages 5    Custom collection results\n *\n * Any --<name> <number> flag is treated as a source filter.\n */\n\nimport { c, args, stripFlags, printResults } from '@/cli/utils.ts';\nimport { createBrain } from '@/cli/factory/index.ts';\n\n/**\n * Parse dynamic source flags: each `--<name> <number>` becomes `{ name: number }`.\n *\n * Known non-source flags (--repo, --depth, etc.) are excluded.\n * Returns sources map + the query string (positional args).\n */\nfunction parseSourceFlags(): { sources: Record<string, number>; query: string } {\n    const NON_SOURCE_FLAGS = new Set([\n        'repo', 'depth', 'collection', 'pattern', 'context', 'name',\n        'keep', 'reranker', 'pruner', 'only', 'docs-path', 'mode', 'limit',\n        'ignore', 'meta', 'k', 'yes', 'y', 'force', 'verbose',\n    ]);\n\n    const sources: Record<string, number> = {};\n    const positional: string[] = [];\n\n    for (let i = 0; i < args.length; i++) {\n        if (args[i].startsWith('--')) {\n            const name = args[i].slice(2);\n\n            // Skip boolean flags\n            if (name === 'yes' || name === 'force' || name === 'verbose') continue;\n\n            // If next arg is a number and flag is not a known non-source flag\n            const next = args[i + 1];\n            if (next !== undefined && /^\\d+$/.test(next) && !NON_SOURCE_FLAGS.has(name)) {\n                sources[name] = parseInt(next, 10);\n                i++; // skip the value\n                continue;\n            }\n\n            // Known value flag — skip its value\n            if (NON_SOURCE_FLAGS.has(name) && next !== undefined && !next.startsWith('--')) {\n                i++;\n            }\n            continue;\n        }\n        positional.push(args[i]);\n    }\n\n    const query = positional.slice(1).join(' '); // skip command name\n    return { sources, query };\n}\n\n/** Print active source filters. */\nfunction printFilterInfo(sources: Record<string, number>): void {\n    const entries = Object.entries(sources);\n    if (entries.length === 0) return;\n    const parts = entries.map(([k, v]) => `${k}=${v}`);\n    console.log(c.dim(`  Sources: ${parts.join(', ')}`));\n}\n\n/** Build search options from sources map. */\nfunction buildSearchOptions(sources: Record<string, number>): { sources: Record<string, number>; source: 'cli' } {\n    return Object.keys(sources).length > 0 ? { sources, source: 'cli' } : { sources: {}, source: 'cli' };\n}\n\nexport async function cmdSearch(): Promise<void> {\n    const { sources, query } = parseSourceFlags();\n    if (!query) {\n        console.log(c.red('Usage: brainbank search <query> [--code <n>] [--git <n>] [--<source> <n>]'));\n        process.exit(1);\n    }\n\n    const brain = await createBrain();\n    console.log(c.bold(`\\n━━━ BrainBank Search: \"${query}\" ━━━\\n`));\n    printFilterInfo(sources);\n\n    const opts = buildSearchOptions(sources);\n    const results = await brain.search(query, opts);\n    printResults(results);\n    brain.close();\n}\n\nexport async function cmdHybridSearch(): Promise<void> {\n    const { sources, query } = parseSourceFlags();\n    if (!query) {\n        console.log(c.red('Usage: brainbank hsearch <query> [--code <n>] [--git <n>] [--docs <n>] [--<source> <n>]'));\n        process.exit(1);\n    }\n\n    const brain = await createBrain();\n    console.log(c.bold(`\\n━━━ BrainBank Hybrid Search: \"${query}\" ━━━`));\n    console.log(c.dim(`  Mode: vector + BM25 → Reciprocal Rank Fusion`));\n    printFilterInfo(sources);\n    console.log('');\n\n    const opts = buildSearchOptions(sources);\n    const results = await brain.hybridSearch(query, opts);\n    printResults(results);\n    brain.close();\n}\n\nexport async function cmdKeywordSearch(): Promise<void> {\n    const { sources, query } = parseSourceFlags();\n    if (!query) {\n        console.log(c.red('Usage: brainbank ksearch <query> [--code <n>] [--git <n>] [--<source> <n>]'));\n        process.exit(1);\n    }\n\n    const brain = await createBrain();\n    await brain.initialize();\n    console.log(c.bold(`\\n━━━ BrainBank Keyword Search: \"${query}\" ━━━`));\n    console.log(c.dim(`  Mode: BM25 full-text (instant)`));\n    printFilterInfo(sources);\n    console.log('');\n\n    const opts = buildSearchOptions(sources);\n    const results = await brain.searchBM25(query, opts);\n    printResults(results);\n    brain.close();\n}\n","/**\n * ServerClient — Lightweight HTTP client for the BrainBank daemon.\n *\n * Used by CLI commands to delegate to a running HTTP server\n * instead of loading models locally. Falls back gracefully\n * (returns null) if the server is unreachable.\n */\n\nimport * as http from 'node:http';\n\nimport { isServerRunning } from '@/services/daemon.ts';\n\ninterface ContextOptions {\n    task: string;\n    repo?: string;\n    sources?: Record<string, number>;\n    pathPrefix?: string;\n    affectedFiles?: string[];\n}\n\n/**\n * Try to get context from the running HTTP server.\n * Returns the context string if successful, null if server is unreachable.\n */\nexport async function tryServerContext(options: ContextOptions): Promise<string | null> {\n    const info = isServerRunning();\n    if (!info) return null;\n\n    try {\n        const body = JSON.stringify({\n            task: options.task,\n            repo: options.repo,\n            sources: options.sources,\n            pathPrefix: options.pathPrefix,\n            affectedFiles: options.affectedFiles,\n        });\n\n        const response = await httpPost(info.port, '/context', body);\n        const data = JSON.parse(response) as { context?: string; error?: string };\n\n        if (data.error) return null;\n        return data.context ?? null;\n    } catch {\n        // Server unreachable or error — fall back to local\n        return null;\n    }\n}\n\n/**\n * Try to trigger indexing on the running HTTP server.\n * Returns the result if successful, null if server is unreachable.\n */\nexport async function tryServerIndex(repo?: string, forceReindex?: boolean): Promise<Record<string, unknown> | null> {\n    const info = isServerRunning();\n    if (!info) return null;\n\n    try {\n        const body = JSON.stringify({ repo, forceReindex });\n        const response = await httpPost(info.port, '/index', body);\n        const data = JSON.parse(response) as { result?: Record<string, unknown>; error?: string };\n\n        if (data.error) return null;\n        return data.result ?? null;\n    } catch {\n        return null;\n    }\n}\n\n/**\n * Check server health. Returns health info or null.\n */\nexport async function serverHealth(): Promise<{\n    ok: boolean;\n    pid: number;\n    port: number;\n    uptime: number;\n    workspaces: number;\n} | null> {\n    const info = isServerRunning();\n    if (!info) return null;\n\n    try {\n        const response = await httpGet(info.port, '/health');\n        return JSON.parse(response) as { ok: boolean; pid: number; port: number; uptime: number; workspaces: number };\n    } catch {\n        return null;\n    }\n}\n\n// ── HTTP helpers ────────────────────────────────────\n\nfunction httpPost(port: number, path: string, body: string): Promise<string> {\n    return new Promise((resolve, reject) => {\n        const req = http.request({\n            hostname: '127.0.0.1',\n            port,\n            path,\n            method: 'POST',\n            headers: {\n                'Content-Type': 'application/json',\n                'Content-Length': Buffer.byteLength(body),\n            },\n            timeout: 120_000, // 2 minutes — context queries can be slow on first load\n        }, (res) => {\n            const chunks: Buffer[] = [];\n            res.on('data', (chunk: Buffer) => chunks.push(chunk));\n            res.on('end', () => resolve(Buffer.concat(chunks).toString('utf8')));\n        });\n\n        req.on('error', reject);\n        req.on('timeout', () => { req.destroy(); reject(new Error('Request timed out')); });\n        req.write(body);\n        req.end();\n    });\n}\n\nfunction httpGet(port: number, path: string): Promise<string> {\n    return new Promise((resolve, reject) => {\n        const req = http.request({\n            hostname: '127.0.0.1',\n            port,\n            path,\n            method: 'GET',\n            timeout: 5_000,\n        }, (res) => {\n            const chunks: Buffer[] = [];\n            res.on('data', (chunk: Buffer) => chunks.push(chunk));\n            res.on('end', () => resolve(Buffer.concat(chunks).toString('utf8')));\n        });\n\n        req.on('error', reject);\n        req.on('timeout', () => { req.destroy(); reject(new Error('Request timed out')); });\n        req.end();\n    });\n}\n","/**\n * brainbank context <task> — Get formatted context for a task\n * brainbank context add <collection> <path> <description>\n * brainbank context list\n *\n * Source filtering (same as search commands):\n *   --code 20    Max code results (default: 20)\n *   --git 5      Max git results\n *   --no-git     Skip git results\n *   --no-code    Skip code results\n *   --path <dir> Filter results to files under this path prefix\n *   --ignore <paths> Exclude paths (comma-separated or repeated: --ignore a,b --ignore c)\n */\n\nimport { c, args, stripFlags, getFlag, getFlagAll, findDocsPlugin } from '@/cli/utils.ts';\nimport { createBrain } from '@/cli/factory/index.ts';\nimport { tryServerContext } from '@/cli/server-client.ts';\n\n/** Parse --code N, --git N, --no-git, --no-code flags into sources map. */\nfunction parseContextFlags(): Record<string, number> {\n    const NON_SOURCE = new Set([\n        'repo', 'depth', 'collection', 'pattern', 'context', 'name',\n        'keep', 'reranker', 'pruner', 'only', 'docs-path', 'mode', 'limit',\n        'ignore', 'meta', 'k', 'yes', 'y', 'force', 'verbose', 'path',\n    ]);\n    const sources: Record<string, number> = {};\n    for (let i = 0; i < args.length; i++) {\n        if (!args[i].startsWith('--')) continue;\n        const name = args[i].slice(2);\n        // --no-git, --no-code → set to 0\n        if (name.startsWith('no-')) {\n            sources[name.slice(3)] = 0;\n            continue;\n        }\n        // --code 20, --git 5\n        const next = args[i + 1];\n        if (next !== undefined && /^\\d+$/.test(next) && !NON_SOURCE.has(name)) {\n            sources[name] = parseInt(next, 10);\n            i++;\n        }\n    }\n    return sources;\n}\n\nexport async function cmdContext(): Promise<void> {\n    const pos = stripFlags(args);\n    const sub = pos[1];\n\n    // brainbank context add <collection> <path> <description>\n    if (sub === 'add') {\n        const collection = pos[2];\n        const path = pos[3];\n        const desc = pos.slice(4).join(' ');\n\n        if (!collection || !path || !desc) {\n            console.log(c.red('Usage: brainbank context add <collection> <path> <description>'));\n            process.exit(1);\n        }\n\n        const brain = await createBrain();\n        await brain.initialize();\n        const docsPlugin = findDocsPlugin(brain);\n        if (!docsPlugin) { console.log(c.red('Docs plugin not loaded.')); process.exit(1); }\n        docsPlugin.addContext(collection, path, desc);\n        console.log(c.green(`✓ Context added: ${collection}:${path} → \"${desc}\"`));\n        brain.close();\n        return;\n    }\n\n    // brainbank context list\n    if (sub === 'list') {\n        const brain = await createBrain();\n        await brain.initialize();\n        const docsPlugin = findDocsPlugin(brain);\n        if (!docsPlugin) { console.log(c.yellow('  Docs plugin not loaded.')); brain.close(); return; }\n        const contexts = docsPlugin.listContexts();\n        if (contexts.length === 0) {\n            console.log(c.yellow('  No contexts configured.'));\n        } else {\n            console.log(c.bold('\\n━━━ Contexts ━━━\\n'));\n            for (const ctx of contexts) {\n                console.log(`  ${c.cyan(ctx.collection)}:${ctx.path} → ${c.dim(ctx.context)}`);\n            }\n        }\n        brain.close();\n        return;\n    }\n\n    // brainbank context <task> — get formatted context\n    const task = stripFlags(args).slice(1).join(' ');\n    if (!task) {\n        console.log(c.red('Usage: brainbank context <task description>'));\n        console.log(c.dim('       brainbank context add <collection> <path> <description>'));\n        console.log(c.dim('       brainbank context list'));\n        process.exit(1);\n    }\n\n    const sources = parseContextFlags();\n    const pathPrefix = getFlag('path');\n    const ignorePaths = getFlagAll('ignore');\n    const repo = getFlag('repo');\n\n    // Parse BrainBankQL field flags\n    const fields = parseFieldFlags();\n\n    // Try HTTP server delegation first\n    const serverResult = await tryServerContext({\n        task,\n        repo: repo ?? process.cwd(),\n        sources: Object.keys(sources).length > 0 ? sources : undefined,\n        pathPrefix,\n    });\n\n    if (serverResult !== null) {\n        console.log(serverResult);\n        return;\n    }\n\n    // Fall back to local\n    const brain = await createBrain();\n    const context = await brain.getContext(task, {\n        sources: Object.keys(sources).length > 0 ? sources : undefined,\n        pathPrefix,\n        ignorePaths: ignorePaths.length > 0 ? ignorePaths : undefined,\n        source: 'cli',\n        fields: Object.keys(fields).length > 0 ? fields : undefined,\n    });\n    console.log(context);\n    brain.close();\n}\n\n/** Parse BrainBankQL field flags: --lines, --symbols, --compact, --no-callTree, --callTree.depth=N, etc. */\nfunction parseFieldFlags(): Record<string, unknown> {\n    const FIELD_BOOLEANS = new Set(['lines', 'symbols', 'compact', 'expander']);\n    const FIELD_NEGATABLE = new Set(['callTree', 'imports']);\n    const fields: Record<string, unknown> = {};\n\n    for (let i = 0; i < args.length; i++) {\n        if (!args[i].startsWith('--')) continue;\n        const raw = args[i].slice(2);\n\n        // --no-callTree, --no-imports → set to false\n        if (raw.startsWith('no-')) {\n            const name = raw.slice(3);\n            if (FIELD_NEGATABLE.has(name)) {\n                fields[name] = false;\n            }\n            continue;\n        }\n\n        // --callTree.depth=4 → { depth: 4 }\n        const dotIdx = raw.indexOf('.');\n        if (dotIdx > 0) {\n            const fieldName = raw.slice(0, dotIdx);\n            const rest = raw.slice(dotIdx + 1);\n            const eqIdx = rest.indexOf('=');\n            if (eqIdx > 0) {\n                const key = rest.slice(0, eqIdx);\n                const val = parseInt(rest.slice(eqIdx + 1), 10);\n                if (!isNaN(val)) {\n                    fields[fieldName] = { [key]: val };\n                }\n            }\n            continue;\n        }\n\n        // --lines, --symbols, --compact, --expander → true\n        if (FIELD_BOOLEANS.has(raw)) {\n            fields[raw] = true;\n        }\n    }\n\n    return fields;\n}\n","/**\n * brainbank files <path|glob> [...paths] [--lines]\n *\n * Fetch full file contents from the index.\n * Use after `brainbank context` to view complete files identified by search.\n */\n\nimport { c, args, getFlag } from '@/cli/utils.ts';\nimport { createBrain } from '@/cli/factory/index.ts';\n\nexport async function cmdFiles(): Promise<void> {\n    // Collect positional args (file patterns) — skip 'files' command itself\n    const patterns: string[] = [];\n    const showLines = args.includes('--lines');\n\n    for (let i = 1; i < args.length; i++) {\n        if (args[i].startsWith('--')) {\n            // Skip --lines and --repo <value>\n            if (args[i] === '--repo') {\n                i++; // skip value\n            }\n            continue;\n        }\n        patterns.push(args[i]);\n    }\n\n    if (patterns.length === 0) {\n        console.log(c.red('Usage: brainbank files <path|glob> [...paths] [--lines]'));\n        console.log(c.dim('  Exact:     brainbank files src/auth/login.ts'));\n        console.log(c.dim('  Directory: brainbank files src/graph/'));\n        console.log(c.dim('  Glob:      brainbank files \"src/**/*.service.ts\"'));\n        console.log(c.dim('  Fuzzy:     brainbank files plugin.ts'));\n        console.log(c.dim('  Lines:     brainbank files src/plugin.ts --lines'));\n        process.exit(1);\n    }\n\n    const brain = await createBrain();\n    await brain.initialize();\n    const results = brain.resolveFiles(patterns);\n\n    if (results.length === 0) {\n        console.log(c.yellow('No matching files found in the index.'));\n        console.log(c.dim('Run `brainbank index` first to index your codebase.'));\n        brain.close();\n        return;\n    }\n\n    // Format output\n    for (const r of results) {\n        const meta = r.metadata as Record<string, unknown>;\n        const startLine = (meta.startLine as number) ?? 1;\n\n        console.log(c.bold(`\\n── ${r.filePath} ──\\n`));\n\n        if (showLines) {\n            const codeLines = r.content.split('\\n');\n            const pad = String(startLine + codeLines.length - 1).length;\n            for (let i = 0; i < codeLines.length; i++) {\n                const lineNum = c.dim(`${String(startLine + i).padStart(pad)}|`);\n                console.log(`${lineNum} ${codeLines[i]}`);\n            }\n        } else {\n            console.log(r.content);\n        }\n    }\n\n    console.log(c.dim(`\\n${results.length} file(s) resolved.`));\n    brain.close();\n}\n","/** brainbank stats — Show index statistics. */\n\nimport { c } from '@/cli/utils.ts';\nimport { createBrain } from '@/cli/factory/index.ts';\n\n/** Convert camelCase/snake_case stat keys to human-readable labels. */\nfunction formatStatKey(key: string): string {\n    return key\n        .replace(/([a-z])([A-Z])/g, '$1 $2')\n        .replace(/_/g, ' ')\n        .replace(/\\b\\w/g, c => c.toUpperCase())\n        .padEnd(16);\n}\n\nexport async function cmdStats(): Promise<void> {\n    const brain = await createBrain();\n    await brain.initialize();\n\n    const s = brain.stats();\n\n    console.log(c.bold('\\n━━━ BrainBank Stats ━━━\\n'));\n    console.log(`  ${c.cyan('Plugins')}: ${brain.plugins.join(', ')}\\n`);\n\n    for (const [name, pluginStats] of Object.entries(s)) {\n        if (!pluginStats) continue;\n        console.log(`  ${c.cyan(name)}`);\n        for (const [key, value] of Object.entries(pluginStats)) {\n            console.log(`    ${formatStatKey(key)}${value}`);\n        }\n        console.log('');\n    }\n\n    const kvNames = brain.listCollectionNames();\n    if (kvNames.length > 0) {\n        console.log(`  ${c.cyan('KV Collections')}`);\n        for (const name of kvNames) {\n            const coll = brain.collection(name);\n            console.log(`    ${name}: ${coll.count()} items`);\n        }\n        console.log('');\n    }\n\n    brain.close();\n}\n","/** brainbank reembed — Re-embed all vectors. */\n\nimport { c } from '@/cli/utils.ts';\nimport { createBrain } from '@/cli/factory/index.ts';\n\nexport async function cmdReembed(): Promise<void> {\n    const brain = await createBrain();\n    await brain.initialize();\n\n    console.log(c.bold('\\n━━━ BrainBank Re-embed ━━━\\n'));\n    console.log(c.dim('  Regenerating vectors with current embedding provider...'));\n    console.log(c.dim('  Text, FTS, and metadata remain unchanged.\\n'));\n\n    const result = await brain.reembed({\n        onProgress: (table: string, current: number, total: number) => {\n            process.stdout.write(`\\r  ${c.cyan(table.padEnd(8))} ${current}/${total}`);\n        },\n    });\n\n    console.log('\\n');\n    for (const [name, count] of Object.entries(result.counts)) {\n        if (count > 0) {\n            const label = name.charAt(0).toUpperCase() + name.slice(1);\n            console.log(`  ${c.green('✓')} ${label.padEnd(8)} ${count} vectors`);\n        }\n    }\n    console.log(`\\n  ${c.bold('Total')}: ${result.total} vectors regenerated\\n`);\n\n    brain.close();\n}\n","/** brainbank watch — Watch for file changes. */\n\nimport { c } from '@/cli/utils.ts';\nimport { createBrain } from '@/cli/factory/index.ts';\nimport { loadConfig } from '@/cli/factory/config-loader.ts';\n\nexport async function cmdWatch(): Promise<void> {\n    const brain = await createBrain();\n    await brain.initialize();\n\n    // Read ignore patterns from config (code.ignore + top-level ignore)\n    const config = await loadConfig(brain.config.repoPath);\n    const codeIgnore = (config?.code as Record<string, unknown> | undefined)?.ignore as string[] ?? [];\n\n    console.log(c.bold('\\n━━━ BrainBank Watch ━━━\\n'));\n    console.log(c.dim(`  Watching ${brain.config.repoPath} for changes...`));\n    if (codeIgnore.length > 0) {\n        console.log(c.dim(`  Ignoring: ${codeIgnore.join(', ')}`));\n    }\n    console.log(c.dim('  Press Ctrl+C to stop.\\n'));\n\n    const watcher = brain.watch({\n        debounceMs: 2000,\n        ignore: codeIgnore,\n        onIndex: (sourceId: string, pluginName: string) => {\n            const ts = new Date().toLocaleTimeString();\n            console.log(`  ${c.dim(ts)} ${c.green('✓')} ${c.cyan(pluginName)}: ${sourceId}`);\n        },\n        onError: (err: Error) => {\n            console.error(`  ${c.red('✗')} ${err.message}`);\n        },\n    });\n\n    process.on('SIGINT', () => {\n        console.log(c.dim('\\n  Stopping watcher...'));\n        watcher.close();\n        brain.close();\n        process.exit(0);\n    });\n\n    await new Promise(() => {});\n}\n\n","/** brainbank mcp — Start MCP server (stdio). Requires @brainbank/mcp. */\n\nimport { c } from '@/cli/utils.ts';\n\nexport async function cmdMcp(): Promise<void> {\n    try {\n        await import('@brainbank/mcp');\n    } catch {\n        console.error(c.red('Error: @brainbank/mcp is not installed.'));\n        console.error(c.dim('  Install: npm i @brainbank/mcp'));\n        process.exit(1);\n    }\n}\n","/**\n * brainbank daemon — HTTP daemon for CLI delegation.\n *\n *   brainbank daemon              → Start foreground\n *   brainbank daemon start        → Start background (fork + PID file)\n *   brainbank daemon stop         → Stop background daemon\n *   brainbank daemon restart      → Stop + start\n */\n\nimport { c, args, getFlag, stripFlags } from '@/cli/utils.ts';\nimport { isServerRunning, removePid, DEFAULT_PORT } from '@/services/daemon.ts';\nimport { createBrain } from '@/cli/factory/index.ts';\n\nexport async function cmdDaemon(): Promise<void> {\n    const pos = stripFlags(args);\n    const sub = pos[1]; // start | stop | undefined\n\n    if (sub === 'stop') return stopDaemon();\n    if (sub === 'restart') { stopDaemon(); return forkDaemon(); }\n    if (sub === 'start') return forkDaemon();\n    return startForeground();\n}\n\n// ── Foreground ──────────────────────────────────\n\nasync function startForeground(): Promise<void> {\n    const port = parseInt(getFlag('port') ?? String(DEFAULT_PORT), 10);\n    const { HttpServer } = await import('@/services/http-server.ts');\n\n    const server = new HttpServer({\n        port,\n        factory: async (repoPath: string) => {\n            const brain = await createBrain(repoPath);\n            await brain.initialize();\n            return brain;\n        },\n        onError: (repo, err) => {\n            const msg = err instanceof Error ? err.message : String(err);\n            console.error(c.red(`  Pool error [${repo}]: ${msg}`));\n        },\n        onLog: (msg) => console.log(c.dim(`  ${msg}`)),\n    });\n\n    console.log(c.bold('\\n━━━ BrainBank HTTP Daemon ━━━\\n'));\n\n    await server.start();\n\n    console.log(c.dim(`  Port: ${port}`));\n    console.log(c.dim('  Press Ctrl+C to stop.\\n'));\n\n    const shutdown = () => {\n        console.log(c.dim('\\n  Shutting down...'));\n        server.close();\n        process.exit(0);\n    };\n    process.on('SIGINT', shutdown);\n    process.on('SIGTERM', shutdown);\n\n    await new Promise(() => {});\n}\n\n// ── Background ──────────────────────────────────\n\nasync function forkDaemon(): Promise<void> {\n    const port = parseInt(getFlag('port') ?? String(DEFAULT_PORT), 10);\n    const { fork } = await import('node:child_process');\n\n    const existing = isServerRunning();\n    if (existing) {\n        console.log(c.yellow(`  Daemon already running (PID ${existing.pid}, port ${existing.port})`));\n        return;\n    }\n\n    const child = fork(process.argv[1], ['daemon', '--port', String(port)], {\n        detached: true,\n        stdio: 'ignore',\n    });\n\n    child.unref();\n\n    console.log(c.green(`  ✓ Daemon started (PID ${child.pid}, port ${port})`));\n    console.log(c.dim('  Stop with: brainbank daemon stop'));\n}\n\nfunction stopDaemon(): void {\n    const info = isServerRunning();\n    if (!info) {\n        console.log(c.yellow('  No daemon running.'));\n        return;\n    }\n\n    try {\n        process.kill(info.pid, 'SIGTERM');\n        removePid();\n        console.log(c.green(`  ✓ Daemon stopped (PID ${info.pid})`));\n    } catch {\n        removePid();\n        console.log(c.yellow(`  PID ${info.pid} not found. Cleaned up stale PID file.`));\n    }\n}\n","/**\n * Status Command — Show BrainBank server status.\n *\n * Usage: brainbank status\n */\n\nimport { c } from '@/cli/utils.ts';\nimport { serverHealth } from '@/cli/server-client.ts';\nimport { isServerRunning } from '@/services/daemon.ts';\n\nfunction formatUptime(seconds: number): string {\n    if (seconds < 60) return `${seconds}s`;\n    const minutes = Math.floor(seconds / 60);\n    if (minutes < 60) return `${minutes}m`;\n    const hours = Math.floor(minutes / 60);\n    const remainMinutes = minutes % 60;\n    return remainMinutes > 0 ? `${hours}h ${remainMinutes}m` : `${hours}h`;\n}\n\nexport async function cmdStatus(): Promise<void> {\n    const info = isServerRunning();\n\n    if (!info) {\n        console.log(`\\n  ${c.dim('HTTP Server:')} ${c.yellow('stopped')}\\n`);\n        console.log(c.dim('  Start with: brainbank daemon'));\n        console.log('');\n        return;\n    }\n\n    // Try to get detailed health from the server\n    const health = await serverHealth();\n\n    if (health) {\n        const uptime = formatUptime(health.uptime);\n        console.log(`\\n  ${c.dim('HTTP Server:')} ${c.green('running')}`);\n        console.log(`  ${c.dim('PID:')}         ${health.pid}`);\n        console.log(`  ${c.dim('Port:')}        ${health.port}`);\n        console.log(`  ${c.dim('Uptime:')}      ${uptime}`);\n        console.log(`  ${c.dim('Workspaces:')}  ${health.workspaces}`);\n        console.log('');\n    } else {\n        // PID file exists but server not responding\n        console.log(`\\n  ${c.dim('HTTP Server:')} ${c.yellow('stale')} (PID ${info.pid} not responding)`);\n        console.log(c.dim('  The PID file may be stale. Restart with: brainbank daemon'));\n        console.log('');\n    }\n}\n","/** brainbank help — Show CLI usage. */\n\nimport { c } from '@/cli/utils.ts';\n\nexport function showHelp(): void {\n    console.log(c.bold('\\n━━━ BrainBank — Semantic Knowledge Bank ━━━\\n'));\n    console.log(c.bold('Indexing:'));\n    console.log(`  ${c.cyan('index')} ${c.dim('(i)')} [path]                  Index code + git history`);\n    console.log(`  ${c.cyan('collection add')} <path> --name      Add a document collection`);\n    console.log(`  ${c.cyan('collection list')}                    List collections`);\n    console.log(`  ${c.cyan('collection remove')} <name>           Remove a collection`);\n    console.log(`  ${c.cyan('docs')} [--collection <name>]         Index document collections`);\n    console.log('');\n    console.log(c.bold('Search:'));\n    console.log(`  ${c.cyan('search')} <query>                     Semantic search (vector)`);\n    console.log(`  ${c.cyan('hsearch')} <query>                    Hybrid search (${c.bold('best quality')})`);\n    console.log(`  ${c.cyan('ksearch')} <query>                    Keyword search (BM25, instant)`);\n    console.log(`  ${c.cyan('dsearch')} <query>                    Document search`);\n    console.log(c.dim('    All search commands accept --<source> <n> to filter by source'));\n    console.log('');\n    console.log(c.bold('Context:'));\n    console.log(`  ${c.cyan('context')} <task>                     Get formatted context for a task`);\n    console.log(`  ${c.cyan('context add')} <col> <path> <desc>    Add context metadata`);\n    console.log(`  ${c.cyan('context list')}                       List all context metadata`);\n    console.log(`  ${c.cyan('files')} <path|glob> [...] [--lines]  View full indexed files directly`);\n    console.log('');\n    console.log(c.bold('KV Store:'));\n    console.log(`  ${c.cyan('kv add')} <coll> <content>            Add item to a collection`);\n    console.log(`  ${c.cyan('kv search')} <coll> <query>           Search a collection`);\n    console.log(`  ${c.cyan('kv list')} [coll]                     List collections or items`);\n    console.log(`  ${c.cyan('kv trim')} <coll> --keep <n>          Keep only N most recent`);\n    console.log(`  ${c.cyan('kv clear')} <coll>                    Clear all items`);\n    console.log('');\n    console.log(c.bold('Utility:'));\n    console.log(`  ${c.cyan('stats')}                              Show index statistics`);\n    console.log(`  ${c.cyan('reembed')}                            Re-embed all vectors`);\n    console.log(`  ${c.cyan('watch')}                              Watch files, auto-re-index`);\n    console.log(`  ${c.cyan('mcp')}                                Start MCP server (stdio)`);\n    console.log(`  ${c.cyan('mcp:export')} [target]                Export MCP config (antigravity)`);\n    console.log(`  ${c.cyan('daemon')}                             Start HTTP daemon (foreground)`);\n    console.log(`  ${c.cyan('daemon start')}                       Start HTTP daemon (background)`);\n    console.log(`  ${c.cyan('daemon stop')}                        Stop background daemon`);\n    console.log(`  ${c.cyan('daemon restart')}                     Restart background daemon`);\n    console.log(`  ${c.cyan('status')}                             Show daemon status`);\n    console.log(`  ${c.cyan('--version')} ${c.dim('(-v)')}                      Show version`);\n    console.log('');\n    console.log(c.bold('Options:'));\n    console.log(`  ${c.dim('--repo <path>')}           Repository path (default: .)`);\n    console.log(`  ${c.dim('--force')}                 Force re-index all files`);\n    console.log(`  ${c.dim('--depth <n>')}             Git history depth (default: 500)`);\n    console.log(`  ${c.dim('--collection <name>')}     Filter by collection`);\n    console.log(`  ${c.dim('--pattern <glob>')}        Collection glob (default: **/*.md)`);\n    console.log(`  ${c.dim('--context <desc>')}        Context description`);\n    console.log(`  ${c.dim('--<source> <n>')}          Source filter: max results from <source> (0 = skip)`);\n    console.log(`  ${c.dim('--path <dir>')}            Filter context results to files under this path prefix`);\n    console.log(`  ${c.dim('--ignore <globs>')}        Ignore glob patterns for code indexing (comma-separated)`);\n    console.log(`  ${c.dim('--yes / -y')}              Skip interactive prompt (auto-select all available)`);\n    console.log(`  ${c.dim('--reranker <name>')}       Reranker to use (qwen3)`);\n    console.log(`  ${c.dim('--port <n>')}              HTTP daemon port (default: 8181)`);\n    console.log('');\n    console.log(c.bold('Examples:'));\n    console.log(c.dim('  brainbank index .'));\n    console.log(c.dim('  brainbank index . --ignore \"sdk/**,vendor/**\"'));\n    console.log(c.dim('  brainbank kv add errors \"Fixed null pointer in api.ts\"'));\n    console.log(c.dim('  brainbank kv search errors \"null pointer\"'));\n    console.log(c.dim('  brainbank kv list'));\n    console.log(c.dim('  brainbank hsearch \"authentication middleware\"'));\n    console.log(c.dim('  brainbank hsearch \"auth\" --code 0 --git 10           # git only'));\n    console.log(c.dim('  brainbank search \"handler\" --git 0                   # code only'));\n    console.log(c.dim('  brainbank hsearch \"api\" --docs 10 --code 0 --git 0   # docs only'));\n    console.log(c.dim('  brainbank context \"auth flow\" | pbcopy               # → clipboard'));\n    console.log(c.dim('  brainbank daemon start                               # background HTTP'));\n    console.log(c.dim('  brainbank mcp                                        # MCP stdio'));\n    console.log(c.dim('  brainbank mcp:export antigravity                     # export MCP config'));\n}\n","#!/usr/bin/env node\n\n/**\n * BrainBank — CLI Entry Point\n *\n * Dispatcher that routes commands to their handler modules.\n */\n\nimport { args, c } from './utils.ts';\nimport { cmdIndex } from './commands/index.ts';\nimport { cmdCollection } from './commands/collection.ts';\nimport { cmdKv } from './commands/kv.ts';\nimport { cmdDocs, cmdDocSearch } from './commands/docs.ts';\nimport { cmdSearch, cmdHybridSearch, cmdKeywordSearch } from './commands/search.ts';\nimport { cmdContext } from './commands/context.ts';\nimport { cmdFiles } from './commands/files.ts';\nimport { cmdStats } from './commands/stats.ts';\nimport { cmdReembed } from './commands/reembed.ts';\nimport { cmdWatch } from './commands/watch.ts';\nimport { cmdMcp } from './commands/mcp.ts';\nimport { cmdMcpExport } from './commands/mcp-export.ts';\nimport { cmdDaemon } from './commands/daemon.ts';\nimport { cmdStatus } from './commands/status.ts';\nimport { showHelp } from './commands/help.ts';\nimport { VERSION } from '@/constants.ts';\n\nconst command = args[0];\n\nasync function main(): Promise<void> {\n    switch (command) {\n        case '--version':\n        case '-v':\n            console.log(`brainbank v${VERSION}`);\n            break;\n        case 'i':\n        case 'index':       return cmdIndex();\n        case 'collection':  return cmdCollection();\n        case 'kv':          return cmdKv();\n        case 'docs':        return cmdDocs();\n        case 'dsearch':     return cmdDocSearch();\n        case 'search':      return cmdSearch();\n        case 'hsearch':     return cmdHybridSearch();\n        case 'ksearch':     return cmdKeywordSearch();\n        case 'context':     return cmdContext();\n        case 'files':       return cmdFiles();\n        case 'stats':       return cmdStats();\n        case 'reembed':     return cmdReembed();\n        case 'watch':       return cmdWatch();\n        case 'mcp':         return cmdMcp();\n        case 'mcp:export':  return cmdMcpExport();\n        case 'serve':        return cmdMcp(); // backward compat\n        case 'daemon':      return cmdDaemon();\n        case 'status':      return cmdStatus();\n        case 'help':\n        case '--help':\n        case '-h':\n            showHelp();\n            break;\n        default:\n            if (command) console.log(c.red(`Unknown command: ${command}\\n`));\n            showHelp();\n            process.exit(command ? 1 : 0);\n    }\n}\n\nmain().catch(err => {\n    console.error(c.red(`Error: ${err.message}`));\n    if (process.env.BRAINBANK_DEBUG) console.error(err.stack);\n    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+{"version":3,"sources":["../src/cli/commands/index.ts","../src/cli/commands/mcp-export.ts","../src/cli/commands/scan.ts","../src/cli/commands/collection.ts","../src/cli/commands/kv.ts","../src/cli/commands/docs.ts","../src/cli/commands/search.ts","../src/cli/server-client.ts","../src/cli/commands/context.ts","../src/cli/commands/files.ts","../src/cli/commands/stats.ts","../src/cli/commands/reembed.ts","../src/cli/commands/watch.ts","../src/cli/commands/mcp.ts","../src/cli/commands/daemon.ts","../src/cli/commands/status.ts","../src/cli/commands/help.ts","../src/cli/index.ts"],"sourcesContent":["/**\n * brainbank index [path] — Interactive scan → select → index\n *\n * Scans the repo first, shows a summary tree, and prompts the user\n * with checkboxes to select which modules to index. Use --yes to skip.\n */\n\nimport type { ScanResult, ScanModule } from './scan.ts';\n\nimport * as fs from 'node:fs';\nimport * as path from 'node:path';\nimport { c, args, getFlag, hasFlag, stripFlags } from '@/cli/utils.ts';\nimport { createBrain, getConfig, registerConfigCollections } from '@/cli/factory/index.ts';\nimport { findDocsPlugin } from '@/cli/utils.ts';\nimport { autoExportMcp } from './mcp-export.ts';\nimport { scanRepo } from './scan.ts';\n\nexport async function cmdIndex(): Promise<void> {\n    const positional = stripFlags(args);\n    const repoPath = positional[1] || '.';\n    const force = hasFlag('force');\n    const depth = parseInt(getFlag('depth') || '500', 10);\n    const onlyRaw = getFlag('only');\n    const docsPath = getFlag('docs');\n    const skipPrompt = hasFlag('yes') || hasFlag('y');\n\n\n    const scan = scanRepo(repoPath);\n    printScanTree(scan, depth);\n\n\n    let modules: string[];\n\n    if (onlyRaw) {\n        // --only flag: explicit module selection\n        modules = onlyRaw.split(',').map(s => s.trim());\n    } else if (scan.config.plugins && scan.config.plugins.length > 0) {\n        // Config exists with plugins field — use it as source of truth\n        modules = scan.config.plugins;\n        console.log(c.dim(`\\n  Using config: plugins = [${modules.join(', ')}]\\n`));\n    } else if (skipPrompt) {\n        modules = buildDefaultModules(scan);\n    } else {\n        modules = await promptModules(scan);\n        if (modules.length === 0) {\n            console.log(c.dim('\\n  Nothing selected. Exiting.\\n'));\n            return;\n        }\n\n        // Clean screen and show selection summary\n        console.clear();\n        console.log(c.bold('\\n━━━ BrainBank ━━━\\n'));\n        console.log('  Selected modules:');\n        for (const m of modules) {\n            console.log(`    ${c.green('✓')} ${m}`);\n        }\n        console.log('');\n    }\n\n    // If --docs is passed, auto-include 'docs' in modules\n    if (docsPath && !modules.includes('docs')) {\n        modules.push('docs');\n    }\n\n    // Auto-generate config.json if it doesn't exist yet\n    if (!scan.config.exists && !skipPrompt) {\n        await saveConfig(scan.repoPath, modules);\n    }\n\n\n    console.log(c.bold(`\\n━━━ Indexing: ${modules.join(', ')} ━━━`));\n\n    const brain = await createBrain(repoPath);\n    await brain.initialize();\n\n    const config = await getConfig(repoPath);\n    await registerConfigCollections(brain, repoPath, config);\n\n    if (docsPath) {\n        const absDocsPath = path.resolve(docsPath);\n        const collName = path.basename(absDocsPath);\n        try {\n            const docsPlugin = findDocsPlugin(brain);\n            await docsPlugin?.addCollection({\n                name: collName,\n                path: absDocsPath,\n                pattern: '**/*.md',\n                ignore: ['deprecated/**', 'node_modules/**'],\n            });\n            console.log(c.dim(`  Registered docs collection: ${collName}`));\n        } catch {\n            console.log(c.yellow(`  Warning: docs module not loaded, skipping --docs`));\n        }\n    }\n\n    const result = await brain.index({\n        modules,\n        forceReindex: force,\n        pluginOptions: { depth },\n        onProgress: (stage, msg) => {\n            process.stdout.write(`\\r  ${c.cyan(stage.toUpperCase())} ${msg}                    `);\n        },\n    });\n\n    console.log('\\n');\n    for (const [name, value] of Object.entries(result)) {\n        if (!value) continue;\n        const v = value as Record<string, unknown>;\n        if (typeof v.indexed === 'number') {\n            const parts = [`${v.indexed} indexed`, `${v.skipped ?? 0} skipped`];\n            if (typeof v.chunks === 'number') parts.push(`${v.chunks} chunks`);\n            if (typeof v.removed === 'number' && v.removed > 0) parts.push(`${v.removed} removed`);\n            console.log(`  ${c.green(name)}: ${parts.join(', ')}`);\n        } else {\n            console.log(`  ${c.green(name)}: done`);\n        }\n    }\n\n    const stats = brain.stats();\n    console.log(`\\n  ${c.bold('Totals')}:`);\n    for (const [name, s] of Object.entries(stats)) {\n        if (!s || typeof s !== 'object') continue;\n        const entries = Object.entries(s as Record<string, unknown>)\n            .map(([k, v]) => `${k}: ${v}`)\n            .join(', ');\n        console.log(`    ${name}: ${entries}`);\n    }\n\n    brain.close();\n\n    // Auto-export MCP config to Antigravity if detected and not already configured\n    await autoExportMcp(repoPath);\n}\n\n\nfunction printScanTree(scan: ScanResult, depth: number): void {\n    console.clear();\n    console.log(c.bold('\\n━━━ BrainBank Scan ━━━'));\n    console.log(c.dim(`  Repo: ${scan.repoPath}`));\n\n    // Multi-repo detection\n    if (scan.gitSubdirs.length > 0) {\n        console.log(c.cyan(`\\n  🔀 Multi-repo — ${scan.gitSubdirs.length} git repos detected`));\n        for (const sub of scan.gitSubdirs) {\n            console.log(c.dim(`     └── ${sub.name}`));\n        }\n    }\n\n    // Dynamic module display\n    for (const mod of scan.modules) {\n        console.log('');\n        if (mod.available) {\n            const extra = mod.name === 'git' ? ` (depth: ${depth})` : '';\n            console.log(`  ${mod.icon} ${c.bold(capitalizeFirst(mod.name))} — ${mod.summary}${extra}`);\n            if (mod.details) {\n                for (const d of mod.details) {\n                    console.log(c.dim(`     ${d}`));\n                }\n            }\n        } else {\n            console.log(`  ${mod.icon} ${c.dim(`${capitalizeFirst(mod.name)} — ${mod.summary}`)}`);\n        }\n    }\n\n    // Config ignore\n    if (scan.config.ignore?.length) {\n        console.log(c.dim(`     Ignore: ${scan.config.ignore.join(', ')}`));\n    }\n\n    // Config & DB\n    console.log('');\n    if (scan.config.exists) {\n        console.log(`  ⚙️  ${c.dim('Config:')} .brainbank/config.json ${c.green('✓')}`);\n    }\n    if (scan.db?.exists) {\n        const ago = scan.db.lastModified ? timeSince(scan.db.lastModified) : '';\n        console.log(`  💾 ${c.dim('DB:')} ${scan.db.sizeMB} MB${ago ? `, last indexed ${ago}` : ''}`);\n    } else {\n        console.log(`  💾 ${c.dim('DB: new (first index)')}`);\n    }\n    console.log('');\n}\n\n\n/** Build the default list of available modules based on scan. */\nfunction buildDefaultModules(scan: ScanResult): string[] {\n    return scan.modules.filter(m => m.available && m.checked).map(m => m.name);\n}\n\n/** Interactive checkbox prompt via @inquirer/prompts. */\nasync function promptModules(scan: ScanResult): Promise<string[]> {\n    const { checkbox } = await import('@inquirer/prompts');\n    console.log(c.dim('  ─────────────────────────────────────────\\n'));\n\n    const choices = scan.modules.map((m: ScanModule) => ({\n        name: `${capitalizeFirst(m.name).padEnd(6)} — ${m.summary}`,\n        value: m.name,\n        checked: m.checked && m.available,\n        disabled: m.available ? undefined : m.disabled,\n    }));\n\n    return checkbox<string>({\n        message: 'Select modules to index:\\n',\n        choices,\n    });\n}\n\n\nfunction timeSince(date: Date): string {\n    const seconds = Math.floor((Date.now() - date.getTime()) / 1000);\n    if (seconds < 60) return 'just now';\n    const minutes = Math.floor(seconds / 60);\n    if (minutes < 60) return `${minutes}m ago`;\n    const hours = Math.floor(minutes / 60);\n    if (hours < 24) return `${hours}h ago`;\n    const days = Math.floor(hours / 24);\n    return `${days}d ago`;\n}\n\n/** Capitalize first letter. */\nfunction capitalizeFirst(s: string): string {\n    return s.charAt(0).toUpperCase() + s.slice(1);\n}\n\n/** Generate .brainbank/config.json from the selected modules. */\nasync function saveConfig(repoPath: string, modules: string[]): Promise<void> {\n    const { select, confirm } = await import('@inquirer/prompts');\n\n    // Embedding provider selection\n    const envEmbedding = process.env.BRAINBANK_EMBEDDING;\n    const embedding = await select<string>({\n        message: 'Embedding provider:',\n        choices: [\n            {\n                name: 'perplexity-context  — best accuracy (recommended)',\n                value: 'perplexity-context',\n            },\n            {\n                name: 'perplexity          — fast, high quality',\n                value: 'perplexity',\n            },\n            {\n                name: 'openai              — text-embedding-3-small',\n                value: 'openai',\n            },\n            {\n                name: 'local               — offline, no API key needed',\n                value: 'local',\n            },\n        ],\n        default: envEmbedding ?? 'perplexity-context',\n    });\n\n    // Pruner selection\n    const pruner = await select<string>({\n        message: 'Noise pruner:',\n        choices: [\n            {\n                name: 'haiku  — AI-powered noise filter (recommended)',\n                value: 'haiku',\n            },\n            {\n                name: 'none   — no pruning',\n                value: 'none',\n            },\n        ],\n        default: 'haiku',\n    });\n\n    const configDir = path.join(repoPath, '.brainbank');\n    const configPath = path.join(configDir, 'config.json');\n\n    const config: Record<string, unknown> = {\n        plugins: modules,\n        embedding,\n    };\n\n    if (pruner !== 'none') {\n        config.pruner = pruner;\n    }\n\n    // Key management: detect available keys and offer to save\n    const detectedKeys: Record<string, string> = {};\n    const needsPerplexity = embedding.startsWith('perplexity');\n    const needsAnthropic = pruner === 'haiku';\n    const needsOpenai = embedding === 'openai';\n\n    if (needsPerplexity && process.env.PERPLEXITY_API_KEY) {\n        detectedKeys.perplexity = process.env.PERPLEXITY_API_KEY;\n    }\n    if (needsAnthropic && process.env.ANTHROPIC_API_KEY) {\n        detectedKeys.anthropic = process.env.ANTHROPIC_API_KEY;\n    }\n    if (needsOpenai && process.env.OPENAI_API_KEY) {\n        detectedKeys.openai = process.env.OPENAI_API_KEY;\n    }\n\n    if (Object.keys(detectedKeys).length > 0) {\n        const keyNames = Object.keys(detectedKeys).join(', ');\n        const saveKeys = await confirm({\n            message: `Save API keys (${keyNames}) to config.json? (portable, no env vars needed)`,\n            default: true,\n        });\n        if (saveKeys) {\n            config.keys = detectedKeys;\n        }\n    }\n\n    fs.mkdirSync(configDir, { recursive: true });\n    fs.writeFileSync(configPath, JSON.stringify(config, null, 2) + '\\n');\n    console.log(c.green(`  ✓ Saved ${path.relative(process.cwd(), configPath)}`));\n}\n\n","/**\n * brainbank mcp:export [target] — Export MCP server config for AI IDEs.\n *\n * Generates the MCP server config block for brainbank and merges it into\n * the target IDE's config file. Currently supports: antigravity.\n *\n * Detects: node path, cli.js path, API keys from config or env vars.\n */\n\nimport type { ProjectConfig } from '@/cli/factory/config-loader.ts';\n\nimport * as fs from 'node:fs';\nimport * as path from 'node:path';\nimport { fileURLToPath } from 'node:url';\nimport { c, args, getFlag } from '@/cli/utils.ts';\nimport { getConfig } from '@/cli/factory/index.ts';\n\nconst __filename = fileURLToPath(import.meta.url);\nconst __dirname = path.dirname(__filename);\n\n/** Supported export targets and their config file paths. */\nconst TARGETS: Record<string, { configPath: string; label: string }> = {\n    antigravity: {\n        configPath: path.join(process.env.HOME ?? '~', '.gemini', 'antigravity', 'mcp_config.json'),\n        label: 'Gemini Antigravity',\n    },\n};\n\ninterface McpServerConfig {\n    command: string;\n    args: string[];\n    env?: Record<string, string>;\n    cwd?: string;\n}\n\ninterface McpConfig {\n    mcpServers: Record<string, McpServerConfig>;\n}\n\n/**\n * Build the brainbank MCP server config block.\n * Resolves node binary, dist/cli.js path, and API keys.\n */\nfunction buildBrainbankMcpBlock(config: ProjectConfig | null): McpServerConfig {\n    const nodeBin = process.execPath;\n\n    // Resolve dist/cli.js from the global install location (node_prefix/lib/node_modules/brainbank/dist/cli.js)\n    const globalCliJs = path.join(path.dirname(nodeBin), '..', 'lib', 'node_modules', 'brainbank', 'dist', 'cli.js');\n    // Fallback: relative to this file (dev / npm link)\n    const localCliJs = path.resolve(__dirname, '..', '..', 'dist', 'cli.js');\n    const resolvedCliJs = fs.existsSync(globalCliJs) ? globalCliJs : localCliJs;\n\n    const env: Record<string, string> = {};\n\n    // Resolve API keys: config.keys > env vars\n    const keys = config?.keys;\n    const perplexityKey = keys?.perplexity ?? process.env.PERPLEXITY_API_KEY;\n    const anthropicKey = keys?.anthropic ?? process.env.ANTHROPIC_API_KEY;\n    const openaiKey = keys?.openai ?? process.env.OPENAI_API_KEY;\n\n    if (perplexityKey) env.PERPLEXITY_API_KEY = perplexityKey;\n    if (anthropicKey) env.ANTHROPIC_API_KEY = anthropicKey;\n    if (openaiKey) env.OPENAI_API_KEY = openaiKey;\n\n    const block: McpServerConfig = {\n        command: nodeBin,\n        args: ['--disable-warning=ExperimentalWarning', resolvedCliJs, 'mcp'],\n    };\n\n    if (Object.keys(env).length > 0) {\n        block.env = env;\n    }\n\n    return block;\n}\n\n/**\n * Load existing MCP config, merge brainbank entry, and write back.\n * Preserves all other server entries.\n */\nfunction mergeAndWrite(targetPath: string, block: McpServerConfig): { created: boolean } {\n    let existing: McpConfig = { mcpServers: {} };\n    const created = !fs.existsSync(targetPath);\n\n    if (!created) {\n        try {\n            const raw = fs.readFileSync(targetPath, 'utf-8');\n            existing = JSON.parse(raw) as McpConfig;\n            if (!existing.mcpServers) existing.mcpServers = {};\n        } catch {\n            // Corrupt or empty file — start fresh\n            existing = { mcpServers: {} };\n        }\n    }\n\n    existing.mcpServers.brainbank = block;\n\n    fs.mkdirSync(path.dirname(targetPath), { recursive: true });\n    fs.writeFileSync(targetPath, JSON.stringify(existing, null, 2) + '\\n');\n\n    return { created };\n}\n\n/** Check if an MCP config already has a brainbank entry. */\nexport function hasBrainbankMcpEntry(targetPath: string): boolean {\n    if (!fs.existsSync(targetPath)) return false;\n    try {\n        const raw = fs.readFileSync(targetPath, 'utf-8');\n        const config = JSON.parse(raw) as McpConfig;\n        return !!config.mcpServers?.brainbank;\n    } catch {\n        return false;\n    }\n}\n\n/** Auto-export: called after index when Antigravity is detected. */\nexport async function autoExportMcp(repoPath: string): Promise<void> {\n    const target = TARGETS.antigravity;\n    if (!target) return;\n\n    // Only auto-export if Antigravity dir exists\n    const antigravityDir = path.dirname(target.configPath);\n    if (!fs.existsSync(antigravityDir)) return;\n\n    // Only auto-export if brainbank isn't already configured\n    if (hasBrainbankMcpEntry(target.configPath)) return;\n\n    const config = await getConfig(repoPath);\n    const block = buildBrainbankMcpBlock(config);\n    mergeAndWrite(target.configPath, block);\n    console.log(`  ${c.green('✓')} Exported MCP config to ${c.dim(path.relative(process.env.HOME ?? '', target.configPath))}`);\n}\n\n// ── GEMINI.md BrainBank Section ──────────────────────────────\n\nconst BRAINBANK_SECTION_MARKER = '<!-- brainbank:start -->';\nconst BRAINBANK_SECTION_END = '<!-- brainbank:end -->';\n\n/** Global GEMINI.md path — ~/.gemini/GEMINI.md (shared across all projects). */\nconst GLOBAL_GEMINI = path.join(process.env.HOME ?? '~', '.gemini', 'GEMINI.md');\n\nfunction buildGeminiSection(): string {\n    return `${BRAINBANK_SECTION_MARKER}\n\n## BrainBank — Code Intelligence\n\nWhen \\`brainbank_context\\` and \\`brainbank_files\\` MCP tools are available, **always use them instead of \\`grep_search\\` or \\`list_dir\\`**.\n\n**\\`brainbank_context\\`** — semantic search. \\`repo\\` is **required** (the project root where \\`brainbank index\\` was run). Use \\`path:\\` to scope within it, \\`compact: false\\`, \\`sources: { code: 25, docs: 0, git: 0 }\\`.\n\n**\\`brainbank_files\\`** — read full indexed files (\\`lines: true\\` always). Only works with files tracked by the index — for \\`.env\\`, \\`docker-compose.yml\\`, etc. use \\`view_file\\`.\n\n**Sources rule:** Default to code-only (\\`docs: 0\\`). Only add \\`docs\\` when the user explicitly asks about documentation. Never mix code and docs in the same query — fire separate queries.\n\n### Output handling (critical)\n\nBrainBank may return results **inline** or save them to an **output file**:\n\n- **Inline:** read and proceed normally.\n- **File result** (saved to \\`output.txt\\`): show the path as a clickable link, ask user to paste, then **STOP and WAIT**:\n\n  📋 Output: [output.txt](file:///path/to/output.txt) — _\"Could you paste the context output here?\"_\n\n  Do **NOT** read the file yourself. Wait for the paste before proceeding.\n\n${BRAINBANK_SECTION_END}\n`;\n}\n\n/** Check if GEMINI.md already has the brainbank section. */\nfunction hasGeminiSection(geminiPath: string): boolean {\n    if (!fs.existsSync(geminiPath)) return false;\n    const content = fs.readFileSync(geminiPath, 'utf-8');\n    return content.includes(BRAINBANK_SECTION_MARKER);\n}\n\n/** Append BrainBank section to GEMINI.md (creates if doesn't exist). */\nfunction appendGeminiSection(geminiPath: string): void {\n    const section = buildGeminiSection();\n    if (fs.existsSync(geminiPath)) {\n        fs.appendFileSync(geminiPath, section);\n    } else {\n        fs.writeFileSync(geminiPath, `# GEMINI.md\\n${section}`);\n    }\n}\n\n/** Replace BrainBank section between markers in GEMINI.md. */\nfunction replaceGeminiSection(geminiPath: string): void {\n    const content = fs.readFileSync(geminiPath, 'utf-8');\n    const startIdx = content.indexOf(BRAINBANK_SECTION_MARKER);\n    const endIdx = content.indexOf(BRAINBANK_SECTION_END);\n    if (startIdx === -1 || endIdx === -1) return;\n\n    const before = content.slice(0, startIdx);\n    const after = content.slice(endIdx + BRAINBANK_SECTION_END.length);\n    const section = buildGeminiSection();\n    fs.writeFileSync(geminiPath, before + section + after);\n}\n\n/** CLI command: brainbank mcp:export [target] [--force] */\nexport async function cmdMcpExport(): Promise<void> {\n    const targetName = args[1] || getFlag('target') || 'antigravity';\n    const repoPath = getFlag('repo') || '.';\n    const force = args.includes('--force') || args.includes('-f');\n\n    const target = TARGETS[targetName];\n    if (!target) {\n        console.error(c.red(`Unknown export target: ${targetName}`));\n        console.error(c.dim(`  Available: ${Object.keys(TARGETS).join(', ')}`));\n        process.exit(1);\n    }\n\n    const config = await getConfig(repoPath);\n    const block = buildBrainbankMcpBlock(config);\n\n    console.log(c.bold(`\\n━━━ MCP Export: ${target.label} ━━━\\n`));\n\n    // ── MCP Config ────────────────────────────────────────────\n    const mcpExists = hasBrainbankMcpEntry(target.configPath);\n    let writeMcp = true;\n\n    if (mcpExists && !force) {\n        console.log(`  ${c.yellow('●')} MCP config already has brainbank entry`);\n        const cliPath = block.args.find(a => !a.startsWith('--')) ?? block.args[0];\n        console.log(`  ${c.dim('  New:')} ${block.command} ${cliPath}`);\n        const envKeys = block.env ? Object.keys(block.env) : [];\n        if (envKeys.length > 0) console.log(`  ${c.dim('  Keys:')} ${envKeys.join(', ')}`);\n        const { confirm } = await import('@inquirer/prompts');\n        writeMcp = await confirm({ message: 'Override existing brainbank MCP entry?', default: true });\n    }\n\n    if (writeMcp) {\n        const { created } = mergeAndWrite(target.configPath, block);\n        console.log(`  ${c.green('✓')} ${created ? 'Created' : 'Updated'} ${c.dim(target.configPath)}`);\n    } else {\n        console.log(`  ${c.dim('MCP config — skipped')}`);\n    }\n\n    // ── Global GEMINI.md (~/.gemini/GEMINI.md) ────────────────\n    const geminiHasSection = hasGeminiSection(GLOBAL_GEMINI);\n\n    if (geminiHasSection) {\n        if (force) {\n            replaceGeminiSection(GLOBAL_GEMINI);\n            console.log(`  ${c.green('✓')} Replaced BrainBank section in ${c.dim('~/.gemini/GEMINI.md')}`);\n        } else {\n            console.log(`  ${c.yellow('●')} ~/.gemini/GEMINI.md already has BrainBank section`);\n            const { confirm } = await import('@inquirer/prompts');\n            const override = await confirm({ message: 'Override existing BrainBank section?', default: false });\n            if (override) {\n                replaceGeminiSection(GLOBAL_GEMINI);\n                console.log(`  ${c.green('✓')} Replaced BrainBank section in ${c.dim('~/.gemini/GEMINI.md')}`);\n            } else {\n                console.log(`  ${c.dim('GEMINI.md — skipped')}`);\n            }\n        }\n    } else {\n        if (force) {\n            appendGeminiSection(GLOBAL_GEMINI);\n            console.log(`  ${c.green('✓')} Added BrainBank section to ${c.dim('~/.gemini/GEMINI.md')}`);\n        } else {\n            const { confirm } = await import('@inquirer/prompts');\n            const addGemini = await confirm({\n                message: 'Add BrainBank instructions to ~/.gemini/GEMINI.md? (teaches AI tools how to use BrainBank)',\n                default: true,\n            });\n            if (addGemini) {\n                appendGeminiSection(GLOBAL_GEMINI);\n                console.log(`  ${c.green('✓')} Added BrainBank section to ${c.dim('~/.gemini/GEMINI.md')}`);\n            }\n        }\n    }\n\n    console.log(`\\n  ${c.dim('Restart your IDE to apply changes.')}\\n`);\n}\n","/**\n * brainbank scan — Lightweight repo scanner for the interactive index flow.\n *\n * Scans the filesystem WITHOUT initializing BrainBank. Returns a ScanResult\n * describing what's available to index via dynamic ScanModule descriptors.\n */\n\nimport * as fs from 'node:fs';\nimport * as path from 'node:path';\nimport { execSync } from 'node:child_process';\nimport { SUPPORTED_EXTENSIONS, isIgnoredDir, isIgnoredFile } from '@/lib/languages.ts';\n\n\n/** A single scannable module (plugin). */\nexport interface ScanModule {\n    /** Plugin name (e.g. 'code', 'git', 'docs'). */\n    name: string;\n    /** Whether there's content available to index. */\n    available: boolean;\n    /** Human-readable summary (e.g. '1243 files (5 languages)'). */\n    summary: string;\n    /** Emoji icon for display. */\n    icon: string;\n    /** Whether checked by default in the prompt. */\n    checked: boolean;\n    /** Reason this module is disabled (shown in prompt). */\n    disabled?: string;\n    /** Detail lines for the scan tree (e.g. per-language breakdown). */\n    details?: string[];\n}\n\nexport interface ScanResult {\n    repoPath: string;\n    modules: ScanModule[];\n    config: { exists: boolean; ignore?: string[]; plugins?: string[] };\n    db: { exists: boolean; sizeMB: number; lastModified?: Date } | null;\n    gitSubdirs: { name: string }[];\n}\n\n\n/** Scan a repo path and return what's available to index. */\nexport function scanRepo(repoPath: string): ScanResult {\n    const resolved = path.resolve(repoPath);\n    const gitSubdirs = scanGitSubdirs(resolved);\n\n    return {\n        repoPath: resolved,\n        modules: scanModules(resolved, gitSubdirs),\n        config: scanConfig(resolved),\n        db: scanDb(resolved),\n        gitSubdirs,\n    };\n}\n\n/** Produce ScanModule descriptors for known plugin types. */\nfunction scanModules(repoPath: string, gitSubdirs: { name: string }[]): ScanModule[] {\n    return [\n        scanCodeModule(repoPath),\n        scanGitModule(repoPath, gitSubdirs),\n        scanDocsModule(repoPath),\n    ];\n}\n\n\n/** Scan for indexable code files. */\nfunction scanCodeModule(repoPath: string): ScanModule {\n    const byLanguage = new Map<string, number>();\n    let total = 0;\n\n    function walk(dir: string): void {\n        let entries: fs.Dirent[];\n        try { entries = fs.readdirSync(dir, { withFileTypes: true }); }\n        catch { return; }\n\n        for (const entry of entries) {\n            const fullPath = path.join(dir, entry.name);\n            const isDir = entry.isDirectory() || (entry.isSymbolicLink() && (() => { try { return fs.statSync(fullPath).isDirectory(); } catch { return false; } })());\n            if (isDir) {\n                if (isIgnoredDir(entry.name)) continue;\n                walk(fullPath);\n            } else if (entry.isFile()) {\n                if (isIgnoredFile(entry.name)) continue;\n                const ext = path.extname(entry.name).toLowerCase();\n                const lang = SUPPORTED_EXTENSIONS[ext];\n                if (!lang) continue;\n                byLanguage.set(lang, (byLanguage.get(lang) ?? 0) + 1);\n                total++;\n            }\n        }\n    }\n\n    walk(repoPath);\n\n    if (total === 0) {\n        return { name: 'code', available: false, summary: 'no supported source files found', icon: '📁', checked: false, disabled: 'nothing to index' };\n    }\n\n    const langCount = byLanguage.size;\n    const sorted = [...byLanguage.entries()].sort((a, b) => b[1] - a[1]);\n    const maxShow = 7;\n    const shown = sorted.slice(0, maxShow);\n    const remaining = sorted.length - maxShow;\n\n    const details: string[] = [];\n    for (let i = 0; i < shown.length; i++) {\n        const [lang, count] = shown[i];\n        const isLast = i === shown.length - 1 && remaining <= 0;\n        const prefix = isLast ? '└──' : '├──';\n        details.push(`${prefix} ${lang.padEnd(14)} ${count} files`);\n    }\n    if (remaining > 0) {\n        details.push(`└── ...and ${remaining} more`);\n    }\n\n    return {\n        name: 'code',\n        available: true,\n        summary: `${total} files (${langCount} language${langCount > 1 ? 's' : ''})`,\n        icon: '📁',\n        checked: true,\n        details,\n    };\n}\n\n/** Scan for git history. */\nfunction scanGitModule(repoPath: string, gitSubdirs: { name: string }[]): ScanModule {\n    const stats = scanGitStats(repoPath, gitSubdirs);\n\n    if (!stats) {\n        return { name: 'git', available: false, summary: 'no .git directory found', icon: '📜', checked: false, disabled: 'not a git repo' };\n    }\n\n    const details: string[] = [];\n    if (stats.lastMessage) {\n        details.push(`Last: ${stats.lastMessage} (${stats.lastDate})`);\n    }\n\n    return {\n        name: 'git',\n        available: true,\n        summary: `${stats.commitCount.toLocaleString()} commits`,\n        icon: '📜',\n        checked: true,\n        details,\n    };\n}\n\n/** Scan for document collections. */\nfunction scanDocsModule(repoPath: string): ScanModule {\n    const collections = scanDocsCollections(repoPath);\n\n    if (collections.length === 0) {\n        return { name: 'docs', available: false, summary: 'no documents found', icon: '📄', checked: false, disabled: 'no .md/.mdx files' };\n    }\n\n    const totalFiles = collections.reduce((s, d) => s + d.fileCount, 0);\n    const details = collections.map((d, i) => {\n        const isLast = i === collections.length - 1;\n        const prefix = isLast ? '└──' : '├──';\n        return `${prefix} ${d.name.padEnd(10)} → ${d.path} (${d.fileCount} files)`;\n    });\n\n    return {\n        name: 'docs',\n        available: true,\n        summary: `${collections.length} collection${collections.length > 1 ? 's' : ''} (${totalFiles} files)`,\n        icon: '📄',\n        checked: true,\n        details,\n    };\n}\n\n\n/** Get git stats. Supports single repo and multi-repo aggregation. */\nfunction scanGitStats(repoPath: string, gitSubdirs: { name: string }[]): { commitCount: number; lastMessage: string; lastDate: string } | null {\n    if (fs.existsSync(path.join(repoPath, '.git'))) {\n        return gitStats(repoPath);\n    }\n\n    if (gitSubdirs.length === 0) return null;\n\n    let totalCommits = 0;\n    let latestMessage = '';\n    let latestDate = '';\n\n    for (const sub of gitSubdirs) {\n        const stats = gitStats(path.join(repoPath, sub.name));\n        if (stats) {\n            totalCommits += stats.commitCount;\n            if (!latestMessage) {\n                latestMessage = stats.lastMessage;\n                latestDate = stats.lastDate;\n            }\n        }\n    }\n\n    return totalCommits > 0\n        ? { commitCount: totalCommits, lastMessage: latestMessage, lastDate: latestDate }\n        : null;\n}\n\n/** Get git stats for a single directory. */\nfunction gitStats(dir: string): { commitCount: number; lastMessage: string; lastDate: string } | null {\n    try {\n        const count = parseInt(execSync('git rev-list --count HEAD', { cwd: dir, encoding: 'utf-8' }).trim(), 10);\n        const log = execSync('git log -1 --format=\"%s|%ar\"', { cwd: dir, encoding: 'utf-8' }).trim();\n        const [lastMessage, lastDate] = log.split('|');\n        return { commitCount: count, lastMessage: lastMessage ?? '', lastDate: lastDate ?? '' };\n    } catch {\n        return null;\n    }\n}\n\n/** Scan for document collections (config + auto-detect). */\nfunction scanDocsCollections(repoPath: string): { name: string; path: string; fileCount: number }[] {\n    const results: { name: string; path: string; fileCount: number }[] = [];\n    const seen = new Set<string>();\n\n    // 1. Read explicit collections from config.json\n    const configPath = path.join(repoPath, '.brainbank', 'config.json');\n    try {\n        if (fs.existsSync(configPath)) {\n            const config = JSON.parse(fs.readFileSync(configPath, 'utf-8')) as Record<string, unknown>;\n            const docsCfg = config?.docs as Record<string, unknown> | undefined;\n            const collections = docsCfg?.collections as { name: string; path: string }[] | undefined;\n            if (collections) {\n                for (const coll of collections) {\n                    const absPath = path.resolve(repoPath, coll.path);\n                    results.push({ name: coll.name, path: coll.path, fileCount: countDocs(absPath) });\n                    seen.add(absPath);\n                }\n            }\n        }\n    } catch {}\n\n    // 2. Auto-detect .md/.mdx in the repo root and top-level dirs\n    const rootDocs = countDocsShallow(repoPath);\n    if (rootDocs > 0) {\n        results.push({ name: '(root)', path: '.', fileCount: rootDocs });\n    }\n\n    try {\n        for (const entry of fs.readdirSync(repoPath, { withFileTypes: true })) {\n            if (!entry.isDirectory()) continue;\n            if (isIgnoredDir(entry.name)) continue;\n            if (entry.name.startsWith('.')) continue;\n\n            const dirPath = path.join(repoPath, entry.name);\n            if (seen.has(dirPath)) continue;\n\n            const count = countDocs(dirPath);\n            if (count > 0) {\n                results.push({ name: entry.name, path: `./${entry.name}`, fileCount: count });\n            }\n        }\n    } catch {}\n\n    return results;\n}\n\n/** Count .md/.mdx files recursively in a directory. */\nfunction countDocs(dir: string): number {\n    let count = 0;\n    try {\n        for (const e of fs.readdirSync(dir, { withFileTypes: true })) {\n            const ePath = path.join(dir, e.name);\n            const isDir = e.isDirectory() || (e.isSymbolicLink() && (() => { try { return fs.statSync(ePath).isDirectory(); } catch { return false; } })());\n            if (isDir) {\n                if (isIgnoredDir(e.name)) continue;\n                count += countDocs(ePath);\n            } else if ((e.isFile() || e.isSymbolicLink()) && /\\.mdx?$/i.test(e.name)) {\n                count++;\n            }\n        }\n    } catch {}\n    return count;\n}\n\n/** Count .md/.mdx files in a directory (non-recursive, root level only). */\nfunction countDocsShallow(dir: string): number {\n    let count = 0;\n    try {\n        for (const e of fs.readdirSync(dir, { withFileTypes: true })) {\n            if (e.isFile() && /\\.mdx?$/i.test(e.name)) count++;\n        }\n    } catch {}\n    return count;\n}\n\n/** Check if config.json exists and read key fields. */\nfunction scanConfig(repoPath: string): ScanResult['config'] {\n    const configPath = path.join(repoPath, '.brainbank', 'config.json');\n    if (!fs.existsSync(configPath)) return { exists: false };\n\n    try {\n        const config = JSON.parse(fs.readFileSync(configPath, 'utf-8')) as Record<string, unknown>;\n        const codeCfg = config?.code as Record<string, unknown> | undefined;\n        return {\n            exists: true,\n            ignore: codeCfg?.ignore as string[] | undefined,\n            plugins: config?.plugins as string[] | undefined,\n        };\n    } catch {\n        return { exists: false };\n    }\n}\n\n/** Check DB existence and size. */\nfunction scanDb(repoPath: string): ScanResult['db'] {\n    const dbPath = path.join(repoPath, '.brainbank', 'data', 'brainbank.db');\n    if (!fs.existsSync(dbPath)) return { exists: false, sizeMB: 0 };\n\n    try {\n        const stat = fs.statSync(dbPath);\n        return {\n            exists: true,\n            sizeMB: Math.round(stat.size / 1024 / 1024 * 10) / 10,\n            lastModified: stat.mtime,\n        };\n    } catch {\n        return { exists: false, sizeMB: 0 };\n    }\n}\n\n/** Detect subdirectories with their own .git (mono-repo). Respects `repos` whitelist from config. */\nfunction scanGitSubdirs(repoPath: string): ScanResult['gitSubdirs'] {\n    if (fs.existsSync(path.join(repoPath, '.git'))) return [];\n\n    try {\n        let subdirs = fs.readdirSync(repoPath, { withFileTypes: true })\n            .filter(e => {\n                if (e.name.startsWith('.')) return false;\n                const isDir = e.isDirectory() || (e.isSymbolicLink() && (() => { try { return fs.statSync(path.join(repoPath, e.name)).isDirectory(); } catch { return false; } })());\n                return isDir;\n            })\n            .filter(e => fs.existsSync(path.join(repoPath, e.name, '.git')))\n            .map(e => ({ name: e.name }));\n\n        // Apply repos whitelist from config if present\n        const configRepos = readReposFromConfig(repoPath);\n        if (configRepos) {\n            subdirs = subdirs.filter(s => configRepos.includes(s.name));\n        }\n\n        return subdirs;\n    } catch {\n        return [];\n    }\n}\n\n/** Read the `repos` whitelist from .brainbank/config.json. Returns null if not set. */\nfunction readReposFromConfig(repoPath: string): string[] | null {\n    const configPath = path.join(repoPath, '.brainbank', 'config.json');\n    try {\n        if (!fs.existsSync(configPath)) return null;\n        const config = JSON.parse(fs.readFileSync(configPath, 'utf-8')) as Record<string, unknown>;\n        const repos = config.repos;\n        if (Array.isArray(repos) && repos.every(r => typeof r === 'string')) {\n            return repos as string[];\n        }\n        return null;\n    } catch {\n        return null;\n    }\n}\n","/**\n * brainbank collection add|list|remove — Document collection management\n */\n\nimport { c, args, getFlag, stripFlags, findDocsPlugin } from '@/cli/utils.ts';\nimport { createBrain } from '@/cli/factory/index.ts';\n\nexport async function cmdCollection(): Promise<void> {\n    const pos = stripFlags(args);\n    const sub = pos[1];\n\n    if (sub === 'add') {\n        const path = pos[2];\n        const name = getFlag('name');\n        const pattern = getFlag('pattern') ?? '**/*.md';\n        const context = getFlag('context');\n        const ignoreRaw = getFlag('ignore');\n\n        if (!path || !name) {\n            console.log(c.red('Usage: brainbank collection add <path> --name <name> [--pattern \"**/*.md\"] [--ignore \"glob\"] [--context \"description\"]'));\n            process.exit(1);\n        }\n\n        const brain = await createBrain();\n        const docsPlugin = findDocsPlugin(brain);\n        if (!docsPlugin) { console.log(c.red('Docs plugin not loaded. Install @brainbank/docs.')); process.exit(1); }\n        await docsPlugin.addCollection({\n            name,\n            path,\n            pattern,\n            ignore: ignoreRaw ? ignoreRaw.split(',') : [],\n            context: context ?? undefined,\n        });\n        console.log(c.green(`✓ Collection '${name}' added: ${path} (${pattern})`));\n        if (context) console.log(c.dim(`  Context: ${context}`));\n        brain.close();\n        return;\n    }\n\n    if (sub === 'list') {\n        const brain = await createBrain();\n        await brain.initialize();\n        const docsPlugin = findDocsPlugin(brain);\n        if (!docsPlugin) { console.log(c.yellow('  Docs plugin not loaded.')); brain.close(); return; }\n        const collections = docsPlugin.listCollections();\n        if (collections.length === 0) {\n            console.log(c.yellow('  No collections registered.'));\n        } else {\n            console.log(c.bold('\\n━━━ Collections ━━━\\n'));\n            for (const col of collections) {\n                console.log(`  ${c.cyan(col.name)} ${c.dim('→')} ${col.path}`);\n                console.log(`    Pattern: ${col.pattern ?? '**/*.md'}`);\n                if (col.context) console.log(`    Context: ${c.dim(col.context)}`);\n            }\n        }\n        brain.close();\n        return;\n    }\n\n    if (sub === 'remove') {\n        const name = pos[2];\n        if (!name) {\n            console.log(c.red('Usage: brainbank collection remove <name>'));\n            process.exit(1);\n        }\n        const brain = await createBrain();\n        const docsPlugin = findDocsPlugin(brain);\n        if (!docsPlugin) { console.log(c.red('Docs plugin not loaded.')); process.exit(1); }\n        await docsPlugin.removeCollection(name);\n        console.log(c.green(`✓ Collection '${name}' removed.`));\n        brain.close();\n        return;\n    }\n\n    console.log(c.red('Usage: brainbank collection <add|list|remove>'));\n    process.exit(1);\n}\n","/**\n * brainbank kv add|search|list|trim|clear — Dynamic KV collection management\n */\n\nimport { c, args, getFlag, stripFlags } from '@/cli/utils.ts';\nimport { createBrain } from '@/cli/factory/index.ts';\n\nexport async function cmdKv(): Promise<void> {\n    const pos = stripFlags(args);\n    const sub = pos[1];\n\n    if (sub === 'add') {\n        const collName = pos[2];\n        const content = pos.slice(3).join(' ');\n        const metaRaw = getFlag('meta');\n\n        if (!collName || !content) {\n            console.log(c.red(\"Usage: brainbank kv add <collection> <content> [--meta '{\\\"key\\\":\\\"val\\\"}']\"));\n            process.exit(1);\n        }\n\n        const brain = await createBrain();\n        await brain.initialize();\n        const coll = brain.collection(collName);\n        const meta = metaRaw ? JSON.parse(metaRaw) : {};\n        const id = await coll.add(content, meta);\n        console.log(c.green(`✓ Added item #${id} to '${collName}'`));\n        brain.close();\n        return;\n    }\n\n    if (sub === 'search') {\n        const collName = pos[2];\n        const query = pos.slice(3).join(' ');\n        const k = parseInt(getFlag('k') || '5', 10);\n        const mode = (getFlag('mode') || 'hybrid') as 'hybrid' | 'vector' | 'keyword';\n\n        if (!collName || !query) {\n            console.log(c.red('Usage: brainbank kv search <collection> <query> [--k 5] [--mode hybrid|keyword|vector]'));\n            process.exit(1);\n        }\n\n        const brain = await createBrain();\n        await brain.initialize();\n        const coll = brain.collection(collName);\n        const results = await coll.search(query, { k, mode });\n\n        if (results.length === 0) {\n            console.log(c.yellow('  No results found.'));\n        } else {\n            console.log(c.bold(`\\n━━━ ${collName}: \"${query}\" ━━━\\n`));\n            for (const r of results) {\n                const score = Math.round((r.score ?? 0) * 100);\n                console.log(`  ${c.cyan(`[${score}%]`)} ${r.content}`);\n                if (Object.keys(r.metadata).length > 0) {\n                    console.log(`    ${c.dim(JSON.stringify(r.metadata))}`);\n                }\n            }\n        }\n        brain.close();\n        return;\n    }\n\n    if (sub === 'list') {\n        const collName = pos[2];\n        const limit = parseInt(getFlag('limit') || '20', 10);\n\n        if (!collName) {\n            const brain = await createBrain();\n            await brain.initialize();\n            const names = brain.listCollectionNames();\n            if (names.length === 0) {\n                console.log(c.yellow('  No KV collections found.'));\n            } else {\n                console.log(c.bold('\\n━━━ KV Collections ━━━\\n'));\n                for (const n of names) {\n                    const coll = brain.collection(n);\n                    console.log(`  ${c.cyan(n)} — ${coll.count()} items`);\n                }\n            }\n            brain.close();\n            return;\n        }\n\n        const brain = await createBrain();\n        await brain.initialize();\n        const coll = brain.collection(collName);\n        const items = coll.list({ limit });\n        if (items.length === 0) {\n            console.log(c.yellow(`  Collection '${collName}' is empty.`));\n        } else {\n            console.log(c.bold(`\\n━━━ ${collName} (${coll.count()} items) ━━━\\n`));\n            for (const item of items) {\n                const age = Math.round((Date.now() / 1000 - item.createdAt) / 60);\n                console.log(`  #${item.id} ${c.dim(`(${age}m ago)`)} ${item.content.slice(0, 80)}`);\n            }\n        }\n        brain.close();\n        return;\n    }\n\n    if (sub === 'trim') {\n        const collName = pos[2];\n        const keep = parseInt(getFlag('keep') || '0', 10);\n\n        if (!collName || keep <= 0) {\n            console.log(c.red('Usage: brainbank kv trim <collection> --keep <n>'));\n            process.exit(1);\n        }\n\n        const brain = await createBrain();\n        await brain.initialize();\n        const coll = brain.collection(collName);\n        const result = await coll.trim({ keep });\n        console.log(c.green(`✓ Trimmed ${result.removed} items from '${collName}' (kept ${keep})`));\n        brain.close();\n        return;\n    }\n\n    if (sub === 'clear') {\n        const collName = pos[2];\n        if (!collName) {\n            console.log(c.red('Usage: brainbank kv clear <collection>'));\n            process.exit(1);\n        }\n\n        const brain = await createBrain();\n        await brain.initialize();\n        const coll = brain.collection(collName);\n        const before = coll.count();\n        coll.clear();\n        console.log(c.green(`✓ Cleared ${before} items from '${collName}'`));\n        brain.close();\n        return;\n    }\n\n    console.log(c.red('Usage: brainbank kv <add|search|list|trim|clear>'));\n    process.exit(1);\n}\n\n","/**\n * brainbank docs — Index document collections\n * brainbank dsearch — Search documents only\n */\n\nimport { c, args, getFlag, stripFlags, findDocsPlugin } from '@/cli/utils.ts';\nimport { createBrain } from '@/cli/factory/index.ts';\n\nexport async function cmdDocs(): Promise<void> {\n    const collection = getFlag('collection');\n    const brain = await createBrain();\n\n    console.log(c.bold('\\n━━━ BrainBank Docs Index ━━━\\n'));\n\n    const opts: { collections?: string[]; onProgress?: (collection: string, file: string, current: number, total: number) => void } = {};\n    if (collection) opts.collections = [collection];\n    opts.onProgress = (col: string, file: string, cur: number, total: number) => {\n        process.stdout.write(`\\r  ${c.cyan(col)} [${cur}/${total}] ${file}                    `);\n    };\n\n    const docsPlugin = findDocsPlugin(brain);\n    if (!docsPlugin) { console.log(c.red('  Docs plugin not loaded. Install @brainbank/docs.')); process.exit(1); }\n\n    const results = await docsPlugin.indexDocs(opts);\n\n    console.log('\\n');\n    for (const [name, stat] of Object.entries(results) as [string, { indexed: number; skipped: number; removed: number; chunks: number }][]) {\n        const removedStr = stat.removed > 0 ? `, ${c.red(String(stat.removed) + ' removed')}` : '';\n        console.log(`  ${c.green(name)}: ${stat.indexed} indexed, ${stat.skipped} skipped${removedStr}, ${stat.chunks} chunks`);\n    }\n\n    brain.close();\n}\n\nexport async function cmdDocSearch(): Promise<void> {\n    const query = stripFlags(args).slice(1).join(' ');\n    if (!query) {\n        console.log(c.red('Usage: brainbank dsearch <query>'));\n        process.exit(1);\n    }\n\n    const brain = await createBrain();\n    const collection = getFlag('collection');\n    const k = parseInt(getFlag('k') || '8', 10);\n\n    console.log(c.bold(`\\n━━━ BrainBank Doc Search: \"${query}\" ━━━\\n`));\n\n    const docsPlugin = findDocsPlugin(brain);\n    if (!docsPlugin) {\n        console.log(c.red('Docs plugin not loaded. Install @brainbank/docs.'));\n        process.exit(1);\n    }\n    const results = await docsPlugin.search(query, { collection: collection ?? undefined, k });\n\n    if (results.length === 0) {\n        console.log(c.yellow('  No results found.'));\n        brain.close();\n        return;\n    }\n\n    for (const r of results) {\n        const score = Math.round(r.score * 100);\n        const ctx = r.context ? ` — ${c.dim(r.context)}` : '';\n        console.log(`${c.magenta(`[DOC ${score}%]`)} ${c.bold(r.filePath!)} [${r.type === 'document' ? r.metadata.collection ?? '' : ''}]${ctx}`);\n        const preview = r.content.split('\\n').slice(0, 4).join('\\n');\n        console.log(c.dim(preview));\n        console.log('');\n    }\n\n    brain.close();\n}\n","/**\n * brainbank search  — Semantic search (vector)\n * brainbank hsearch — Hybrid search (vector + BM25)\n * brainbank ksearch — Keyword search (BM25)\n *\n * Source filtering:\n *   --code 10             Max code results\n *   --git 0               Skip git results\n *   --docs 5              Max document results\n *   --notes 10            Custom plugin results\n *   --slack_messages 5    Custom collection results\n *\n * Any --<name> <number> flag is treated as a source filter.\n */\n\nimport { c, args, stripFlags, printResults } from '@/cli/utils.ts';\nimport { createBrain } from '@/cli/factory/index.ts';\n\n/**\n * Parse dynamic source flags: each `--<name> <number>` becomes `{ name: number }`.\n *\n * Known non-source flags (--repo, --depth, etc.) are excluded.\n * Returns sources map + the query string (positional args).\n */\nfunction parseSourceFlags(): { sources: Record<string, number>; query: string } {\n    const NON_SOURCE_FLAGS = new Set([\n        'repo', 'depth', 'collection', 'pattern', 'context', 'name',\n        'keep', 'reranker', 'pruner', 'only', 'docs-path', 'mode', 'limit',\n        'ignore', 'meta', 'k', 'yes', 'y', 'force', 'verbose',\n    ]);\n\n    const sources: Record<string, number> = {};\n    const positional: string[] = [];\n\n    for (let i = 0; i < args.length; i++) {\n        if (args[i].startsWith('--')) {\n            const name = args[i].slice(2);\n\n            // Skip boolean flags\n            if (name === 'yes' || name === 'force' || name === 'verbose') continue;\n\n            // If next arg is a number and flag is not a known non-source flag\n            const next = args[i + 1];\n            if (next !== undefined && /^\\d+$/.test(next) && !NON_SOURCE_FLAGS.has(name)) {\n                sources[name] = parseInt(next, 10);\n                i++; // skip the value\n                continue;\n            }\n\n            // Known value flag — skip its value\n            if (NON_SOURCE_FLAGS.has(name) && next !== undefined && !next.startsWith('--')) {\n                i++;\n            }\n            continue;\n        }\n        positional.push(args[i]);\n    }\n\n    const query = positional.slice(1).join(' '); // skip command name\n    return { sources, query };\n}\n\n/** Print active source filters. */\nfunction printFilterInfo(sources: Record<string, number>): void {\n    const entries = Object.entries(sources);\n    if (entries.length === 0) return;\n    const parts = entries.map(([k, v]) => `${k}=${v}`);\n    console.log(c.dim(`  Sources: ${parts.join(', ')}`));\n}\n\n/** Build search options from sources map. */\nfunction buildSearchOptions(sources: Record<string, number>): { sources: Record<string, number>; source: 'cli' } {\n    return Object.keys(sources).length > 0 ? { sources, source: 'cli' } : { sources: {}, source: 'cli' };\n}\n\nexport async function cmdSearch(): Promise<void> {\n    const { sources, query } = parseSourceFlags();\n    if (!query) {\n        console.log(c.red('Usage: brainbank search <query> [--code <n>] [--git <n>] [--<source> <n>]'));\n        process.exit(1);\n    }\n\n    const brain = await createBrain();\n    console.log(c.bold(`\\n━━━ BrainBank Search: \"${query}\" ━━━\\n`));\n    printFilterInfo(sources);\n\n    const opts = buildSearchOptions(sources);\n    const results = await brain.search(query, opts);\n    printResults(results);\n    brain.close();\n}\n\nexport async function cmdHybridSearch(): Promise<void> {\n    const { sources, query } = parseSourceFlags();\n    if (!query) {\n        console.log(c.red('Usage: brainbank hsearch <query> [--code <n>] [--git <n>] [--docs <n>] [--<source> <n>]'));\n        process.exit(1);\n    }\n\n    const brain = await createBrain();\n    console.log(c.bold(`\\n━━━ BrainBank Hybrid Search: \"${query}\" ━━━`));\n    console.log(c.dim(`  Mode: vector + BM25 → Reciprocal Rank Fusion`));\n    printFilterInfo(sources);\n    console.log('');\n\n    const opts = buildSearchOptions(sources);\n    const results = await brain.hybridSearch(query, opts);\n    printResults(results);\n    brain.close();\n}\n\nexport async function cmdKeywordSearch(): Promise<void> {\n    const { sources, query } = parseSourceFlags();\n    if (!query) {\n        console.log(c.red('Usage: brainbank ksearch <query> [--code <n>] [--git <n>] [--<source> <n>]'));\n        process.exit(1);\n    }\n\n    const brain = await createBrain();\n    await brain.initialize();\n    console.log(c.bold(`\\n━━━ BrainBank Keyword Search: \"${query}\" ━━━`));\n    console.log(c.dim(`  Mode: BM25 full-text (instant)`));\n    printFilterInfo(sources);\n    console.log('');\n\n    const opts = buildSearchOptions(sources);\n    const results = await brain.searchBM25(query, opts);\n    printResults(results);\n    brain.close();\n}\n","/**\n * ServerClient — Lightweight HTTP client for the BrainBank daemon.\n *\n * Used by CLI commands to delegate to a running HTTP server\n * instead of loading models locally. Falls back gracefully\n * (returns null) if the server is unreachable.\n */\n\nimport * as http from 'node:http';\n\nimport { isServerRunning } from '@/services/daemon.ts';\n\ninterface ContextOptions {\n    task: string;\n    repo?: string;\n    sources?: Record<string, number>;\n    pathPrefix?: string;\n    affectedFiles?: string[];\n}\n\n/**\n * Try to get context from the running HTTP server.\n * Returns the context string if successful, null if server is unreachable.\n */\nexport async function tryServerContext(options: ContextOptions): Promise<string | null> {\n    const info = isServerRunning();\n    if (!info) return null;\n\n    try {\n        const body = JSON.stringify({\n            task: options.task,\n            repo: options.repo,\n            sources: options.sources,\n            pathPrefix: options.pathPrefix,\n            affectedFiles: options.affectedFiles,\n        });\n\n        const response = await httpPost(info.port, '/context', body);\n        const data = JSON.parse(response) as { context?: string; error?: string };\n\n        if (data.error) return null;\n        return data.context ?? null;\n    } catch {\n        // Server unreachable or error — fall back to local\n        return null;\n    }\n}\n\n/**\n * Try to trigger indexing on the running HTTP server.\n * Returns the result if successful, null if server is unreachable.\n */\nexport async function tryServerIndex(repo?: string, forceReindex?: boolean): Promise<Record<string, unknown> | null> {\n    const info = isServerRunning();\n    if (!info) return null;\n\n    try {\n        const body = JSON.stringify({ repo, forceReindex });\n        const response = await httpPost(info.port, '/index', body);\n        const data = JSON.parse(response) as { result?: Record<string, unknown>; error?: string };\n\n        if (data.error) return null;\n        return data.result ?? null;\n    } catch {\n        return null;\n    }\n}\n\n/**\n * Check server health. Returns health info or null.\n */\nexport async function serverHealth(): Promise<{\n    ok: boolean;\n    pid: number;\n    port: number;\n    uptime: number;\n    workspaces: number;\n} | null> {\n    const info = isServerRunning();\n    if (!info) return null;\n\n    try {\n        const response = await httpGet(info.port, '/health');\n        return JSON.parse(response) as { ok: boolean; pid: number; port: number; uptime: number; workspaces: number };\n    } catch {\n        return null;\n    }\n}\n\n// ── HTTP helpers ────────────────────────────────────\n\nfunction httpPost(port: number, path: string, body: string): Promise<string> {\n    return new Promise((resolve, reject) => {\n        const req = http.request({\n            hostname: '127.0.0.1',\n            port,\n            path,\n            method: 'POST',\n            headers: {\n                'Content-Type': 'application/json',\n                'Content-Length': Buffer.byteLength(body),\n            },\n            timeout: 120_000, // 2 minutes — context queries can be slow on first load\n        }, (res) => {\n            const chunks: Buffer[] = [];\n            res.on('data', (chunk: Buffer) => chunks.push(chunk));\n            res.on('end', () => resolve(Buffer.concat(chunks).toString('utf8')));\n        });\n\n        req.on('error', reject);\n        req.on('timeout', () => { req.destroy(); reject(new Error('Request timed out')); });\n        req.write(body);\n        req.end();\n    });\n}\n\nfunction httpGet(port: number, path: string): Promise<string> {\n    return new Promise((resolve, reject) => {\n        const req = http.request({\n            hostname: '127.0.0.1',\n            port,\n            path,\n            method: 'GET',\n            timeout: 5_000,\n        }, (res) => {\n            const chunks: Buffer[] = [];\n            res.on('data', (chunk: Buffer) => chunks.push(chunk));\n            res.on('end', () => resolve(Buffer.concat(chunks).toString('utf8')));\n        });\n\n        req.on('error', reject);\n        req.on('timeout', () => { req.destroy(); reject(new Error('Request timed out')); });\n        req.end();\n    });\n}\n","/**\n * brainbank context <task> — Get formatted context for a task\n * brainbank context add <collection> <path> <description>\n * brainbank context list\n *\n * Source filtering (same as search commands):\n *   --code 20    Max code results (default: 20)\n *   --git 5      Max git results\n *   --no-git     Skip git results\n *   --no-code    Skip code results\n *   --path <dir> Filter results to files under this path prefix\n *   --ignore <paths> Exclude paths (comma-separated or repeated: --ignore a,b --ignore c)\n */\n\nimport { c, args, stripFlags, getFlag, getFlagAll, findDocsPlugin } from '@/cli/utils.ts';\nimport { createBrain } from '@/cli/factory/index.ts';\nimport { tryServerContext } from '@/cli/server-client.ts';\n\n/** Parse --code N, --git N, --no-git, --no-code flags into sources map. */\nfunction parseContextFlags(): Record<string, number> {\n    const NON_SOURCE = new Set([\n        'repo', 'depth', 'collection', 'pattern', 'context', 'name',\n        'keep', 'reranker', 'pruner', 'only', 'docs-path', 'mode', 'limit',\n        'ignore', 'meta', 'k', 'yes', 'y', 'force', 'verbose', 'path',\n    ]);\n    const sources: Record<string, number> = {};\n    for (let i = 0; i < args.length; i++) {\n        if (!args[i].startsWith('--')) continue;\n        const name = args[i].slice(2);\n        // --no-git, --no-code → set to 0\n        if (name.startsWith('no-')) {\n            sources[name.slice(3)] = 0;\n            continue;\n        }\n        // --code 20, --git 5\n        const next = args[i + 1];\n        if (next !== undefined && /^\\d+$/.test(next) && !NON_SOURCE.has(name)) {\n            sources[name] = parseInt(next, 10);\n            i++;\n        }\n    }\n    return sources;\n}\n\nexport async function cmdContext(): Promise<void> {\n    const pos = stripFlags(args);\n    const sub = pos[1];\n\n    // brainbank context add <collection> <path> <description>\n    if (sub === 'add') {\n        const collection = pos[2];\n        const path = pos[3];\n        const desc = pos.slice(4).join(' ');\n\n        if (!collection || !path || !desc) {\n            console.log(c.red('Usage: brainbank context add <collection> <path> <description>'));\n            process.exit(1);\n        }\n\n        const brain = await createBrain();\n        await brain.initialize();\n        const docsPlugin = findDocsPlugin(brain);\n        if (!docsPlugin) { console.log(c.red('Docs plugin not loaded.')); process.exit(1); }\n        docsPlugin.addContext(collection, path, desc);\n        console.log(c.green(`✓ Context added: ${collection}:${path} → \"${desc}\"`));\n        brain.close();\n        return;\n    }\n\n    // brainbank context list\n    if (sub === 'list') {\n        const brain = await createBrain();\n        await brain.initialize();\n        const docsPlugin = findDocsPlugin(brain);\n        if (!docsPlugin) { console.log(c.yellow('  Docs plugin not loaded.')); brain.close(); return; }\n        const contexts = docsPlugin.listContexts();\n        if (contexts.length === 0) {\n            console.log(c.yellow('  No contexts configured.'));\n        } else {\n            console.log(c.bold('\\n━━━ Contexts ━━━\\n'));\n            for (const ctx of contexts) {\n                console.log(`  ${c.cyan(ctx.collection)}:${ctx.path} → ${c.dim(ctx.context)}`);\n            }\n        }\n        brain.close();\n        return;\n    }\n\n    // brainbank context <task> — get formatted context\n    const task = stripFlags(args).slice(1).join(' ');\n    if (!task) {\n        console.log(c.red('Usage: brainbank context <task description>'));\n        console.log(c.dim('       brainbank context add <collection> <path> <description>'));\n        console.log(c.dim('       brainbank context list'));\n        process.exit(1);\n    }\n\n    const sources = parseContextFlags();\n    const pathPrefix = getFlag('path');\n    const ignorePaths = getFlagAll('ignore');\n    const repo = getFlag('repo');\n\n    // Parse BrainBankQL field flags\n    const fields = parseFieldFlags();\n\n    // Try HTTP server delegation first\n    const serverResult = await tryServerContext({\n        task,\n        repo: repo ?? process.cwd(),\n        sources: Object.keys(sources).length > 0 ? sources : undefined,\n        pathPrefix,\n    });\n\n    if (serverResult !== null) {\n        console.log(serverResult);\n        return;\n    }\n\n    // Fall back to local\n    const brain = await createBrain();\n    const context = await brain.getContext(task, {\n        sources: Object.keys(sources).length > 0 ? sources : undefined,\n        pathPrefix,\n        ignorePaths: ignorePaths.length > 0 ? ignorePaths : undefined,\n        source: 'cli',\n        fields: Object.keys(fields).length > 0 ? fields : undefined,\n    });\n    console.log(context);\n    brain.close();\n}\n\n/** Parse BrainBankQL field flags: --lines, --symbols, --compact, --no-callTree, --callTree.depth=N, etc. */\nfunction parseFieldFlags(): Record<string, unknown> {\n    const FIELD_BOOLEANS = new Set(['lines', 'symbols', 'compact', 'expander']);\n    const FIELD_NEGATABLE = new Set(['callTree', 'imports']);\n    const fields: Record<string, unknown> = {};\n\n    for (let i = 0; i < args.length; i++) {\n        if (!args[i].startsWith('--')) continue;\n        const raw = args[i].slice(2);\n\n        // --no-callTree, --no-imports → set to false\n        if (raw.startsWith('no-')) {\n            const name = raw.slice(3);\n            if (FIELD_NEGATABLE.has(name)) {\n                fields[name] = false;\n            }\n            continue;\n        }\n\n        // --callTree.depth=4 → { depth: 4 }\n        const dotIdx = raw.indexOf('.');\n        if (dotIdx > 0) {\n            const fieldName = raw.slice(0, dotIdx);\n            const rest = raw.slice(dotIdx + 1);\n            const eqIdx = rest.indexOf('=');\n            if (eqIdx > 0) {\n                const key = rest.slice(0, eqIdx);\n                const val = parseInt(rest.slice(eqIdx + 1), 10);\n                if (!isNaN(val)) {\n                    fields[fieldName] = { [key]: val };\n                }\n            }\n            continue;\n        }\n\n        // --lines, --symbols, --compact, --expander → true\n        if (FIELD_BOOLEANS.has(raw)) {\n            fields[raw] = true;\n        }\n    }\n\n    return fields;\n}\n","/**\n * brainbank files <path|glob> [...paths] [--lines]\n *\n * Fetch full file contents from the index.\n * Use after `brainbank context` to view complete files identified by search.\n */\n\nimport { c, args, getFlag } from '@/cli/utils.ts';\nimport { createBrain } from '@/cli/factory/index.ts';\n\nexport async function cmdFiles(): Promise<void> {\n    // Collect positional args (file patterns) — skip 'files' command itself\n    const patterns: string[] = [];\n    const showLines = args.includes('--lines');\n\n    for (let i = 1; i < args.length; i++) {\n        if (args[i].startsWith('--')) {\n            // Skip --lines and --repo <value>\n            if (args[i] === '--repo') {\n                i++; // skip value\n            }\n            continue;\n        }\n        patterns.push(args[i]);\n    }\n\n    if (patterns.length === 0) {\n        console.log(c.red('Usage: brainbank files <path|glob> [...paths] [--lines]'));\n        console.log(c.dim('  Exact:     brainbank files src/auth/login.ts'));\n        console.log(c.dim('  Directory: brainbank files src/graph/'));\n        console.log(c.dim('  Glob:      brainbank files \"src/**/*.service.ts\"'));\n        console.log(c.dim('  Fuzzy:     brainbank files plugin.ts'));\n        console.log(c.dim('  Lines:     brainbank files src/plugin.ts --lines'));\n        process.exit(1);\n    }\n\n    const brain = await createBrain();\n    await brain.initialize();\n    const results = brain.resolveFiles(patterns);\n\n    if (results.length === 0) {\n        console.log(c.yellow('No matching files found in the index.'));\n        console.log(c.dim('Run `brainbank index` first to index your codebase.'));\n        brain.close();\n        return;\n    }\n\n    // Format output\n    for (const r of results) {\n        const meta = r.metadata as Record<string, unknown>;\n        const startLine = (meta.startLine as number) ?? 1;\n\n        console.log(c.bold(`\\n── ${r.filePath} ──\\n`));\n\n        if (showLines) {\n            const codeLines = r.content.split('\\n');\n            const pad = String(startLine + codeLines.length - 1).length;\n            for (let i = 0; i < codeLines.length; i++) {\n                const lineNum = c.dim(`${String(startLine + i).padStart(pad)}|`);\n                console.log(`${lineNum} ${codeLines[i]}`);\n            }\n        } else {\n            console.log(r.content);\n        }\n    }\n\n    console.log(c.dim(`\\n${results.length} file(s) resolved.`));\n    brain.close();\n}\n","/** brainbank stats — Show index statistics. */\n\nimport { c } from '@/cli/utils.ts';\nimport { createBrain } from '@/cli/factory/index.ts';\n\n/** Convert camelCase/snake_case stat keys to human-readable labels. */\nfunction formatStatKey(key: string): string {\n    return key\n        .replace(/([a-z])([A-Z])/g, '$1 $2')\n        .replace(/_/g, ' ')\n        .replace(/\\b\\w/g, c => c.toUpperCase())\n        .padEnd(16);\n}\n\nexport async function cmdStats(): Promise<void> {\n    const brain = await createBrain();\n    await brain.initialize();\n\n    const s = brain.stats();\n\n    console.log(c.bold('\\n━━━ BrainBank Stats ━━━\\n'));\n    console.log(`  ${c.cyan('Plugins')}: ${brain.plugins.join(', ')}\\n`);\n\n    for (const [name, pluginStats] of Object.entries(s)) {\n        if (!pluginStats) continue;\n        console.log(`  ${c.cyan(name)}`);\n        for (const [key, value] of Object.entries(pluginStats)) {\n            console.log(`    ${formatStatKey(key)}${value}`);\n        }\n        console.log('');\n    }\n\n    const kvNames = brain.listCollectionNames();\n    if (kvNames.length > 0) {\n        console.log(`  ${c.cyan('KV Collections')}`);\n        for (const name of kvNames) {\n            const coll = brain.collection(name);\n            console.log(`    ${name}: ${coll.count()} items`);\n        }\n        console.log('');\n    }\n\n    brain.close();\n}\n","/** brainbank reembed — Re-embed all vectors. */\n\nimport { c } from '@/cli/utils.ts';\nimport { createBrain } from '@/cli/factory/index.ts';\n\nexport async function cmdReembed(): Promise<void> {\n    const brain = await createBrain();\n    await brain.initialize();\n\n    console.log(c.bold('\\n━━━ BrainBank Re-embed ━━━\\n'));\n    console.log(c.dim('  Regenerating vectors with current embedding provider...'));\n    console.log(c.dim('  Text, FTS, and metadata remain unchanged.\\n'));\n\n    const result = await brain.reembed({\n        onProgress: (table: string, current: number, total: number) => {\n            process.stdout.write(`\\r  ${c.cyan(table.padEnd(8))} ${current}/${total}`);\n        },\n    });\n\n    console.log('\\n');\n    for (const [name, count] of Object.entries(result.counts)) {\n        if (count > 0) {\n            const label = name.charAt(0).toUpperCase() + name.slice(1);\n            console.log(`  ${c.green('✓')} ${label.padEnd(8)} ${count} vectors`);\n        }\n    }\n    console.log(`\\n  ${c.bold('Total')}: ${result.total} vectors regenerated\\n`);\n\n    brain.close();\n}\n","/** brainbank watch — Watch for file changes. */\n\nimport { c } from '@/cli/utils.ts';\nimport { createBrain } from '@/cli/factory/index.ts';\nimport { loadConfig } from '@/cli/factory/config-loader.ts';\n\nexport async function cmdWatch(): Promise<void> {\n    const brain = await createBrain();\n    await brain.initialize();\n\n    // Read ignore patterns from config (code.ignore + top-level ignore)\n    const config = await loadConfig(brain.config.repoPath);\n    const codeIgnore = (config?.code as Record<string, unknown> | undefined)?.ignore as string[] ?? [];\n\n    console.log(c.bold('\\n━━━ BrainBank Watch ━━━\\n'));\n    console.log(c.dim(`  Watching ${brain.config.repoPath} for changes...`));\n    if (codeIgnore.length > 0) {\n        console.log(c.dim(`  Ignoring: ${codeIgnore.join(', ')}`));\n    }\n    console.log(c.dim('  Press Ctrl+C to stop.\\n'));\n\n    const watcher = brain.watch({\n        debounceMs: 2000,\n        ignore: codeIgnore,\n        onIndex: (sourceId: string, pluginName: string) => {\n            const ts = new Date().toLocaleTimeString();\n            console.log(`  ${c.dim(ts)} ${c.green('✓')} ${c.cyan(pluginName)}: ${sourceId}`);\n        },\n        onError: (err: Error) => {\n            console.error(`  ${c.red('✗')} ${err.message}`);\n        },\n    });\n\n    process.on('SIGINT', () => {\n        console.log(c.dim('\\n  Stopping watcher...'));\n        watcher.close();\n        brain.close();\n        process.exit(0);\n    });\n\n    await new Promise(() => {});\n}\n\n","/** brainbank mcp — Start MCP server (stdio). Requires @brainbank/mcp. */\n\nimport { c } from '@/cli/utils.ts';\n\nexport async function cmdMcp(): Promise<void> {\n    try {\n        await import('@brainbank/mcp');\n    } catch {\n        console.error(c.red('Error: @brainbank/mcp is not installed.'));\n        console.error(c.dim('  Install: npm i @brainbank/mcp'));\n        process.exit(1);\n    }\n}\n","/**\n * brainbank daemon — HTTP daemon for CLI delegation.\n *\n *   brainbank daemon              → Start foreground\n *   brainbank daemon start        → Start background (fork + PID file)\n *   brainbank daemon stop         → Stop background daemon\n *   brainbank daemon restart      → Stop + start\n */\n\nimport { c, args, getFlag, stripFlags } from '@/cli/utils.ts';\nimport { isServerRunning, removePid, DEFAULT_PORT } from '@/services/daemon.ts';\nimport { createBrain } from '@/cli/factory/index.ts';\n\nexport async function cmdDaemon(): Promise<void> {\n    const pos = stripFlags(args);\n    const sub = pos[1]; // start | stop | undefined\n\n    if (sub === 'stop') return stopDaemon();\n    if (sub === 'restart') { stopDaemon(); return forkDaemon(); }\n    if (sub === 'start') return forkDaemon();\n    return startForeground();\n}\n\n// ── Foreground ──────────────────────────────────\n\nasync function startForeground(): Promise<void> {\n    const port = parseInt(getFlag('port') ?? String(DEFAULT_PORT), 10);\n    const { HttpServer } = await import('@/services/http-server.ts');\n\n    const server = new HttpServer({\n        port,\n        factory: async (repoPath: string) => {\n            const brain = await createBrain(repoPath);\n            await brain.initialize();\n            return brain;\n        },\n        onError: (repo, err) => {\n            const msg = err instanceof Error ? err.message : String(err);\n            console.error(c.red(`  Pool error [${repo}]: ${msg}`));\n        },\n        onLog: (msg) => console.log(c.dim(`  ${msg}`)),\n    });\n\n    console.log(c.bold('\\n━━━ BrainBank HTTP Daemon ━━━\\n'));\n\n    await server.start();\n\n    console.log(c.dim(`  Port: ${port}`));\n    console.log(c.dim('  Press Ctrl+C to stop.\\n'));\n\n    const shutdown = () => {\n        console.log(c.dim('\\n  Shutting down...'));\n        server.close();\n        process.exit(0);\n    };\n    process.on('SIGINT', shutdown);\n    process.on('SIGTERM', shutdown);\n\n    await new Promise(() => {});\n}\n\n// ── Background ──────────────────────────────────\n\nasync function forkDaemon(): Promise<void> {\n    const port = parseInt(getFlag('port') ?? String(DEFAULT_PORT), 10);\n    const { fork } = await import('node:child_process');\n\n    const existing = isServerRunning();\n    if (existing) {\n        console.log(c.yellow(`  Daemon already running (PID ${existing.pid}, port ${existing.port})`));\n        return;\n    }\n\n    const child = fork(process.argv[1], ['daemon', '--port', String(port)], {\n        detached: true,\n        stdio: 'ignore',\n    });\n\n    child.unref();\n\n    console.log(c.green(`  ✓ Daemon started (PID ${child.pid}, port ${port})`));\n    console.log(c.dim('  Stop with: brainbank daemon stop'));\n}\n\nfunction stopDaemon(): void {\n    const info = isServerRunning();\n    if (!info) {\n        console.log(c.yellow('  No daemon running.'));\n        return;\n    }\n\n    try {\n        process.kill(info.pid, 'SIGTERM');\n        removePid();\n        console.log(c.green(`  ✓ Daemon stopped (PID ${info.pid})`));\n    } catch {\n        removePid();\n        console.log(c.yellow(`  PID ${info.pid} not found. Cleaned up stale PID file.`));\n    }\n}\n","/**\n * Status Command — Show BrainBank server status.\n *\n * Usage: brainbank status\n */\n\nimport { c } from '@/cli/utils.ts';\nimport { serverHealth } from '@/cli/server-client.ts';\nimport { isServerRunning } from '@/services/daemon.ts';\n\nfunction formatUptime(seconds: number): string {\n    if (seconds < 60) return `${seconds}s`;\n    const minutes = Math.floor(seconds / 60);\n    if (minutes < 60) return `${minutes}m`;\n    const hours = Math.floor(minutes / 60);\n    const remainMinutes = minutes % 60;\n    return remainMinutes > 0 ? `${hours}h ${remainMinutes}m` : `${hours}h`;\n}\n\nexport async function cmdStatus(): Promise<void> {\n    const info = isServerRunning();\n\n    if (!info) {\n        console.log(`\\n  ${c.dim('HTTP Server:')} ${c.yellow('stopped')}\\n`);\n        console.log(c.dim('  Start with: brainbank daemon'));\n        console.log('');\n        return;\n    }\n\n    // Try to get detailed health from the server\n    const health = await serverHealth();\n\n    if (health) {\n        const uptime = formatUptime(health.uptime);\n        console.log(`\\n  ${c.dim('HTTP Server:')} ${c.green('running')}`);\n        console.log(`  ${c.dim('PID:')}         ${health.pid}`);\n        console.log(`  ${c.dim('Port:')}        ${health.port}`);\n        console.log(`  ${c.dim('Uptime:')}      ${uptime}`);\n        console.log(`  ${c.dim('Workspaces:')}  ${health.workspaces}`);\n        console.log('');\n    } else {\n        // PID file exists but server not responding\n        console.log(`\\n  ${c.dim('HTTP Server:')} ${c.yellow('stale')} (PID ${info.pid} not responding)`);\n        console.log(c.dim('  The PID file may be stale. Restart with: brainbank daemon'));\n        console.log('');\n    }\n}\n","/** brainbank help — Show CLI usage. */\n\nimport { c } from '@/cli/utils.ts';\n\nexport function showHelp(): void {\n    console.log(c.bold('\\n━━━ BrainBank — Semantic Knowledge Bank ━━━\\n'));\n    console.log(c.bold('Indexing:'));\n    console.log(`  ${c.cyan('index')} ${c.dim('(i)')} [path]                  Index code + git history`);\n    console.log(`  ${c.cyan('collection add')} <path> --name      Add a document collection`);\n    console.log(`  ${c.cyan('collection list')}                    List collections`);\n    console.log(`  ${c.cyan('collection remove')} <name>           Remove a collection`);\n    console.log(`  ${c.cyan('docs')} [--collection <name>]         Index document collections`);\n    console.log('');\n    console.log(c.bold('Search:'));\n    console.log(`  ${c.cyan('search')} <query>                     Semantic search (vector)`);\n    console.log(`  ${c.cyan('hsearch')} <query>                    Hybrid search (${c.bold('best quality')})`);\n    console.log(`  ${c.cyan('ksearch')} <query>                    Keyword search (BM25, instant)`);\n    console.log(`  ${c.cyan('dsearch')} <query>                    Document search`);\n    console.log(c.dim('    All search commands accept --<source> <n> to filter by source'));\n    console.log('');\n    console.log(c.bold('Context:'));\n    console.log(`  ${c.cyan('context')} <task>                     Get formatted context for a task`);\n    console.log(`  ${c.cyan('context add')} <col> <path> <desc>    Add context metadata`);\n    console.log(`  ${c.cyan('context list')}                       List all context metadata`);\n    console.log(`  ${c.cyan('files')} <path|glob> [...] [--lines]  View full indexed files directly`);\n    console.log('');\n    console.log(c.bold('KV Store:'));\n    console.log(`  ${c.cyan('kv add')} <coll> <content>            Add item to a collection`);\n    console.log(`  ${c.cyan('kv search')} <coll> <query>           Search a collection`);\n    console.log(`  ${c.cyan('kv list')} [coll]                     List collections or items`);\n    console.log(`  ${c.cyan('kv trim')} <coll> --keep <n>          Keep only N most recent`);\n    console.log(`  ${c.cyan('kv clear')} <coll>                    Clear all items`);\n    console.log('');\n    console.log(c.bold('Utility:'));\n    console.log(`  ${c.cyan('stats')}                              Show index statistics`);\n    console.log(`  ${c.cyan('reembed')}                            Re-embed all vectors`);\n    console.log(`  ${c.cyan('watch')}                              Watch files, auto-re-index`);\n    console.log(`  ${c.cyan('mcp')}                                Start MCP server (stdio)`);\n    console.log(`  ${c.cyan('mcp:export')} [target]                Export MCP config (antigravity)`);\n    console.log(`  ${c.cyan('daemon')}                             Start HTTP daemon (foreground)`);\n    console.log(`  ${c.cyan('daemon start')}                       Start HTTP daemon (background)`);\n    console.log(`  ${c.cyan('daemon stop')}                        Stop background daemon`);\n    console.log(`  ${c.cyan('daemon restart')}                     Restart background daemon`);\n    console.log(`  ${c.cyan('status')}                             Show daemon status`);\n    console.log(`  ${c.cyan('--version')} ${c.dim('(-v)')}                      Show version`);\n    console.log('');\n    console.log(c.bold('Options:'));\n    console.log(`  ${c.dim('--repo <path>')}           Repository path (default: .)`);\n    console.log(`  ${c.dim('--force')}                 Force re-index all files`);\n    console.log(`  ${c.dim('--depth <n>')}             Git history depth (default: 500)`);\n    console.log(`  ${c.dim('--collection <name>')}     Filter by collection`);\n    console.log(`  ${c.dim('--pattern <glob>')}        Collection glob (default: **/*.md)`);\n    console.log(`  ${c.dim('--context <desc>')}        Context description`);\n    console.log(`  ${c.dim('--<source> <n>')}          Source filter: max results from <source> (0 = skip)`);\n    console.log(`  ${c.dim('--path <dir>')}            Filter context results to files under this path prefix`);\n    console.log(`  ${c.dim('--ignore <globs>')}        Ignore glob patterns for code indexing (comma-separated)`);\n    console.log(`  ${c.dim('--yes / -y')}              Skip interactive prompt (auto-select all available)`);\n    console.log(`  ${c.dim('--reranker <name>')}       Reranker to use (qwen3)`);\n    console.log(`  ${c.dim('--port <n>')}              HTTP daemon port (default: 8181)`);\n    console.log('');\n    console.log(c.bold('Examples:'));\n    console.log(c.dim('  brainbank index .'));\n    console.log(c.dim('  brainbank index . --ignore \"sdk/**,vendor/**\"'));\n    console.log(c.dim('  brainbank kv add errors \"Fixed null pointer in api.ts\"'));\n    console.log(c.dim('  brainbank kv search errors \"null pointer\"'));\n    console.log(c.dim('  brainbank kv list'));\n    console.log(c.dim('  brainbank hsearch \"authentication middleware\"'));\n    console.log(c.dim('  brainbank hsearch \"auth\" --code 0 --git 10           # git only'));\n    console.log(c.dim('  brainbank search \"handler\" --git 0                   # code only'));\n    console.log(c.dim('  brainbank hsearch \"api\" --docs 10 --code 0 --git 0   # docs only'));\n    console.log(c.dim('  brainbank context \"auth flow\" | pbcopy               # → clipboard'));\n    console.log(c.dim('  brainbank daemon start                               # background HTTP'));\n    console.log(c.dim('  brainbank mcp                                        # MCP stdio'));\n    console.log(c.dim('  brainbank mcp:export antigravity                     # export MCP config'));\n}\n","#!/usr/bin/env node\n\n/**\n * BrainBank — CLI Entry Point\n *\n * Dispatcher that routes commands to their handler modules.\n */\n\nimport { args, c } from './utils.ts';\nimport { cmdIndex } from './commands/index.ts';\nimport { cmdCollection } from './commands/collection.ts';\nimport { cmdKv } from './commands/kv.ts';\nimport { cmdDocs, cmdDocSearch } from './commands/docs.ts';\nimport { cmdSearch, cmdHybridSearch, cmdKeywordSearch } from './commands/search.ts';\nimport { cmdContext } from './commands/context.ts';\nimport { cmdFiles } from './commands/files.ts';\nimport { cmdStats } from './commands/stats.ts';\nimport { cmdReembed } from './commands/reembed.ts';\nimport { cmdWatch } from './commands/watch.ts';\nimport { cmdMcp } from './commands/mcp.ts';\nimport { cmdMcpExport } from './commands/mcp-export.ts';\nimport { cmdDaemon } from './commands/daemon.ts';\nimport { cmdStatus } from './commands/status.ts';\nimport { showHelp } from './commands/help.ts';\nimport { VERSION } from '@/constants.ts';\n\nconst command = args[0];\n\nasync function main(): Promise<void> {\n    switch (command) {\n        case '--version':\n        case '-v':\n            console.log(`brainbank v${VERSION}`);\n            break;\n        case 'i':\n        case 'index':       return cmdIndex();\n        case 'collection':  return cmdCollection();\n        case 'kv':          return cmdKv();\n        case 'docs':        return cmdDocs();\n        case 'dsearch':     return cmdDocSearch();\n        case 'search':      return cmdSearch();\n        case 'hsearch':     return cmdHybridSearch();\n        case 'ksearch':     return cmdKeywordSearch();\n        case 'context':     return cmdContext();\n        case 'files':       return cmdFiles();\n        case 'stats':       return cmdStats();\n        case 'reembed':     return cmdReembed();\n        case 'watch':       return cmdWatch();\n        case 'mcp':         return cmdMcp();\n        case 'mcp:export':  return cmdMcpExport();\n        case 'serve':        return cmdMcp(); // backward compat\n        case 'daemon':      return cmdDaemon();\n        case 'status':      return cmdStatus();\n        case 'help':\n        case '--help':\n        case '-h':\n            showHelp();\n            break;\n        default:\n            if (command) console.log(c.red(`Unknown command: ${command}\\n`));\n            showHelp();\n            process.exit(command ? 1 : 0);\n    }\n}\n\nmain().catch(err => {\n    console.error(c.red(`Error: ${err.message}`));\n    if (process.env.BRAINBANK_DEBUG) console.error(err.stack);\n    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package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "brainbank",
-    "version": "0.9.5",
+    "version": "0.9.6",
     "description": "Pluggable semantic memory for AI agents — hybrid search (vector + BM25) in a single SQLite file. Built-in code, git, and docs indexers. Bring your own.",
     "type": "module",
     "main": "dist/index.js",

package/src/cli/commands/mcp-export.ts

@@ -41,7 +41,7 @@ interface McpConfig {
  * Build the brainbank MCP server config block.
  * Resolves node binary, dist/cli.js path, and API keys.
  */
-function buildBrainbankMcpBlock(config: ProjectConfig | null, repoPath: string): McpServerConfig {
+function buildBrainbankMcpBlock(config: ProjectConfig | null): McpServerConfig {
     const nodeBin = process.execPath;
 
     // Resolve dist/cli.js from the global install location (node_prefix/lib/node_modules/brainbank/dist/cli.js)
@@ -62,9 +62,6 @@ function buildBrainbankMcpBlock(config: ProjectConfig | null, repoPath: string):
     if (anthropicKey) env.ANTHROPIC_API_KEY = anthropicKey;
     if (openaiKey) env.OPENAI_API_KEY = openaiKey;
 
-    // Inject repo path so the MCP server knows where the index lives
-    env.BRAINBANK_REPO = path.resolve(repoPath);
-
     const block: McpServerConfig = {
         command: nodeBin,
         args: ['--disable-warning=ExperimentalWarning', resolvedCliJs, 'mcp'],
@@ -129,7 +126,7 @@ export async function autoExportMcp(repoPath: string): Promise<void> {
     if (hasBrainbankMcpEntry(target.configPath)) return;
 
     const config = await getConfig(repoPath);
-    const block = buildBrainbankMcpBlock(config, repoPath);
+    const block = buildBrainbankMcpBlock(config);
     mergeAndWrite(target.configPath, block);
     console.log(`  ${c.green('✓')} Exported MCP config to ${c.dim(path.relative(process.env.HOME ?? '', target.configPath))}`);
 }
@@ -200,11 +197,11 @@ function replaceGeminiSection(geminiPath: string): void {
     fs.writeFileSync(geminiPath, before + section + after);
 }
 
-/** CLI command: brainbank mcp:export [target] */
+/** CLI command: brainbank mcp:export [target] [--force] */
 export async function cmdMcpExport(): Promise<void> {
     const targetName = args[1] || getFlag('target') || 'antigravity';
     const repoPath = getFlag('repo') || '.';
-    const { confirm } = await import('@inquirer/prompts');
+    const force = args.includes('--force') || args.includes('-f');
 
     const target = TARGETS[targetName];
     if (!target) {
@@ -214,7 +211,7 @@ export async function cmdMcpExport(): Promise<void> {
     }
 
     const config = await getConfig(repoPath);
-    const block = buildBrainbankMcpBlock(config, repoPath);
+    const block = buildBrainbankMcpBlock(config);
 
     console.log(c.bold(`\n━━━ MCP Export: ${target.label} ━━━\n`));
 
@@ -222,12 +219,13 @@ export async function cmdMcpExport(): Promise<void> {
     const mcpExists = hasBrainbankMcpEntry(target.configPath);
     let writeMcp = true;
 
-    if (mcpExists) {
+    if (mcpExists && !force) {
         console.log(`  ${c.yellow('●')} MCP config already has brainbank entry`);
         const cliPath = block.args.find(a => !a.startsWith('--')) ?? block.args[0];
         console.log(`  ${c.dim('  New:')} ${block.command} ${cliPath}`);
         const envKeys = block.env ? Object.keys(block.env) : [];
         if (envKeys.length > 0) console.log(`  ${c.dim('  Keys:')} ${envKeys.join(', ')}`);
+        const { confirm } = await import('@inquirer/prompts');
         writeMcp = await confirm({ message: 'Override existing brainbank MCP entry?', default: true });
     }
 
@@ -242,22 +240,34 @@ export async function cmdMcpExport(): Promise<void> {
     const geminiHasSection = hasGeminiSection(GLOBAL_GEMINI);
 
     if (geminiHasSection) {
-        console.log(`  ${c.yellow('●')} ~/.gemini/GEMINI.md already has BrainBank section`);
-        const override = await confirm({ message: 'Override existing BrainBank section?', default: false });
-        if (override) {
+        if (force) {
             replaceGeminiSection(GLOBAL_GEMINI);
             console.log(`  ${c.green('✓')} Replaced BrainBank section in ${c.dim('~/.gemini/GEMINI.md')}`);
         } else {
-            console.log(`  ${c.dim('GEMINI.md — skipped')}`);
+            console.log(`  ${c.yellow('●')} ~/.gemini/GEMINI.md already has BrainBank section`);
+            const { confirm } = await import('@inquirer/prompts');
+            const override = await confirm({ message: 'Override existing BrainBank section?', default: false });
+            if (override) {
+                replaceGeminiSection(GLOBAL_GEMINI);
+                console.log(`  ${c.green('✓')} Replaced BrainBank section in ${c.dim('~/.gemini/GEMINI.md')}`);
+            } else {
+                console.log(`  ${c.dim('GEMINI.md — skipped')}`);
+            }
         }
     } else {
-        const addGemini = await confirm({
-            message: 'Add BrainBank instructions to ~/.gemini/GEMINI.md? (teaches AI tools how to use BrainBank)',
-            default: true,
-        });
-        if (addGemini) {
+        if (force) {
             appendGeminiSection(GLOBAL_GEMINI);
             console.log(`  ${c.green('✓')} Added BrainBank section to ${c.dim('~/.gemini/GEMINI.md')}`);
+        } else {
+            const { confirm } = await import('@inquirer/prompts');
+            const addGemini = await confirm({
+                message: 'Add BrainBank instructions to ~/.gemini/GEMINI.md? (teaches AI tools how to use BrainBank)',
+                default: true,
+            });
+            if (addGemini) {
+                appendGeminiSection(GLOBAL_GEMINI);
+                console.log(`  ${c.green('✓')} Added BrainBank section to ${c.dim('~/.gemini/GEMINI.md')}`);
+            }
         }
     }