brainbank 0.6.0 → 0.7.0

package/dist/{chunk-C4KDZGRX.js.map → chunk-VQ27YUHH.js.map}

@@ -1 +1 @@
-{"version":3,"sources":["../src/indexers/docs/docs-indexer.ts","../src/search/vector/rerank.ts","../src/indexers/docs/document-search.ts","../src/indexers/docs/docs-plugin.ts"],"sourcesContent":["/**\n * BrainBank — Document Indexer\n * \n * Indexes generic document collections (markdown, text, etc.)\n * with heading-aware smart chunking, inspired by qmd.\n * \n *   const indexer = new DocsIndexer(db, embedding, hnsw, vecCache);\n *   await indexer.indexCollection('notes', '/path/to/notes', '**\\/*.md');\n */\n\nimport * as fs from 'node:fs';\nimport * as path from 'node:path';\nimport { createHash } from 'node:crypto';\n\nimport type { Database } from '@/db/database.ts';\nimport type { EmbeddingProvider, VectorIndex } from '@/types.ts';\nimport type { HNSWIndex } from '@/providers/vector/hnsw-index.ts';\n\n// ── Break Point Scoring (qmd-inspired) ──────────────\n\ninterface BreakPoint {\n    pos: number;      // character position\n    score: number;    // break quality (higher = better)\n}\n\nconst BREAK_SCORES: [RegExp, number][] = [\n    [/^# /,      100],   // H1\n    [/^## /,      90],   // H2\n    [/^### /,     80],   // H3\n    [/^#### /,    70],   // H4\n    [/^##### /,   60],   // H5\n    [/^###### /,  50],   // H6\n    [/^```/,      80],   // Code fence\n    [/^---$/,     60],   // Horizontal rule\n    [/^\\*\\*\\*$/,  60],   // Horizontal rule alt\n    [/^$/,        20],   // Blank line (paragraph break)\n    [/^[-*+] /,    5],   // List item\n];\n\n// ── Chunk Target ────────────────────────────────────\n\nconst TARGET_CHARS = 3000;       // ~900 tokens\nconst WINDOW_CHARS = 600;        // search window before cutoff\nconst MIN_CHUNK_CHARS = 200;     // don't create tiny chunks\n\n\n/** Ignored output/vendor directories when walking docs. */\nconst IGNORED_DOC_DIRS = new Set([\n    'node_modules', '.git', '.hg', '.svn',\n    'dist', 'build', 'out', 'coverage', '.next',\n    '__pycache__', '.tox', '.venv', 'venv',\n    'vendor', 'target', '.cache', '.turbo',\n]);\n\n// ── DocsIndexer ──────────────────────────────────────\n\nexport class DocsIndexer {\n    constructor(\n        private _db: Database,\n        private _embedding: EmbeddingProvider,\n        private _hnsw: HNSWIndex,\n        private _vecCache: Map<number, Float32Array>,\n    ) {}\n\n    /**\n     * Index all documents in a collection.\n     * Incremental — skips unchanged files (by content hash).\n     */\n    async indexCollection(\n        collection: string,\n        dirPath: string,\n        pattern: string = '**/*.md',\n        options: {\n            ignore?: string[];\n            onProgress?: (file: string, current: number, total: number) => void;\n        } = {},\n    ): Promise<{ indexed: number; skipped: number; chunks: number }> {\n        const absDir = path.resolve(dirPath);\n        if (!fs.existsSync(absDir)) {\n            throw new Error(`Collection path does not exist: ${absDir}`);\n        }\n\n        const files = this._walkFiles(absDir, pattern, options.ignore);\n        let indexed = 0, skipped = 0, totalChunks = 0;\n\n        for (let i = 0; i < files.length; i++) {\n            const relPath = files[i];\n            options.onProgress?.(relPath, i + 1, files.length);\n\n            const absPath = path.join(absDir, relPath);\n            const content = fs.readFileSync(absPath, 'utf-8');\n            const hash = createHash('sha256').update(content).digest('hex').slice(0, 16);\n\n            if (this._isUnchanged(collection, relPath, hash)) {\n                skipped++;\n                continue;\n            }\n\n            this._removeOldChunks(collection, relPath);\n            const chunkCount = await this._indexFile(collection, relPath, content, hash);\n            indexed++;\n            totalChunks += chunkCount;\n        }\n\n        return { indexed, skipped, chunks: totalChunks };\n    }\n\n    /** Walk directory tree and collect matching files. */\n    private _walkFiles(absDir: string, pattern: string, ignore?: string[]): string[] {\n        const patternExt = pattern.match(/\\.([\\w]+)$/)?.[1];\n        const files: string[] = [];\n\n        const walk = (dir: string, base: string): void => {\n            let entries: fs.Dirent[];\n            try { entries = fs.readdirSync(dir, { withFileTypes: true }); }\n            catch { return; }\n            for (const e of entries) {\n                const rel = base ? `${base}/${e.name}` : e.name;\n                if (e.isDirectory()) {\n                    if (IGNORED_DOC_DIRS.has(e.name)) continue;\n                    walk(path.join(dir, e.name), rel);\n                } else if (e.isFile()) {\n                    if (this._isIgnoredFile(rel, ignore)) continue;\n                    const ext = path.extname(e.name).slice(1);\n                    if (!patternExt || ext === patternExt) files.push(rel);\n                }\n            }\n        };\n        walk(absDir, '');\n        return files;\n    }\n\n    /** Check if a file matches any ignore patterns. */\n    private _isIgnoredFile(relPath: string, ignore?: string[]): boolean {\n        if (!ignore) return false;\n        return ignore.some(ig => {\n            const regex = ig\n                .replace(/\\*\\*/g, '{{GLOBSTAR}}')\n                .replace(/\\*/g, '{{STAR}}')\n                .replace(/[.+?^${}()|[\\]\\\\]/g, '\\\\$&')\n                .replace(/\\{\\{GLOBSTAR\\}\\}/g, '.*')\n                .replace(/\\{\\{STAR\\}\\}/g, '[^/]*');\n            return new RegExp(regex).test(relPath);\n        });\n    }\n\n    /** Check if all chunks for a file match the current hash and have vectors. */\n    private _isUnchanged(collection: string, relPath: string, hash: string): boolean {\n        const existing = this._db.prepare(\n            `SELECT dc.id, dc.content_hash, dv.chunk_id AS has_vector\n             FROM doc_chunks dc\n             LEFT JOIN doc_vectors dv ON dv.chunk_id = dc.id\n             WHERE dc.collection = ? AND dc.file_path = ?`\n        ).all(collection, relPath) as any[];\n\n        return existing.length > 0 &&\n            existing.every((c: any) => c.content_hash === hash && c.has_vector != null);\n    }\n\n    /** Remove old chunks and their HNSW vectors for a file. */\n    private _removeOldChunks(collection: string, relPath: string): void {\n        const oldChunks = this._db.prepare(\n            'SELECT id FROM doc_chunks WHERE collection = ? AND file_path = ?'\n        ).all(collection, relPath) as any[];\n\n        for (const old of oldChunks) {\n            this._hnsw.remove(old.id);\n            this._vecCache.delete(old.id);\n        }\n        this._db.prepare(\n            'DELETE FROM doc_chunks WHERE collection = ? AND file_path = ?'\n        ).run(collection, relPath);\n    }\n\n    /** Index a single file: chunk, embed, store in DB + HNSW. */\n    private async _indexFile(\n        collection: string, relPath: string, content: string, hash: string,\n    ): Promise<number> {\n        const title = this._extractTitle(content, relPath);\n        const chunks = this._smartChunk(content);\n\n        const insertChunk = this._db.prepare(`\n            INSERT INTO doc_chunks (collection, file_path, title, content, seq, pos, content_hash)\n            VALUES (?, ?, ?, ?, ?, ?, ?)\n        `);\n\n        const chunkIds: number[] = [];\n        this._db.transaction(() => {\n            for (let seq = 0; seq < chunks.length; seq++) {\n                const result = insertChunk.run(\n                    collection, relPath, title, chunks[seq].text, seq, chunks[seq].pos, hash,\n                );\n                chunkIds.push(Number(result.lastInsertRowid));\n            }\n        });\n\n        const texts = chunks.map(c => `title: ${title} | text: ${c.text}`);\n        const embeddings = await this._embedding.embedBatch(texts);\n\n        const insertVec = this._db.prepare(\n            'INSERT OR REPLACE INTO doc_vectors (chunk_id, embedding) VALUES (?, ?)'\n        );\n        this._db.transaction(() => {\n            for (let j = 0; j < chunkIds.length; j++) {\n                insertVec.run(chunkIds[j], Buffer.from(embeddings[j].buffer));\n            }\n        });\n\n        for (let j = 0; j < chunkIds.length; j++) {\n            this._hnsw.add(embeddings[j], chunkIds[j]);\n            this._vecCache.set(chunkIds[j], embeddings[j]);\n        }\n\n        return chunks.length;\n    }\n\n    /** Remove all indexed data for a collection. */\n    removeCollection(collection: string): void {\n        const chunks = this._db.prepare(\n            'SELECT id FROM doc_chunks WHERE collection = ?'\n        ).all(collection) as any[];\n        for (const chunk of chunks) {\n            this._hnsw.remove(chunk.id);\n            this._vecCache.delete(chunk.id);\n        }\n\n        this._db.prepare('DELETE FROM doc_chunks WHERE collection = ?').run(collection);\n        this._db.prepare('DELETE FROM collections WHERE name = ?').run(collection);\n        this._db.prepare('DELETE FROM path_contexts WHERE collection = ?').run(collection);\n    }\n\n    // ── Smart Chunking ──────────────────────────────\n\n    /** Split document into chunks at natural markdown boundaries. */\n    private _smartChunk(text: string): { text: string; pos: number }[] {\n        if (text.length <= TARGET_CHARS) {\n            return [{ text, pos: 0 }];\n        }\n\n        const lines = text.split('\\n');\n        const breakPoints = this._findBreakPoints(lines);\n        const chunks: { text: string; pos: number }[] = [];\n        let chunkStart = 0;\n\n        while (chunkStart < text.length) {\n            const remaining = text.length - chunkStart;\n            if (remaining <= TARGET_CHARS + WINDOW_CHARS) {\n                this._flushRemainder(text, chunkStart, chunks);\n                break;\n            }\n\n            const bestBreak = this._findBestBreak(chunkStart, breakPoints);\n            const chunkText = text.slice(chunkStart, bestBreak).trim();\n            if (chunkText.length >= MIN_CHUNK_CHARS) {\n                chunks.push({ text: chunkText, pos: chunkStart });\n            }\n            chunkStart = bestBreak;\n        }\n\n        return chunks;\n    }\n\n    /** Handle the last chunk: merge if too small, otherwise push. */\n    private _flushRemainder(\n        text: string, chunkStart: number, chunks: { text: string; pos: number }[],\n    ): void {\n        const lastText = text.slice(chunkStart).trim();\n        if (lastText.length >= MIN_CHUNK_CHARS) {\n            chunks.push({ text: lastText, pos: chunkStart });\n        } else if (chunks.length > 0) {\n            chunks[chunks.length - 1].text += '\\n' + lastText;\n        } else {\n            chunks.push({ text: lastText, pos: chunkStart });\n        }\n    }\n\n    /** Find the best break position within the target window. */\n    private _findBestBreak(chunkStart: number, breakPoints: BreakPoint[]): number {\n        const targetEnd = chunkStart + TARGET_CHARS;\n        const windowStart = targetEnd - WINDOW_CHARS;\n\n        let bestBreak = targetEnd;\n        let bestScore = 0;\n\n        for (const bp of breakPoints) {\n            if (bp.pos <= chunkStart) continue;\n            if (bp.pos > targetEnd + WINDOW_CHARS / 2) break;\n            if (bp.pos < windowStart) continue;\n\n            const distance = Math.abs(bp.pos - targetEnd);\n            const decay = 1 - (distance / WINDOW_CHARS) ** 2 * 0.7;\n            const finalScore = bp.score * decay;\n\n            if (finalScore > bestScore) {\n                bestScore = finalScore;\n                bestBreak = bp.pos;\n            }\n        }\n\n        return bestBreak;\n    }\n\n    /** Find all potential break points in the document with scores. */\n    private _findBreakPoints(lines: string[]): BreakPoint[] {\n        const points: BreakPoint[] = [];\n        let charPos = 0;\n        let inCodeBlock = false;\n\n        for (const line of lines) {\n            if (line.trimStart().startsWith('```')) {\n                inCodeBlock = !inCodeBlock;\n                if (!inCodeBlock) {\n                    points.push({ pos: charPos + line.length + 1, score: 80 });\n                }\n                charPos += line.length + 1;\n                continue;\n            }\n\n            if (inCodeBlock) {\n                charPos += line.length + 1;\n                continue;\n            }\n\n            for (const [pattern, score] of BREAK_SCORES) {\n                if (pattern.test(line.trim())) {\n                    points.push({ pos: charPos, score });\n                    break;\n                }\n            }\n\n            charPos += line.length + 1;\n        }\n\n        return points;\n    }\n\n    /** Extract document title from first heading or filename. */\n    private _extractTitle(content: string, filePath: string): string {\n        const match = content.match(/^#{1,3}\\s+(.+)$/m);\n        if (match) return match[1].trim();\n        return path.basename(filePath, path.extname(filePath));\n    }\n}\n","/**\n * BrainBank — Rerank\n * \n * Position-aware score blending between retrieval and reranker.\n * Pure function — no state.\n * \n * Top 1-3:  75% retrieval / 25% reranker (preserves exact matches)\n * Top 4-10: 60% retrieval / 40% reranker\n * Top 11+:  40% retrieval / 60% reranker (trust reranker more)\n */\n\nimport type { Reranker, SearchResult } from '@/types.ts';\n\n/** Re-rank results using position-aware blending. */\nexport async function rerank(\n    query: string,\n    results: SearchResult[],\n    reranker: Reranker,\n): Promise<SearchResult[]> {\n    const documents = results.map(r => r.content);\n    const scores = await reranker.rank(query, documents);\n\n    const blended = results.map((r, i) => {\n        const pos = i + 1;\n        const rrfWeight = pos <= 3 ? 0.75 : pos <= 10 ? 0.60 : 0.40;\n        return {\n            ...r,\n            score: rrfWeight * r.score + (1 - rrfWeight) * (scores[i] ?? 0),\n        };\n    });\n\n    return blended.sort((a, b) => b.score - a.score);\n}\n","/**\n * BrainBank — Document Search\n *\n * Hybrid search (vector + BM25 → RRF) for indexed documents.\n * Extracted from DocsPlugin to keep plugin management separate from search logic.\n */\n\nimport type { HNSWIndex } from '@/providers/vector/hnsw-index.ts';\nimport type { Database } from '@/db/database.ts';\nimport type { EmbeddingProvider, SearchResult, Reranker } from '@/types.ts';\nimport { reciprocalRankFusion } from '@/lib/rrf.ts';\nimport { rerank } from '@/search/vector/rerank.ts';\nimport { normalizeBM25 } from '@/lib/fts.ts';\n\nexport interface DocumentSearchDeps {\n    db: Database;\n    embedding: EmbeddingProvider;\n    hnsw: HNSWIndex;\n    vecCache: Map<number, Float32Array>;\n    reranker?: Reranker;\n}\n\nexport class DocumentSearch {\n    constructor(private _d: DocumentSearchDeps) {}\n\n    /** Hybrid search (vector + BM25 → RRF), with dedup and optional reranking. */\n    async search(query: string, options?: {\n        collection?: string;\n        k?: number;\n        minScore?: number;\n        mode?: 'hybrid' | 'vector' | 'keyword';\n    }): Promise<SearchResult[]> {\n        const k = options?.k ?? 8;\n        const mode = options?.mode ?? 'hybrid';\n        const minScore = options?.minScore ?? 0;\n\n        if (mode === 'keyword') return this._dedup(this._searchBM25(query, k * 2, minScore, options?.collection), k);\n        if (mode === 'vector') return this._dedup(await this._searchVector(query, k * 2, minScore, options?.collection), k);\n\n        // Hybrid: over-fetch from both, fuse with RRF, then dedup by file\n        const fetchK = k * 2;\n        const [vecHits, bm25Hits] = await Promise.all([\n            this._searchVector(query, fetchK, 0, options?.collection),\n            Promise.resolve(this._searchBM25(query, fetchK, 0, options?.collection)),\n        ]);\n\n        if (vecHits.length === 0 && bm25Hits.length === 0) return [];\n        if (bm25Hits.length === 0) return this._dedup(vecHits.filter(h => h.score >= minScore), k);\n        if (vecHits.length === 0) return this._dedup(bm25Hits.filter(h => h.score >= minScore), k);\n\n        const fused = reciprocalRankFusion([vecHits, bm25Hits]);\n\n        // Map fused results back to doc SearchResults\n        const allById = new Map<number, SearchResult>();\n        for (const h of [...vecHits, ...bm25Hits]) {\n            const id = (h.metadata as any)?.chunkId;\n            if (id != null) allById.set(id, h);\n        }\n\n        const results: SearchResult[] = [];\n        for (const r of fused) {\n            const chunkId = (r.metadata as any)?.chunkId;\n            const original = allById.get(chunkId);\n            if (!original) continue;\n            const merged = { ...original, score: r.score };\n            if (merged.score >= minScore) results.push(merged);\n        }\n\n        const deduped = this._dedup(results, k);\n        return this._rerankResults(query, deduped);\n    }\n\n    /** Apply reranking if a reranker is configured. */\n    private async _rerankResults(query: string, results: SearchResult[]): Promise<SearchResult[]> {\n        if (!this._d.reranker || results.length <= 1) return results;\n        return rerank(query, results, this._d.reranker);\n    }\n\n    /** Deduplicate results by file path — keep best-scoring chunk per file. */\n    private _dedup(results: SearchResult[], k: number): SearchResult[] {\n        const seen = new Map<string, SearchResult>();\n        for (const r of results) {\n            const key = r.filePath ?? '';\n            if (!seen.has(key) || (seen.get(key)!.score < r.score)) {\n                seen.set(key, r);\n            }\n        }\n        return [...seen.values()]\n            .sort((a, b) => b.score - a.score)\n            .slice(0, k);\n    }\n\n    /** Vector-only search via HNSW. */\n    private async _searchVector(query: string, k: number, minScore: number, collection?: string): Promise<SearchResult[]> {\n        if (this._d.hnsw.size === 0) return [];\n        const queryVec = await this._d.embedding.embed(query);\n\n        let searchK = k;\n        if (collection && this._d.hnsw.size > 0) {\n            const collectionCount = (this._d.db.prepare(\n                'SELECT COUNT(*) as c FROM doc_chunks WHERE collection = ?'\n            ).get(collection) as any)?.c ?? 0;\n            const totalChunks = (this._d.db.prepare(\n                'SELECT COUNT(*) as c FROM doc_chunks'\n            ).get() as any)?.c ?? 1;\n            const ratio = collectionCount > 0\n                ? Math.max(3, Math.min(50, Math.ceil(totalChunks / collectionCount)))\n                : 3;\n            searchK = Math.min(k * ratio, this._d.hnsw.size);\n        }\n\n        const hits = this._d.hnsw.search(queryVec, searchK);\n        const results: SearchResult[] = [];\n\n        for (const hit of hits) {\n            if (minScore && hit.score < minScore) continue;\n            const chunk = this._d.db.prepare('SELECT * FROM doc_chunks WHERE id = ?').get(hit.id) as any;\n            if (!chunk) continue;\n            if (collection && chunk.collection !== collection) continue;\n\n            results.push({\n                type: 'document',\n                score: hit.score,\n                filePath: chunk.file_path,\n                content: chunk.content,\n                context: this._getDocContext(chunk.collection, chunk.file_path),\n                metadata: {\n                    collection: chunk.collection,\n                    title: chunk.title,\n                    seq: chunk.seq,\n                    chunkId: chunk.id,\n                },\n            });\n\n            if (results.length >= k) break;\n        }\n\n        return results;\n    }\n\n    /** BM25 keyword search via FTS5 (OR-mode for natural language). */\n    private _searchBM25(query: string, k: number, minScore: number, collection?: string): SearchResult[] {\n        const ftsQuery = this._buildDocsFTS(query);\n        if (!ftsQuery) return [];\n\n        try {\n            const collectionFilter = collection ? 'AND d.collection = ?' : '';\n            const params: any[] = [ftsQuery];\n            if (collection) params.push(collection);\n            params.push(k * 2);\n\n            const rows = this._d.db.prepare(`\n                SELECT d.*, bm25(fts_docs, 10.0, 2.0, 5.0, 1.0) AS bm25_score\n                FROM fts_docs f\n                JOIN doc_chunks d ON d.id = f.rowid\n                WHERE fts_docs MATCH ? ${collectionFilter}\n                ORDER BY bm25_score ASC\n                LIMIT ?\n            `).all(...params) as any[];\n\n            return rows\n                .map(r => ({\n                    type: 'document' as const,\n                    score: normalizeBM25(r.bm25_score),\n                    filePath: r.file_path,\n                    content: r.content,\n                    context: this._getDocContext(r.collection, r.file_path),\n                    metadata: {\n                        collection: r.collection,\n                        title: r.title,\n                        seq: r.seq,\n                        chunkId: r.id,\n                    },\n                }))\n                .filter(r => r.score >= minScore)\n                .slice(0, k);\n        } catch {\n            return [];\n        }\n    }\n\n    /** Build OR-mode FTS5 query for natural language doc search. */\n    private _buildDocsFTS(query: string): string {\n        const STOP_WORDS = new Set([\n            'the', 'is', 'at', 'which', 'on', 'a', 'an', 'and', 'or', 'but',\n            'in', 'with', 'to', 'for', 'of', 'by', 'from', 'as', 'it', 'its',\n            'this', 'that', 'be', 'are', 'was', 'were', 'been', 'has', 'have',\n            'had', 'do', 'does', 'did', 'can', 'could', 'will', 'would', 'how',\n            'what', 'when', 'where', 'who', 'why', 'not', 'no', 'so', 'if',\n        ]);\n\n        const clean = query\n            .replace(/[{}[\\]()^~*:\"]/g, ' ')\n            .replace(/\\bAND\\b|\\bOR\\b|\\bNOT\\b|\\bNEAR\\b/gi, '')\n            .replace(/[_\\-./\\\\]/g, ' ')\n            .trim();\n\n        const words = clean.split(/\\s+/)\n            .filter(w => w.length >= 3 && !STOP_WORDS.has(w.toLowerCase()));\n\n        if (words.length === 0) return '';\n        return words.map(w => `\"${w}\"`).join(' OR ');\n    }\n\n    /** Resolve context for a document (checks path_contexts tree → collection context). */\n    private _getDocContext(collection: string, filePath: string): string | undefined {\n        const parts = filePath.split('/');\n        for (let i = parts.length; i >= 0; i--) {\n            const checkPath = i === 0 ? '/' : '/' + parts.slice(0, i).join('/');\n            const ctx = this._d.db.prepare(\n                'SELECT context FROM path_contexts WHERE collection = ? AND path = ?'\n            ).get(collection, checkPath) as any;\n            if (ctx) return ctx.context;\n        }\n\n        const coll = this._d.db.prepare(\n            'SELECT context FROM collections WHERE name = ?'\n        ).get(collection) as any;\n        return coll?.context ?? undefined;\n    }\n}\n","/**\n * BrainBank — Docs Module\n * \n * Index any folder of markdown/text files (notes, docs, wikis).\n * Heading-aware smart chunking inspired by qmd.\n * \n *   import { docs } from 'brainbank/docs';\n *   brain.use(docs());\n */\n\nimport type { Plugin, PluginContext } from '@/indexers/base.ts';\nimport type { HNSWIndex } from '@/providers/vector/hnsw-index.ts';\nimport type { Database } from '@/db/database.ts';\nimport type { EmbeddingProvider, DocumentCollection, SearchResult } from '@/types.ts';\nimport { DocsIndexer } from './docs-indexer.ts';\nimport { DocumentSearch } from './document-search.ts';\n\nclass DocsPlugin implements Plugin {\n    readonly name = 'docs';\n    hnsw!: HNSWIndex;\n    indexer!: DocsIndexer;\n    vecCache = new Map<number, Float32Array>();\n    private _db!: Database;\n    private _search!: DocumentSearch;\n\n    async initialize(ctx: PluginContext): Promise<void> {\n        this._db = ctx.db;\n        this.hnsw = await ctx.createHnsw();\n        ctx.loadVectors('doc_vectors', 'chunk_id', this.hnsw, this.vecCache);\n        this.indexer = new DocsIndexer(ctx.db, ctx.embedding, this.hnsw, this.vecCache);\n        this._search = new DocumentSearch({\n            db: ctx.db,\n            embedding: ctx.embedding,\n            hnsw: this.hnsw,\n            vecCache: this.vecCache,\n            reranker: ctx.config.reranker,\n        });\n    }\n\n    /** Register a document collection. */\n    addCollection(collection: DocumentCollection): void {\n        this._db.prepare(`\n            INSERT OR REPLACE INTO collections (name, path, pattern, ignore_json, context)\n            VALUES (?, ?, ?, ?, ?)\n        `).run(\n            collection.name,\n            collection.path,\n            collection.pattern ?? '**/*.md',\n            JSON.stringify(collection.ignore ?? []),\n            collection.context ?? null,\n        );\n    }\n\n    /** Remove a collection and its indexed data. */\n    removeCollection(name: string): void {\n        this.indexer.removeCollection(name);\n    }\n\n    /** List all registered collections. */\n    listCollections(): DocumentCollection[] {\n        return (this._db.prepare('SELECT * FROM collections').all() as any[]).map(row => ({\n            name: row.name,\n            path: row.path,\n            pattern: row.pattern,\n            ignore: JSON.parse(row.ignore_json),\n            context: row.context,\n        }));\n    }\n\n    /** Index all (or specific) collections. Incremental. */\n    async indexCollections(options: {\n        collections?: string[];\n        onProgress?: (collection: string, file: string, current: number, total: number) => void;\n    } = {}): Promise<Record<string, { indexed: number; skipped: number; chunks: number }>> {\n        const allCollections = this.listCollections();\n        const toIndex = options.collections\n            ? allCollections.filter(c => options.collections!.includes(c.name))\n            : allCollections;\n\n        const results: Record<string, { indexed: number; skipped: number; chunks: number }> = {};\n\n        for (const coll of toIndex) {\n            results[coll.name] = await this.indexer.indexCollection(\n                coll.name,\n                coll.path,\n                coll.pattern,\n                {\n                    ignore: coll.ignore,\n                    onProgress: (file, cur, total) => options.onProgress?.(coll.name, file, cur, total),\n                },\n            );\n        }\n\n        return results;\n    }\n\n    /** Search documents using hybrid search (vector + BM25 → RRF). */\n    async search(query: string, options?: {\n        collection?: string;\n        k?: number;\n        minScore?: number;\n        mode?: 'hybrid' | 'vector' | 'keyword';\n    }): Promise<SearchResult[]> {\n        return this._search.search(query, options);\n    }\n\n    /** Add context description for a document path. */\n    addContext(collection: string, path: string, context: string): void {\n        this._db.prepare(`\n            INSERT OR REPLACE INTO path_contexts (collection, path, context)\n            VALUES (?, ?, ?)\n        `).run(collection, path, context);\n    }\n\n    /** Remove context for a path. */\n    removeContext(collection: string, path: string): void {\n        this._db.prepare(\n            'DELETE FROM path_contexts WHERE collection = ? 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+{"version":3,"sources":["../src/indexers/docs/docs-indexer.ts","../src/search/vector/rerank.ts","../src/indexers/docs/document-search.ts","../src/indexers/docs/docs-plugin.ts"],"sourcesContent":["/**\n * BrainBank — Document Indexer\n * \n * Indexes generic document collections (markdown, text, etc.)\n * with heading-aware smart chunking, inspired by qmd.\n * \n *   const indexer = new DocsIndexer(db, embedding, hnsw, vecCache);\n *   await indexer.indexCollection('notes', '/path/to/notes', '**\\/*.md');\n */\n\nimport * as fs from 'node:fs';\nimport * as path from 'node:path';\nimport { createHash } from 'node:crypto';\n\nimport type { Database } from '@/db/database.ts';\nimport type { EmbeddingProvider, VectorIndex } from '@/types.ts';\nimport type { HNSWIndex } from '@/providers/vector/hnsw-index.ts';\n\n// ── Break Point Scoring (qmd-inspired) ──────────────\n\ninterface BreakPoint {\n    pos: number;      // character position\n    score: number;    // break quality (higher = better)\n}\n\nconst BREAK_SCORES: [RegExp, number][] = [\n    [/^# /,      100],   // H1\n    [/^## /,      90],   // H2\n    [/^### /,     80],   // H3\n    [/^#### /,    70],   // H4\n    [/^##### /,   60],   // H5\n    [/^###### /,  50],   // H6\n    [/^```/,      80],   // Code fence\n    [/^---$/,     60],   // Horizontal rule\n    [/^\\*\\*\\*$/,  60],   // Horizontal rule alt\n    [/^$/,        20],   // Blank line (paragraph break)\n    [/^[-*+] /,    5],   // List item\n];\n\n// ── Chunk Target ────────────────────────────────────\n\nconst TARGET_CHARS = 3000;       // ~900 tokens\nconst WINDOW_CHARS = 600;        // search window before cutoff\nconst MIN_CHUNK_CHARS = 200;     // don't create tiny chunks\n\n\n/** Ignored output/vendor directories when walking docs. */\nconst IGNORED_DOC_DIRS = new Set([\n    'node_modules', '.git', '.hg', '.svn',\n    'dist', 'build', 'out', 'coverage', '.next',\n    '__pycache__', '.tox', '.venv', 'venv',\n    'vendor', 'target', '.cache', '.turbo',\n]);\n\n// ── DocsIndexer ──────────────────────────────────────\n\nexport class DocsIndexer {\n    constructor(\n        private _db: Database,\n        private _embedding: EmbeddingProvider,\n        private _hnsw: HNSWIndex,\n        private _vecCache: Map<number, Float32Array>,\n    ) {}\n\n    /**\n     * Index all documents in a collection.\n     * Incremental — skips unchanged files (by content hash).\n     */\n    async indexCollection(\n        collection: string,\n        dirPath: string,\n        pattern: string = '**/*.md',\n        options: {\n            ignore?: string[];\n            onProgress?: (file: string, current: number, total: number) => void;\n        } = {},\n    ): Promise<{ indexed: number; skipped: number; chunks: number }> {\n        const absDir = path.resolve(dirPath);\n        if (!fs.existsSync(absDir)) {\n            throw new Error(`Collection path does not exist: ${absDir}`);\n        }\n\n        const files = this._walkFiles(absDir, pattern, options.ignore);\n        let indexed = 0, skipped = 0, totalChunks = 0;\n\n        for (let i = 0; i < files.length; i++) {\n            const relPath = files[i];\n            options.onProgress?.(relPath, i + 1, files.length);\n\n            const absPath = path.join(absDir, relPath);\n            const content = fs.readFileSync(absPath, 'utf-8');\n            const hash = createHash('sha256').update(content).digest('hex').slice(0, 16);\n\n            if (this._isUnchanged(collection, relPath, hash)) {\n                skipped++;\n                continue;\n            }\n\n            this._removeOldChunks(collection, relPath);\n            const chunkCount = await this._indexFile(collection, relPath, content, hash);\n            indexed++;\n            totalChunks += chunkCount;\n        }\n\n        return { indexed, skipped, chunks: totalChunks };\n    }\n\n    /** Walk directory tree and collect matching files. */\n    private _walkFiles(absDir: string, pattern: string, ignore?: string[]): string[] {\n        const patternExt = pattern.match(/\\.([\\w]+)$/)?.[1];\n        const files: string[] = [];\n\n        const walk = (dir: string, base: string): void => {\n            let entries: fs.Dirent[];\n            try { entries = fs.readdirSync(dir, { withFileTypes: true }); }\n            catch { return; }\n            for (const e of entries) {\n                const rel = base ? `${base}/${e.name}` : e.name;\n                if (e.isDirectory()) {\n                    if (IGNORED_DOC_DIRS.has(e.name)) continue;\n                    walk(path.join(dir, e.name), rel);\n                } else if (e.isFile()) {\n                    if (this._isIgnoredFile(rel, ignore)) continue;\n                    const ext = path.extname(e.name).slice(1);\n                    if (!patternExt || ext === patternExt) files.push(rel);\n                }\n            }\n        };\n        walk(absDir, '');\n        return files;\n    }\n\n    /** Check if a file matches any ignore patterns. */\n    private _isIgnoredFile(relPath: string, ignore?: string[]): boolean {\n        if (!ignore) return false;\n        return ignore.some(ig => {\n            const regex = ig\n                .replace(/\\*\\*/g, '{{GLOBSTAR}}')\n                .replace(/\\*/g, '{{STAR}}')\n                .replace(/[.+?^${}()|[\\]\\\\]/g, '\\\\$&')\n                .replace(/\\{\\{GLOBSTAR\\}\\}/g, '.*')\n                .replace(/\\{\\{STAR\\}\\}/g, '[^/]*');\n            return new RegExp(regex).test(relPath);\n        });\n    }\n\n    /** Check if all chunks for a file match the current hash and have vectors. */\n    private _isUnchanged(collection: string, relPath: string, hash: string): boolean {\n        const existing = this._db.prepare(\n            `SELECT dc.id, dc.content_hash, dv.chunk_id AS has_vector\n             FROM doc_chunks dc\n             LEFT JOIN doc_vectors dv ON dv.chunk_id = dc.id\n             WHERE dc.collection = ? AND dc.file_path = ?`\n        ).all(collection, relPath) as any[];\n\n        return existing.length > 0 &&\n            existing.every((c: any) => c.content_hash === hash && c.has_vector != null);\n    }\n\n    /** Remove old chunks and their HNSW vectors for a file. */\n    private _removeOldChunks(collection: string, relPath: string): void {\n        const oldChunks = this._db.prepare(\n            'SELECT id FROM doc_chunks WHERE collection = ? AND file_path = ?'\n        ).all(collection, relPath) as any[];\n\n        for (const old of oldChunks) {\n            this._hnsw.remove(old.id);\n            this._vecCache.delete(old.id);\n        }\n        this._db.prepare(\n            'DELETE FROM doc_chunks WHERE collection = ? AND file_path = ?'\n        ).run(collection, relPath);\n    }\n\n    /** Index a single file: chunk, embed, store in DB + HNSW. */\n    private async _indexFile(\n        collection: string, relPath: string, content: string, hash: string,\n    ): Promise<number> {\n        const title = this._extractTitle(content, relPath);\n        const chunks = this._smartChunk(content);\n\n        const insertChunk = this._db.prepare(`\n            INSERT INTO doc_chunks (collection, file_path, title, content, seq, pos, content_hash)\n            VALUES (?, ?, ?, ?, ?, ?, ?)\n        `);\n\n        const chunkIds: number[] = [];\n        this._db.transaction(() => {\n            for (let seq = 0; seq < chunks.length; seq++) {\n                const result = insertChunk.run(\n                    collection, relPath, title, chunks[seq].text, seq, chunks[seq].pos, hash,\n                );\n                chunkIds.push(Number(result.lastInsertRowid));\n            }\n        });\n\n        const texts = chunks.map(c => `title: ${title} | text: ${c.text}`);\n        const embeddings = await this._embedding.embedBatch(texts);\n\n        const insertVec = this._db.prepare(\n            'INSERT OR REPLACE INTO doc_vectors (chunk_id, embedding) VALUES (?, ?)'\n        );\n        this._db.transaction(() => {\n            for (let j = 0; j < chunkIds.length; j++) {\n                insertVec.run(chunkIds[j], Buffer.from(embeddings[j].buffer));\n            }\n        });\n\n        for (let j = 0; j < chunkIds.length; j++) {\n            this._hnsw.add(embeddings[j], chunkIds[j]);\n            this._vecCache.set(chunkIds[j], embeddings[j]);\n        }\n\n        return chunks.length;\n    }\n\n    /** Remove all indexed data for a collection. */\n    removeCollection(collection: string): void {\n        const chunks = this._db.prepare(\n            'SELECT id FROM doc_chunks WHERE collection = ?'\n        ).all(collection) as any[];\n        for (const chunk of chunks) {\n            this._hnsw.remove(chunk.id);\n            this._vecCache.delete(chunk.id);\n        }\n\n        this._db.prepare('DELETE FROM doc_chunks WHERE collection = ?').run(collection);\n        this._db.prepare('DELETE FROM collections WHERE name = ?').run(collection);\n        this._db.prepare('DELETE FROM path_contexts WHERE collection = ?').run(collection);\n    }\n\n    // ── Smart Chunking ──────────────────────────────\n\n    /** Split document into chunks at natural markdown boundaries. */\n    private _smartChunk(text: string): { text: string; pos: number }[] {\n        if (text.length <= TARGET_CHARS) {\n            return [{ text, pos: 0 }];\n        }\n\n        const lines = text.split('\\n');\n        const breakPoints = this._findBreakPoints(lines);\n        const chunks: { text: string; pos: number }[] = [];\n        let chunkStart = 0;\n\n        while (chunkStart < text.length) {\n            const remaining = text.length - chunkStart;\n            if (remaining <= TARGET_CHARS + WINDOW_CHARS) {\n                this._flushRemainder(text, chunkStart, chunks);\n                break;\n            }\n\n            const bestBreak = this._findBestBreak(chunkStart, breakPoints);\n            const chunkText = text.slice(chunkStart, bestBreak).trim();\n            if (chunkText.length >= MIN_CHUNK_CHARS) {\n                chunks.push({ text: chunkText, pos: chunkStart });\n            }\n            chunkStart = bestBreak;\n        }\n\n        return chunks;\n    }\n\n    /** Handle the last chunk: merge if too small, otherwise push. */\n    private _flushRemainder(\n        text: string, chunkStart: number, chunks: { text: string; pos: number }[],\n    ): void {\n        const lastText = text.slice(chunkStart).trim();\n        if (lastText.length >= MIN_CHUNK_CHARS) {\n            chunks.push({ text: lastText, pos: chunkStart });\n        } else if (chunks.length > 0) {\n            chunks[chunks.length - 1].text += '\\n' + lastText;\n        } else {\n            chunks.push({ text: lastText, pos: chunkStart });\n        }\n    }\n\n    /** Find the best break position within the target window. */\n    private _findBestBreak(chunkStart: number, breakPoints: BreakPoint[]): number {\n        const targetEnd = chunkStart + TARGET_CHARS;\n        const windowStart = targetEnd - WINDOW_CHARS;\n\n        let bestBreak = targetEnd;\n        let bestScore = 0;\n\n        for (const bp of breakPoints) {\n            if (bp.pos <= chunkStart) continue;\n            if (bp.pos > targetEnd + WINDOW_CHARS / 2) break;\n            if (bp.pos < windowStart) continue;\n\n            const distance = Math.abs(bp.pos - targetEnd);\n            const decay = 1 - (distance / WINDOW_CHARS) ** 2 * 0.7;\n            const finalScore = bp.score * decay;\n\n            if (finalScore > bestScore) {\n                bestScore = finalScore;\n                bestBreak = bp.pos;\n            }\n        }\n\n        return bestBreak;\n    }\n\n    /** Find all potential break points in the document with scores. */\n    private _findBreakPoints(lines: string[]): BreakPoint[] {\n        const points: BreakPoint[] = [];\n        let charPos = 0;\n        let inCodeBlock = false;\n\n        for (const line of lines) {\n            if (line.trimStart().startsWith('```')) {\n                inCodeBlock = !inCodeBlock;\n                if (!inCodeBlock) {\n                    points.push({ pos: charPos + line.length + 1, score: 80 });\n                }\n                charPos += line.length + 1;\n                continue;\n            }\n\n            if (inCodeBlock) {\n                charPos += line.length + 1;\n                continue;\n            }\n\n            for (const [pattern, score] of BREAK_SCORES) {\n                if (pattern.test(line.trim())) {\n                    points.push({ pos: charPos, score });\n                    break;\n                }\n            }\n\n            charPos += line.length + 1;\n        }\n\n        return points;\n    }\n\n    /** Extract document title from first heading or filename. */\n    private _extractTitle(content: string, filePath: string): string {\n        const match = content.match(/^#{1,3}\\s+(.+)$/m);\n        if (match) return match[1].trim();\n        return path.basename(filePath, path.extname(filePath));\n    }\n}\n","/**\n * BrainBank — Rerank\n * \n * Position-aware score blending between retrieval and reranker.\n * Pure function — no state.\n * \n * Top 1-3:  75% retrieval / 25% reranker (preserves exact matches)\n * Top 4-10: 60% retrieval / 40% reranker\n * Top 11+:  40% retrieval / 60% reranker (trust reranker more)\n */\n\nimport type { Reranker, SearchResult } from '@/types.ts';\n\n/** Re-rank results using position-aware blending. */\nexport async function rerank(\n    query: string,\n    results: SearchResult[],\n    reranker: Reranker,\n): Promise<SearchResult[]> {\n    const documents = results.map(r => r.content);\n    const scores = await reranker.rank(query, documents);\n\n    const blended = results.map((r, i) => {\n        const pos = i + 1;\n        const rrfWeight = pos <= 3 ? 0.75 : pos <= 10 ? 0.60 : 0.40;\n        return {\n            ...r,\n            score: rrfWeight * r.score + (1 - rrfWeight) * (scores[i] ?? 0),\n        };\n    });\n\n    return blended.sort((a, b) => b.score - a.score);\n}\n","/**\n * BrainBank — Document Search\n *\n * Hybrid search (vector + BM25 → RRF) for indexed documents.\n * Extracted from DocsPlugin to keep plugin management separate from search logic.\n */\n\nimport type { HNSWIndex } from '@/providers/vector/hnsw-index.ts';\nimport type { Database } from '@/db/database.ts';\nimport type { EmbeddingProvider, SearchResult, Reranker } from '@/types.ts';\nimport { reciprocalRankFusion } from '@/lib/rrf.ts';\nimport { rerank } from '@/search/vector/rerank.ts';\nimport { normalizeBM25 } from '@/lib/fts.ts';\n\nexport interface DocumentSearchDeps {\n    db: Database;\n    embedding: EmbeddingProvider;\n    hnsw: HNSWIndex;\n    vecCache: Map<number, Float32Array>;\n    reranker?: Reranker;\n}\n\nexport class DocumentSearch {\n    constructor(private _d: DocumentSearchDeps) {}\n\n    /** Hybrid search (vector + BM25 → RRF), with dedup and optional reranking. */\n    async search(query: string, options?: {\n        collection?: string;\n        k?: number;\n        minScore?: number;\n        mode?: 'hybrid' | 'vector' | 'keyword';\n    }): Promise<SearchResult[]> {\n        const k = options?.k ?? 8;\n        const mode = options?.mode ?? 'hybrid';\n        const minScore = options?.minScore ?? 0;\n\n        if (mode === 'keyword') return this._dedup(this._searchBM25(query, k * 2, minScore, options?.collection), k);\n        if (mode === 'vector') return this._dedup(await this._searchVector(query, k * 2, minScore, options?.collection), k);\n\n        // Hybrid: over-fetch from both, fuse with RRF, then dedup by file\n        const fetchK = k * 2;\n        const [vecHits, bm25Hits] = await Promise.all([\n            this._searchVector(query, fetchK, 0, options?.collection),\n            Promise.resolve(this._searchBM25(query, fetchK, 0, options?.collection)),\n        ]);\n\n        if (vecHits.length === 0 && bm25Hits.length === 0) return [];\n        if (bm25Hits.length === 0) return this._dedup(vecHits.filter(h => h.score >= minScore), k);\n        if (vecHits.length === 0) return this._dedup(bm25Hits.filter(h => h.score >= minScore), k);\n\n        const fused = reciprocalRankFusion([vecHits, bm25Hits]);\n\n        // Map fused results back to doc SearchResults\n        const allById = new Map<number, SearchResult>();\n        for (const h of [...vecHits, ...bm25Hits]) {\n            const id = (h.metadata as any)?.chunkId;\n            if (id != null) allById.set(id, h);\n        }\n\n        const results: SearchResult[] = [];\n        for (const r of fused) {\n            const chunkId = (r.metadata as any)?.chunkId;\n            const original = allById.get(chunkId);\n            if (!original) continue;\n            const merged = { ...original, score: r.score };\n            if (merged.score >= minScore) results.push(merged);\n        }\n\n        const deduped = this._dedup(results, k);\n        return this._rerankResults(query, deduped);\n    }\n\n    /** Apply reranking if a reranker is configured. */\n    private async _rerankResults(query: string, results: SearchResult[]): Promise<SearchResult[]> {\n        if (!this._d.reranker || results.length <= 1) return results;\n        return rerank(query, results, this._d.reranker);\n    }\n\n    /** Deduplicate results by file path — keep best-scoring chunk per file. */\n    private _dedup(results: SearchResult[], k: number): SearchResult[] {\n        const seen = new Map<string, SearchResult>();\n        for (const r of results) {\n            const key = r.filePath ?? '';\n            if (!seen.has(key) || (seen.get(key)!.score < r.score)) {\n                seen.set(key, r);\n            }\n        }\n        return [...seen.values()]\n            .sort((a, b) => b.score - a.score)\n            .slice(0, k);\n    }\n\n    /** Vector-only search via HNSW. */\n    private async _searchVector(query: string, k: number, minScore: number, collection?: string): Promise<SearchResult[]> {\n        if (this._d.hnsw.size === 0) return [];\n        const queryVec = await this._d.embedding.embed(query);\n\n        let searchK = k;\n        if (collection && this._d.hnsw.size > 0) {\n            const collectionCount = (this._d.db.prepare(\n                'SELECT COUNT(*) as c FROM doc_chunks WHERE collection = ?'\n            ).get(collection) as any)?.c ?? 0;\n            const totalChunks = (this._d.db.prepare(\n                'SELECT COUNT(*) as c FROM doc_chunks'\n            ).get() as any)?.c ?? 1;\n            const ratio = collectionCount > 0\n                ? Math.max(3, Math.min(50, Math.ceil(totalChunks / collectionCount)))\n                : 3;\n            searchK = Math.min(k * ratio, this._d.hnsw.size);\n        }\n\n        const hits = this._d.hnsw.search(queryVec, searchK);\n        const results: SearchResult[] = [];\n\n        for (const hit of hits) {\n            if (minScore && hit.score < minScore) continue;\n            const chunk = this._d.db.prepare('SELECT * FROM doc_chunks WHERE id = ?').get(hit.id) as any;\n            if (!chunk) continue;\n            if (collection && chunk.collection !== collection) continue;\n\n            results.push({\n                type: 'document',\n                score: hit.score,\n                filePath: chunk.file_path,\n                content: chunk.content,\n                context: this._getDocContext(chunk.collection, chunk.file_path),\n                metadata: {\n                    collection: chunk.collection,\n                    title: chunk.title,\n                    seq: chunk.seq,\n                    chunkId: chunk.id,\n                },\n            });\n\n            if (results.length >= k) break;\n        }\n\n        return results;\n    }\n\n    /** BM25 keyword search via FTS5 (OR-mode for natural language). */\n    private _searchBM25(query: string, k: number, minScore: number, collection?: string): SearchResult[] {\n        const ftsQuery = this._buildDocsFTS(query);\n        if (!ftsQuery) return [];\n\n        try {\n            const collectionFilter = collection ? 'AND d.collection = ?' : '';\n            const params: any[] = [ftsQuery];\n            if (collection) params.push(collection);\n            params.push(k * 2);\n\n            const rows = this._d.db.prepare(`\n                SELECT d.*, bm25(fts_docs, 10.0, 2.0, 5.0, 1.0) AS bm25_score\n                FROM fts_docs f\n                JOIN doc_chunks d ON d.id = f.rowid\n                WHERE fts_docs MATCH ? ${collectionFilter}\n                ORDER BY bm25_score ASC\n                LIMIT ?\n            `).all(...params) as any[];\n\n            return rows\n                .map(r => ({\n                    type: 'document' as const,\n                    score: normalizeBM25(r.bm25_score),\n                    filePath: r.file_path,\n                    content: r.content,\n                    context: this._getDocContext(r.collection, r.file_path),\n                    metadata: {\n                        collection: r.collection,\n                        title: r.title,\n                        seq: r.seq,\n                        chunkId: r.id,\n                    },\n                }))\n                .filter(r => r.score >= minScore)\n                .slice(0, k);\n        } catch {\n            return [];\n        }\n    }\n\n    /** Build OR-mode FTS5 query for natural language doc search. */\n    private _buildDocsFTS(query: string): string {\n        const STOP_WORDS = new Set([\n            'the', 'is', 'at', 'which', 'on', 'a', 'an', 'and', 'or', 'but',\n            'in', 'with', 'to', 'for', 'of', 'by', 'from', 'as', 'it', 'its',\n            'this', 'that', 'be', 'are', 'was', 'were', 'been', 'has', 'have',\n            'had', 'do', 'does', 'did', 'can', 'could', 'will', 'would', 'how',\n            'what', 'when', 'where', 'who', 'why', 'not', 'no', 'so', 'if',\n        ]);\n\n        const clean = query\n            .replace(/[{}[\\]()^~*:\"]/g, ' ')\n            .replace(/\\bAND\\b|\\bOR\\b|\\bNOT\\b|\\bNEAR\\b/gi, '')\n            .replace(/[_\\-./\\\\]/g, ' ')\n            .trim();\n\n        const words = clean.split(/\\s+/)\n            .filter(w => w.length >= 3 && !STOP_WORDS.has(w.toLowerCase()));\n\n        if (words.length === 0) return '';\n        return words.map(w => `\"${w}\"`).join(' OR ');\n    }\n\n    /** Resolve context for a document (checks path_contexts tree → collection context). */\n    private _getDocContext(collection: string, filePath: string): string | undefined {\n        const parts = filePath.split('/');\n        for (let i = parts.length; i >= 0; i--) {\n            const checkPath = i === 0 ? '/' : '/' + parts.slice(0, i).join('/');\n            const ctx = this._d.db.prepare(\n                'SELECT context FROM path_contexts WHERE collection = ? AND path = ?'\n            ).get(collection, checkPath) as any;\n            if (ctx) return ctx.context;\n        }\n\n        const coll = this._d.db.prepare(\n            'SELECT context FROM collections WHERE name = ?'\n        ).get(collection) as any;\n        return coll?.context ?? undefined;\n    }\n}\n","/**\n * BrainBank — Docs Module\n * \n * Index any folder of markdown/text files (notes, docs, wikis).\n * Heading-aware smart chunking inspired by qmd.\n * \n *   import { docs } from 'brainbank/docs';\n *   brain.use(docs());\n */\n\nimport type { Plugin, PluginContext } from '@/indexers/base.ts';\nimport type { HNSWIndex } from '@/providers/vector/hnsw-index.ts';\nimport type { Database } from '@/db/database.ts';\nimport type { EmbeddingProvider, DocumentCollection, SearchResult } from '@/types.ts';\nimport { DocsIndexer } from './docs-indexer.ts';\nimport { DocumentSearch } from './document-search.ts';\n\nclass DocsPlugin implements Plugin {\n    readonly name = 'docs';\n    hnsw!: HNSWIndex;\n    indexer!: DocsIndexer;\n    vecCache = new Map<number, Float32Array>();\n    private _db!: Database;\n    private _search!: DocumentSearch;\n\n    constructor(private opts: { embeddingProvider?: EmbeddingProvider } = {}) {}\n\n    async initialize(ctx: PluginContext): Promise<void> {\n        this._db = ctx.db;\n        const embedding = this.opts.embeddingProvider ?? ctx.embedding;\n\n        this.hnsw = await ctx.createHnsw(undefined, embedding.dims);\n        ctx.loadVectors('doc_vectors', 'chunk_id', this.hnsw, this.vecCache);\n        this.indexer = new DocsIndexer(ctx.db, embedding, this.hnsw, this.vecCache);\n        this._search = new DocumentSearch({\n            db: ctx.db,\n            embedding,\n            hnsw: this.hnsw,\n            vecCache: this.vecCache,\n            reranker: ctx.config.reranker,\n        });\n    }\n\n    /** Register a document collection. */\n    addCollection(collection: DocumentCollection): void {\n        this._db.prepare(`\n            INSERT OR REPLACE INTO collections (name, path, pattern, ignore_json, context)\n            VALUES (?, ?, ?, ?, ?)\n        `).run(\n            collection.name,\n            collection.path,\n            collection.pattern ?? '**/*.md',\n            JSON.stringify(collection.ignore ?? []),\n            collection.context ?? null,\n        );\n    }\n\n    /** Remove a collection and its indexed data. */\n    removeCollection(name: string): void {\n        this.indexer.removeCollection(name);\n    }\n\n    /** List all registered collections. */\n    listCollections(): DocumentCollection[] {\n        return (this._db.prepare('SELECT * FROM collections').all() as any[]).map(row => ({\n            name: row.name,\n            path: row.path,\n            pattern: row.pattern,\n            ignore: JSON.parse(row.ignore_json),\n            context: row.context,\n        }));\n    }\n\n    /** Index all (or specific) collections. Incremental. */\n    async indexCollections(options: {\n        collections?: string[];\n        onProgress?: (collection: string, file: string, current: number, total: number) => void;\n    } = {}): Promise<Record<string, { indexed: number; skipped: number; chunks: number }>> {\n        const allCollections = this.listCollections();\n        const toIndex = options.collections\n            ? allCollections.filter(c => options.collections!.includes(c.name))\n            : allCollections;\n\n        const results: Record<string, { indexed: number; skipped: number; chunks: number }> = {};\n\n        for (const coll of toIndex) {\n            results[coll.name] = await this.indexer.indexCollection(\n                coll.name,\n                coll.path,\n                coll.pattern,\n                {\n                    ignore: coll.ignore,\n                    onProgress: (file, cur, total) => options.onProgress?.(coll.name, file, cur, total),\n                },\n            );\n        }\n\n        return results;\n    }\n\n    /** Search documents using hybrid search (vector + BM25 → RRF). */\n    async search(query: string, options?: {\n        collection?: string;\n        k?: number;\n        minScore?: number;\n        mode?: 'hybrid' | 'vector' | 'keyword';\n    }): Promise<SearchResult[]> {\n        return this._search.search(query, options);\n    }\n\n    /** Add context description for a document path. */\n    addContext(collection: string, path: string, context: string): void {\n        this._db.prepare(`\n            INSERT OR REPLACE INTO path_contexts (collection, path, context)\n            VALUES (?, ?, ?)\n        `).run(collection, path, context);\n    }\n\n    /** Remove context for a path. */\n    removeContext(collection: string, path: string): void {\n        this._db.prepare(\n            'DELETE FROM path_contexts WHERE collection = ? AND path = ?'\n        ).run(collection, path);\n    }\n\n    /** List all context entries. */\n    listContexts(): { collection: string; path: string; context: string }[] {\n        return this._db.prepare('SELECT * FROM path_contexts').all() as any[];\n    }\n\n    stats(): Record<string, any> {\n        return {\n            collections: (this._db.prepare('SELECT COUNT(*) as c FROM collections').get() as any).c,\n            documents: (this._db.prepare('SELECT COUNT(DISTINCT file_path) as c FROM doc_chunks').get() as any).c,\n            chunks: (this._db.prepare('SELECT COUNT(*) as c FROM doc_chunks').get() as any).c,\n            hnswSize: this.hnsw.size,\n        };\n    }\n}\n\nexport interface DocsPluginOptions {\n    /** Per-plugin embedding provider. Default: global embedding from BrainBank config. */\n    embeddingProvider?: EmbeddingProvider;\n}\n\n/** Create a document collections plugin. */\nexport function docs(opts?: DocsPluginOptions): Plugin {\n    return new 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package/dist/cli.js

@@ -1,17 +1,17 @@
 #!/usr/bin/env node
 import {
   BrainBank
-} from "./chunk-YC4ZQLDN.js";
+} from "./chunk-DI3H6JVZ.js";
 import "./chunk-B77KABWH.js";
 import {
   code
-} from "./chunk-PXK62M5W.js";
+} from "./chunk-FGL32LUJ.js";
 import {
   git
-} from "./chunk-HPNUMUIF.js";
+} from "./chunk-JRSKWF6K.js";
 import {
   docs
-} from "./chunk-C4KDZGRX.js";
+} from "./chunk-VQ27YUHH.js";
 import "./chunk-YOLKSYWK.js";
 import "./chunk-U2Q2XGPZ.js";
 import {
@@ -107,7 +107,7 @@ import * as path2 from "path";
 // src/cli/factory.ts
 import * as path from "path";
 import * as fs from "fs";
-var CONFIG_NAMES = ["config.ts", "config.js", "config.mjs"];
+var CONFIG_NAMES = ["config.json", "config.ts", "config.js", "config.mjs"];
 var INDEXER_EXTENSIONS = [".ts", ".js", ".mjs"];
 var NOT_LOADED = /* @__PURE__ */ Symbol("not-loaded");
 var _configCache = NOT_LOADED;
@@ -118,21 +118,34 @@ async function loadConfig() {
   const brainbankDir = path.resolve(repoPath, ".brainbank");
   for (const name of CONFIG_NAMES) {
     const configPath = path.join(brainbankDir, name);
-    if (fs.existsSync(configPath)) {
-      try {
+    if (!fs.existsSync(configPath)) continue;
+    try {
+      if (name === "config.json") {
+        const raw = fs.readFileSync(configPath, "utf-8");
+        _configCache = JSON.parse(raw);
+      } else {
         const mod = await import(configPath);
         _configCache = mod.default ?? mod;
-        return _configCache;
-      } catch (err) {
-        console.error(c.red(`Error loading .brainbank/${name}: ${err.message}`));
-        process.exit(1);
       }
+      return _configCache;
+    } catch (err) {
+      console.error(c.red(`Error loading .brainbank/${name}: ${err.message}`));
+      process.exit(1);
     }
   }
   _configCache = null;
   return null;
 }
 __name(loadConfig, "loadConfig");
+async function getConfig() {
+  return loadConfig();
+}
+__name(getConfig, "getConfig");
+async function resolveEmbeddingKey(key) {
+  const { resolveEmbedding } = await import("./resolve-CUJWY6HP.js");
+  return resolveEmbedding(key);
+}
+__name(resolveEmbeddingKey, "resolveEmbeddingKey");
 async function discoverFolderPlugins() {
   if (_folderPluginsCache !== NOT_LOADED) return _folderPluginsCache;
   const repoPath = getFlag("repo") ?? ".";
@@ -177,10 +190,11 @@ async function createBrain(repoPath) {
   const config = await loadConfig();
   const folderIndexers = await discoverFolderPlugins();
   const brainOpts = { repoPath: rp, ...config?.brainbank ?? {} };
-  await setupProviders(brainOpts);
+  if (config?.maxFileSize) brainOpts.maxFileSize = config.maxFileSize;
+  await setupProviders(brainOpts, config);
   const brain = new BrainBank(brainOpts);
-  const builtins = config?.builtins ?? ["code", "git", "docs"];
-  registerBuiltins(brain, rp, builtins);
+  const builtins = config?.plugins ?? config?.builtins ?? ["code", "git", "docs"];
+  await registerBuiltins(brain, rp, builtins, config);
   for (const indexer of folderIndexers) brain.use(indexer);
   if (config?.indexers) {
     for (const indexer of config.indexers) brain.use(indexer);
@@ -188,38 +202,87 @@ async function createBrain(repoPath) {
   return brain;
 }
 __name(createBrain, "createBrain");
-async function setupProviders(brainOpts) {
-  const rerankerFlag = getFlag("reranker");
+async function setupProviders(brainOpts, config) {
+  const rerankerFlag = getFlag("reranker") ?? config?.reranker;
   if (rerankerFlag === "qwen3") {
     const { Qwen3Reranker } = await import("./qwen3-reranker-3MHEENT5.js");
     brainOpts.reranker = new Qwen3Reranker();
   }
-  const embFlag = getFlag("embedding");
+  const embFlag = getFlag("embedding") ?? config?.embedding;
   if (embFlag) {
-    const { resolveEmbedding } = await import("./resolve-CUJWY6HP.js");
-    const provider = await resolveEmbedding(embFlag);
+    const provider = await resolveEmbeddingKey(embFlag);
     brainOpts.embeddingProvider = provider;
     brainOpts.embeddingDims = provider.dims;
   }
 }
 __name(setupProviders, "setupProviders");
-function registerBuiltins(brain, rp, builtins) {
+async function registerBuiltins(brain, rp, builtins, config) {
   const resolvedRp = path.resolve(rp);
   const hasRootGit = fs.existsSync(path.join(resolvedRp, ".git"));
   const gitSubdirs = !hasRootGit ? detectGitSubdirs(resolvedRp) : [];
+  const codeEmb = config?.code?.embedding ? await resolveEmbeddingKey(config.code.embedding) : void 0;
+  const gitEmb = config?.git?.embedding ? await resolveEmbeddingKey(config.git.embedding) : void 0;
+  const docsEmb = config?.docs?.embedding ? await resolveEmbeddingKey(config.docs.embedding) : void 0;
   if (gitSubdirs.length > 0 && (builtins.includes("code") || builtins.includes("git"))) {
     console.log(c.cyan(`  Multi-repo: found ${gitSubdirs.length} git repos: ${gitSubdirs.map((d) => d.name).join(", ")}`));
     for (const sub of gitSubdirs) {
-      if (builtins.includes("code")) brain.use(code({ repoPath: sub.path, name: `code:${sub.name}` }));
-      if (builtins.includes("git")) brain.use(git({ repoPath: sub.path, name: `git:${sub.name}` }));
+      if (builtins.includes("code")) {
+        brain.use(code({
+          repoPath: sub.path,
+          name: `code:${sub.name}`,
+          embeddingProvider: codeEmb,
+          maxFileSize: config?.code?.maxFileSize
+        }));
+      }
+      if (builtins.includes("git")) {
+        brain.use(git({
+          repoPath: sub.path,
+          name: `git:${sub.name}`,
+          embeddingProvider: gitEmb,
+          depth: config?.git?.depth,
+          maxDiffBytes: config?.git?.maxDiffBytes
+        }));
+      }
     }
   } else {
-    if (builtins.includes("code")) brain.use(code({ repoPath: rp }));
-    if (builtins.includes("git")) brain.use(git());
+    if (builtins.includes("code")) {
+      brain.use(code({
+        repoPath: rp,
+        embeddingProvider: codeEmb,
+        maxFileSize: config?.code?.maxFileSize
+      }));
+    }
+    if (builtins.includes("git")) {
+      brain.use(git({
+        embeddingProvider: gitEmb,
+        depth: config?.git?.depth,
+        maxDiffBytes: config?.git?.maxDiffBytes
+      }));
+    }
+  }
+  if (builtins.includes("docs")) {
+    brain.use(docs({ embeddingProvider: docsEmb }));
   }
-  if (builtins.includes("docs")) brain.use(docs());
 }
 __name(registerBuiltins, "registerBuiltins");
+async function registerConfigCollections(brain, config) {
+  const collections = config?.docs?.collections;
+  if (!collections?.length) return;
+  for (const coll of collections) {
+    const absPath = path.resolve(coll.path);
+    try {
+      await brain.addCollection({
+        name: coll.name,
+        path: absPath,
+        pattern: coll.pattern ?? "**/*.md",
+        ignore: coll.ignore,
+        context: coll.context
+      });
+    } catch {
+    }
+  }
+}
+__name(registerConfigCollections, "registerConfigCollections");
 
 // src/cli/commands/index-cmd.ts
 async function cmdIndex() {
@@ -239,6 +302,8 @@ async function cmdIndex() {
   if (modules) console.log(c.dim(`  Modules: ${modules.join(", ")}`));
   if (docsPath) console.log(c.dim(`  Docs path: ${docsPath}`));
   const brain = await createBrain(repoPath);
+  const config = await getConfig();
+  await registerConfigCollections(brain, config);
   if (docsPath) {
     const absDocsPath = path2.resolve(docsPath);
     const collName = path2.basename(absDocsPath);