brainbank 0.1.3 → 0.1.4

package/dist/chunk-4ZKBQ33J.js

@@ -1,56 +0,0 @@
-import {
-  __name
-} from "./chunk-7QVYU63E.js";
-
-// src/query/rrf.ts
-function reciprocalRankFusion(resultSets, k = 60, maxResults = 15) {
-  const fused = /* @__PURE__ */ new Map();
-  for (const results of resultSets) {
-    for (let rank = 0; rank < results.length; rank++) {
-      const r = results[rank];
-      const key = resultKey(r);
-      const rrfContribution = 1 / (k + rank + 1);
-      const existing = fused.get(key);
-      if (existing) {
-        existing.rrfScore += rrfContribution;
-        if (r.score > existing.result.score) {
-          existing.result = { ...r };
-        }
-      } else {
-        fused.set(key, {
-          result: { ...r },
-          rrfScore: rrfContribution
-        });
-      }
-    }
-  }
-  const sorted = Array.from(fused.values()).sort((a, b) => b.rrfScore - a.rrfScore).slice(0, maxResults);
-  const maxRRF = sorted[0]?.rrfScore ?? 1;
-  return sorted.map((entry) => ({
-    ...entry.result,
-    score: entry.rrfScore / maxRRF,
-    metadata: {
-      ...entry.result.metadata,
-      rrfScore: entry.rrfScore
-    }
-  }));
-}
-__name(reciprocalRankFusion, "reciprocalRankFusion");
-function resultKey(r) {
-  switch (r.type) {
-    case "code":
-      return `code:${r.filePath}:${r.metadata.startLine}-${r.metadata.endLine}`;
-    case "commit":
-      return `commit:${r.metadata.hash || r.metadata.shortHash}`;
-    case "pattern":
-      return `pattern:${r.metadata.taskType}:${r.content?.slice(0, 60)}`;
-    default:
-      return `${r.type}:${r.content?.slice(0, 80)}`;
-  }
-}
-__name(resultKey, "resultKey");
-
-export {
-  reciprocalRankFusion
-};
-//# sourceMappingURL=chunk-4ZKBQ33J.js.map

package/dist/chunk-4ZKBQ33J.js.map

@@ -1 +0,0 @@
-{"version":3,"sources":["../src/query/rrf.ts"],"sourcesContent":["/**\n * BrainBank — Reciprocal Rank Fusion (RRF)\n * \n * Combines results from multiple search systems (vector + BM25)\n * using the RRF algorithm: score = Σ 1/(k + rank_i)\n * \n * This is the same algorithm used by Elasticsearch, QMD, and most\n * production hybrid search systems. Simple but very effective.\n * \n * Reference: Cormack et al., \"Reciprocal Rank Fusion outperforms\n * Condorcet and individual Rank Learning Methods\" (2009)\n */\n\nimport type { SearchResult } from '../types.ts';\n\n/**\n * Fuse ranked lists from different search systems into a single ranked list.\n * \n * @param resultSets - Arrays of SearchResult from different systems (e.g. vector, BM25)\n * @param k - Smoothing constant. Default: 60 (standard value). Higher = less emphasis on top ranks.\n * @param maxResults - Maximum results to return.\n */\nexport function reciprocalRankFusion(\n    resultSets: SearchResult[][],\n    k: number = 60,\n    maxResults: number = 15,\n): SearchResult[] {\n    // Build a map: unique key → { bestResult, rrfScore }\n    const fused = new Map<string, { result: SearchResult; rrfScore: number }>();\n\n    for (const results of resultSets) {\n        for (let rank = 0; rank < results.length; rank++) {\n            const r = results[rank];\n            const key = resultKey(r);\n            const rrfContribution = 1.0 / (k + rank + 1);\n\n            const existing = fused.get(key);\n            if (existing) {\n                existing.rrfScore += rrfContribution;\n                // Keep the result with the higher original score\n                if (r.score > existing.result.score) {\n                    existing.result = { ...r };\n                }\n            } else {\n                fused.set(key, {\n                    result: { ...r },\n                    rrfScore: rrfContribution,\n                });\n            }\n        }\n    }\n\n    // Sort by RRF score descending, normalize, and return\n    const sorted = Array.from(fused.values())\n        .sort((a, b) => b.rrfScore - a.rrfScore)\n        .slice(0, maxResults);\n\n    // Normalize RRF scores to 0..1 range\n    const maxRRF = sorted[0]?.rrfScore ?? 1;\n    return sorted.map(entry => ({\n        ...entry.result,\n        score: entry.rrfScore / maxRRF,\n        metadata: {\n            ...entry.result.metadata,\n            rrfScore: entry.rrfScore,\n        },\n    }));\n}\n\n/**\n * Generate a unique key for a search result to detect duplicates across systems.\n */\nfunction resultKey(r: SearchResult): string {\n    switch (r.type) {\n        case 'code':\n            return `code:${r.filePath}:${r.metadata.startLine}-${r.metadata.endLine}`;\n        case 'commit':\n            return `commit:${r.metadata.hash || r.metadata.shortHash}`;\n        case 'pattern':\n            return `pattern:${r.metadata.taskType}:${r.content?.slice(0, 60)}`;\n        default:\n            return `${r.type}:${r.content?.slice(0, 80)}`;\n    }\n}\n"],"mappings":";;;;;AAsBO,SAAS,qBACZ,YACA,IAAY,IACZ,aAAqB,IACP;AAEd,QAAM,QAAQ,oBAAI,IAAwD;AAE1E,aAAW,WAAW,YAAY;AAC9B,aAAS,OAAO,GAAG,OAAO,QAAQ,QAAQ,QAAQ;AAC9C,YAAM,IAAI,QAAQ,IAAI;AACtB,YAAM,MAAM,UAAU,CAAC;AACvB,YAAM,kBAAkB,KAAO,IAAI,OAAO;AAE1C,YAAM,WAAW,MAAM,IAAI,GAAG;AAC9B,UAAI,UAAU;AACV,iBAAS,YAAY;AAErB,YAAI,EAAE,QAAQ,SAAS,OAAO,OAAO;AACjC,mBAAS,SAAS,EAAE,GAAG,EAAE;AAAA,QAC7B;AAAA,MACJ,OAAO;AACH,cAAM,IAAI,KAAK;AAAA,UACX,QAAQ,EAAE,GAAG,EAAE;AAAA,UACf,UAAU;AAAA,QACd,CAAC;AAAA,MACL;AAAA,IACJ;AAAA,EACJ;AAGA,QAAM,SAAS,MAAM,KAAK,MAAM,OAAO,CAAC,EACnC,KAAK,CAAC,GAAG,MAAM,EAAE,WAAW,EAAE,QAAQ,EACtC,MAAM,GAAG,UAAU;AAGxB,QAAM,SAAS,OAAO,CAAC,GAAG,YAAY;AACtC,SAAO,OAAO,IAAI,YAAU;AAAA,IACxB,GAAG,MAAM;AAAA,IACT,OAAO,MAAM,WAAW;AAAA,IACxB,UAAU;AAAA,MACN,GAAG,MAAM,OAAO;AAAA,MAChB,UAAU,MAAM;AAAA,IACpB;AAAA,EACJ,EAAE;AACN;AA7CgB;AAkDhB,SAAS,UAAU,GAAyB;AACxC,UAAQ,EAAE,MAAM;AAAA,IACZ,KAAK;AACD,aAAO,QAAQ,EAAE,QAAQ,IAAI,EAAE,SAAS,SAAS,IAAI,EAAE,SAAS,OAAO;AAAA,IAC3E,KAAK;AACD,aAAO,UAAU,EAAE,SAAS,QAAQ,EAAE,SAAS,SAAS;AAAA,IAC5D,KAAK;AACD,aAAO,WAAW,EAAE,SAAS,QAAQ,IAAI,EAAE,SAAS,MAAM,GAAG,EAAE,CAAC;AAAA,IACpE;AACI,aAAO,GAAG,EAAE,IAAI,IAAI,EAAE,SAAS,MAAM,GAAG,EAAE,CAAC;AAAA,EACnD;AACJ;AAXS;","names":[]}

package/dist/chunk-7QVYU63E.js

@@ -1,7 +0,0 @@
-var __defProp = Object.defineProperty;
-var __name = (target, value) => __defProp(target, "name", { value, configurable: true });
-
-export {
-  __name
-};
-//# sourceMappingURL=chunk-7QVYU63E.js.map

package/dist/chunk-GOUBW7UA.js

@@ -1,373 +0,0 @@
-import {
-  __name
-} from "./chunk-7QVYU63E.js";
-
-// src/indexers/doc-indexer.ts
-import * as fs from "fs";
-import * as path from "path";
-import { createHash } from "crypto";
-import { glob } from "fs/promises";
-var BREAK_SCORES = [
-  [/^# /, 100],
-  // H1
-  [/^## /, 90],
-  // H2
-  [/^### /, 80],
-  // H3
-  [/^#### /, 70],
-  // H4
-  [/^##### /, 60],
-  // H5
-  [/^###### /, 50],
-  // H6
-  [/^```/, 80],
-  // Code fence
-  [/^---$/, 60],
-  // Horizontal rule
-  [/^\*\*\*$/, 60],
-  // Horizontal rule alt
-  [/^$/, 20],
-  // Blank line (paragraph break)
-  [/^[-*+] /, 5]
-  // List item
-];
-var TARGET_CHARS = 3e3;
-var WINDOW_CHARS = 600;
-var MIN_CHUNK_CHARS = 200;
-var DocIndexer = class {
-  constructor(_db, _embedding, _hnsw, _vecCache) {
-    this._db = _db;
-    this._embedding = _embedding;
-    this._hnsw = _hnsw;
-    this._vecCache = _vecCache;
-  }
-  static {
-    __name(this, "DocIndexer");
-  }
-  /**
-   * Index all documents in a collection.
-   * Incremental — skips unchanged files (by content hash).
-   */
-  async indexCollection(collection, dirPath, pattern = "**/*.md", options = {}) {
-    const absDir = path.resolve(dirPath);
-    if (!fs.existsSync(absDir)) {
-      throw new Error(`Collection path does not exist: ${absDir}`);
-    }
-    const files = [];
-    for await (const entry of glob(pattern, { cwd: absDir })) {
-      const fullPath = path.join(absDir, entry);
-      const stat = fs.statSync(fullPath);
-      if (stat.isFile()) {
-        const shouldIgnore = options.ignore?.some((ig) => {
-          const igRegex = new RegExp(ig.replace(/\*\*/g, ".*").replace(/\*/g, "[^/]*"));
-          return igRegex.test(entry);
-        });
-        if (!shouldIgnore) {
-          files.push(entry);
-        }
-      }
-    }
-    let indexed = 0;
-    let skipped = 0;
-    let totalChunks = 0;
-    for (let i = 0; i < files.length; i++) {
-      const relPath = files[i];
-      const absPath = path.join(absDir, relPath);
-      options.onProgress?.(relPath, i + 1, files.length);
-      const content = fs.readFileSync(absPath, "utf-8");
-      const hash = createHash("sha256").update(content).digest("hex").slice(0, 16);
-      const existing = this._db.prepare(
-        "SELECT id FROM doc_chunks WHERE collection = ? AND file_path = ? AND content_hash = ? LIMIT 1"
-      ).get(collection, relPath, hash);
-      if (existing) {
-        skipped++;
-        continue;
-      }
-      this._db.prepare(
-        "DELETE FROM doc_chunks WHERE collection = ? AND file_path = ?"
-      ).run(collection, relPath);
-      const title = this._extractTitle(content, relPath);
-      const chunks = this._smartChunk(content);
-      const insertChunk = this._db.prepare(`
-                INSERT INTO doc_chunks (collection, file_path, title, content, seq, pos, content_hash)
-                VALUES (?, ?, ?, ?, ?, ?, ?)
-            `);
-      const chunkIds = [];
-      this._db.transaction(() => {
-        for (let seq = 0; seq < chunks.length; seq++) {
-          const chunk = chunks[seq];
-          const result = insertChunk.run(
-            collection,
-            relPath,
-            title,
-            chunk.text,
-            seq,
-            chunk.pos,
-            hash
-          );
-          chunkIds.push(Number(result.lastInsertRowid));
-        }
-      });
-      const texts = chunks.map((c) => `title: ${title} | text: ${c.text}`);
-      const embeddings = await this._embedding.embedBatch(texts);
-      const insertVec = this._db.prepare(
-        "INSERT OR REPLACE INTO doc_vectors (chunk_id, embedding) VALUES (?, ?)"
-      );
-      this._db.transaction(() => {
-        for (let j = 0; j < chunkIds.length; j++) {
-          const buf = Buffer.from(embeddings[j].buffer);
-          insertVec.run(chunkIds[j], buf);
-          this._hnsw.add(embeddings[j], chunkIds[j]);
-          this._vecCache.set(chunkIds[j], embeddings[j]);
-        }
-      });
-      indexed++;
-      totalChunks += chunks.length;
-    }
-    return { indexed, skipped, chunks: totalChunks };
-  }
-  /**
-   * Remove all indexed data for a collection.
-   */
-  removeCollection(collection) {
-    this._db.prepare("DELETE FROM doc_chunks WHERE collection = ?").run(collection);
-    this._db.prepare("DELETE FROM collections WHERE name = ?").run(collection);
-    this._db.prepare("DELETE FROM path_contexts WHERE collection = ?").run(collection);
-  }
-  // ── Smart Chunking ──────────────────────────────
-  /**
-   * Split document into chunks at natural markdown boundaries.
-   * Uses heading-aware scoring like qmd.
-   */
-  _smartChunk(text) {
-    if (text.length <= TARGET_CHARS) {
-      return [{ text, pos: 0 }];
-    }
-    const lines = text.split("\n");
-    const breakPoints = this._findBreakPoints(lines);
-    const chunks = [];
-    let chunkStart = 0;
-    let lineStart = 0;
-    while (chunkStart < text.length) {
-      const remaining = text.length - chunkStart;
-      if (remaining <= TARGET_CHARS + WINDOW_CHARS) {
-        const lastText = text.slice(chunkStart).trim();
-        if (lastText.length >= MIN_CHUNK_CHARS) {
-          chunks.push({ text: lastText, pos: chunkStart });
-        } else if (chunks.length > 0) {
-          chunks[chunks.length - 1].text += "\n" + lastText;
-        } else {
-          chunks.push({ text: lastText, pos: chunkStart });
-        }
-        break;
-      }
-      const targetEnd = chunkStart + TARGET_CHARS;
-      const windowStart = targetEnd - WINDOW_CHARS;
-      let bestBreak = targetEnd;
-      let bestScore = 0;
-      for (const bp of breakPoints) {
-        if (bp.pos <= chunkStart) continue;
-        if (bp.pos > targetEnd + WINDOW_CHARS / 2) break;
-        if (bp.pos < windowStart) continue;
-        const distance = Math.abs(bp.pos - targetEnd);
-        const decay = 1 - (distance / WINDOW_CHARS) ** 2 * 0.7;
-        const finalScore = bp.score * decay;
-        if (finalScore > bestScore) {
-          bestScore = finalScore;
-          bestBreak = bp.pos;
-        }
-      }
-      const chunkText = text.slice(chunkStart, bestBreak).trim();
-      if (chunkText.length >= MIN_CHUNK_CHARS) {
-        chunks.push({ text: chunkText, pos: chunkStart });
-      }
-      chunkStart = bestBreak;
-    }
-    return chunks;
-  }
-  /**
-   * Find all potential break points in the document with scores.
-   */
-  _findBreakPoints(lines) {
-    const points = [];
-    let charPos = 0;
-    let inCodeBlock = false;
-    for (const line of lines) {
-      if (line.trimStart().startsWith("```")) {
-        inCodeBlock = !inCodeBlock;
-        if (!inCodeBlock) {
-          points.push({ pos: charPos + line.length + 1, score: 80 });
-        }
-        charPos += line.length + 1;
-        continue;
-      }
-      if (inCodeBlock) {
-        charPos += line.length + 1;
-        continue;
-      }
-      for (const [pattern, score] of BREAK_SCORES) {
-        if (pattern.test(line.trim())) {
-          points.push({ pos: charPos, score });
-          break;
-        }
-      }
-      charPos += line.length + 1;
-    }
-    return points;
-  }
-  /**
-   * Extract document title from first heading or filename.
-   */
-  _extractTitle(content, filePath) {
-    const match = content.match(/^#{1,3}\s+(.+)$/m);
-    if (match) return match[1].trim();
-    return path.basename(filePath, path.extname(filePath));
-  }
-};
-
-// src/plugins/docs.ts
-var DocsModuleImpl = class {
-  constructor(opts = {}) {
-    this.opts = opts;
-  }
-  static {
-    __name(this, "DocsModuleImpl");
-  }
-  name = "docs";
-  hnsw;
-  indexer;
-  vecCache = /* @__PURE__ */ new Map();
-  _db;
-  _embedding;
-  async initialize(ctx) {
-    this._db = ctx.db;
-    this._embedding = ctx.embedding;
-    this.hnsw = await ctx.createHnsw();
-    ctx.loadVectors("doc_vectors", "chunk_id", this.hnsw, this.vecCache);
-    this.indexer = new DocIndexer(ctx.db, ctx.embedding, this.hnsw, this.vecCache);
-  }
-  /** Register a document collection. */
-  addCollection(collection) {
-    this._db.prepare(`
-            INSERT OR REPLACE INTO collections (name, path, pattern, ignore_json, context)
-            VALUES (?, ?, ?, ?, ?)
-        `).run(
-      collection.name,
-      collection.path,
-      collection.pattern ?? "**/*.md",
-      JSON.stringify(collection.ignore ?? []),
-      collection.context ?? null
-    );
-  }
-  /** Remove a collection and its indexed data. */
-  removeCollection(name) {
-    this.indexer.removeCollection(name);
-  }
-  /** List all registered collections. */
-  listCollections() {
-    return this._db.prepare("SELECT * FROM collections").all().map((row) => ({
-      name: row.name,
-      path: row.path,
-      pattern: row.pattern,
-      ignore: JSON.parse(row.ignore_json),
-      context: row.context
-    }));
-  }
-  /** Index all (or specific) collections. Incremental. */
-  async indexCollections(options = {}) {
-    const allCollections = this.listCollections();
-    const toIndex = options.collections ? allCollections.filter((c) => options.collections.includes(c.name)) : allCollections;
-    const results = {};
-    for (const coll of toIndex) {
-      results[coll.name] = await this.indexer.indexCollection(
-        coll.name,
-        coll.path,
-        coll.pattern,
-        {
-          ignore: coll.ignore,
-          onProgress: /* @__PURE__ */ __name((file, cur, total) => options.onProgress?.(coll.name, file, cur, total), "onProgress")
-        }
-      );
-    }
-    return results;
-  }
-  /** Search documents only. */
-  async search(query, options) {
-    const k = options?.k ?? 8;
-    const queryVec = await this._embedding.embed(query);
-    const hits = this.hnsw.search(queryVec, k);
-    const results = [];
-    for (const hit of hits) {
-      if (options?.minScore && hit.score < options.minScore) continue;
-      const chunk = this._db.prepare(
-        "SELECT * FROM doc_chunks WHERE id = ?"
-      ).get(hit.id);
-      if (!chunk) continue;
-      if (options?.collection && chunk.collection !== options.collection) continue;
-      const ctx = this._getDocContext(chunk.collection, chunk.file_path);
-      results.push({
-        type: "document",
-        score: hit.score,
-        filePath: chunk.file_path,
-        content: chunk.content,
-        context: ctx,
-        metadata: {
-          collection: chunk.collection,
-          title: chunk.title,
-          seq: chunk.seq
-        }
-      });
-    }
-    return results;
-  }
-  /** Add context description for a document path. */
-  addContext(collection, path2, context) {
-    this._db.prepare(`
-            INSERT OR REPLACE INTO path_contexts (collection, path, context)
-            VALUES (?, ?, ?)
-        `).run(collection, path2, context);
-  }
-  /** Remove context for a path. */
-  removeContext(collection, path2) {
-    this._db.prepare(
-      "DELETE FROM path_contexts WHERE collection = ? AND path = ?"
-    ).run(collection, path2);
-  }
-  /** List all context entries. */
-  listContexts() {
-    return this._db.prepare("SELECT * FROM path_contexts").all();
-  }
-  stats() {
-    return {
-      collections: this._db.prepare("SELECT COUNT(*) as c FROM collections").get().c,
-      documents: this._db.prepare("SELECT COUNT(DISTINCT file_path) as c FROM doc_chunks").get().c,
-      chunks: this._db.prepare("SELECT COUNT(*) as c FROM doc_chunks").get().c,
-      hnswSize: this.hnsw.size
-    };
-  }
-  /** Resolve context for a document (checks path_contexts tree → collection context). */
-  _getDocContext(collection, filePath) {
-    const parts = filePath.split("/");
-    for (let i = parts.length; i >= 0; i--) {
-      const checkPath = i === 0 ? "/" : "/" + parts.slice(0, i).join("/");
-      const ctx = this._db.prepare(
-        "SELECT context FROM path_contexts WHERE collection = ? AND path = ?"
-      ).get(collection, checkPath);
-      if (ctx) return ctx.context;
-    }
-    const coll = this._db.prepare(
-      "SELECT context FROM collections WHERE name = ?"
-    ).get(collection);
-    return coll?.context ?? void 0;
-  }
-};
-function docs(opts) {
-  return new DocsModuleImpl(opts);
-}
-__name(docs, "docs");
-
-export {
-  DocIndexer,
-  docs
-};
-//# sourceMappingURL=chunk-GOUBW7UA.js.map

package/dist/chunk-GOUBW7UA.js.map

@@ -1 +0,0 @@
-{"version":3,"sources":["../src/indexers/doc-indexer.ts","../src/plugins/docs.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 DocIndexer(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';\nimport { glob } from 'node:fs/promises';\nimport type { Database } from '../storage/database.ts';\nimport type { EmbeddingProvider, VectorIndex } from '../types.ts';\nimport type { HNSWIndex } from '../vector/hnsw.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// ── DocIndexer ──────────────────────────────────────\n\nexport class DocIndexer {\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        // Resolve absolute path\n        const absDir = path.resolve(dirPath);\n        if (!fs.existsSync(absDir)) {\n            throw new Error(`Collection path does not exist: ${absDir}`);\n        }\n\n        // Find files matching pattern\n        const files: string[] = [];\n        for await (const entry of glob(pattern, { cwd: absDir })) {\n            const fullPath = path.join(absDir, entry);\n            const stat = fs.statSync(fullPath);\n            if (stat.isFile()) {\n                // Check ignore patterns\n                const shouldIgnore = options.ignore?.some(ig => {\n                    const igRegex = new RegExp(ig.replace(/\\*\\*/g, '.*').replace(/\\*/g, '[^/]*'));\n                    return igRegex.test(entry);\n                });\n                if (!shouldIgnore) {\n                    files.push(entry); // relative path\n                }\n            }\n        }\n\n        let indexed = 0;\n        let skipped = 0;\n        let totalChunks = 0;\n\n        for (let i = 0; i < files.length; i++) {\n            const relPath = files[i];\n            const absPath = path.join(absDir, relPath);\n\n            options.onProgress?.(relPath, i + 1, files.length);\n\n            // Read content and hash\n            const content = fs.readFileSync(absPath, 'utf-8');\n            const hash = createHash('sha256').update(content).digest('hex').slice(0, 16);\n\n            // Check if already indexed with same hash\n            const existing = this._db.prepare(\n                'SELECT id FROM doc_chunks WHERE collection = ? AND file_path = ? AND content_hash = ? LIMIT 1'\n            ).get(collection, relPath, hash) as any;\n\n            if (existing) {\n                skipped++;\n                continue;\n            }\n\n            // Remove old chunks for this file\n            this._db.prepare(\n                'DELETE FROM doc_chunks WHERE collection = ? AND file_path = ?'\n            ).run(collection, relPath);\n\n            // Extract title and chunk\n            const title = this._extractTitle(content, relPath);\n            const chunks = this._smartChunk(content);\n\n            // Insert chunks\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\n            this._db.transaction(() => {\n                for (let seq = 0; seq < chunks.length; seq++) {\n                    const chunk = chunks[seq];\n                    const result = insertChunk.run(\n                        collection, relPath, title, chunk.text, seq, chunk.pos, hash,\n                    );\n                    chunkIds.push(Number(result.lastInsertRowid));\n                }\n            });\n\n            // Generate embeddings\n            const texts = chunks.map(c => `title: ${title} | text: ${c.text}`);\n            const embeddings = await this._embedding.embedBatch(texts);\n\n            // Store vectors\n            const insertVec = this._db.prepare(\n                'INSERT OR REPLACE INTO doc_vectors (chunk_id, embedding) VALUES (?, ?)'\n            );\n\n            this._db.transaction(() => {\n                for (let j = 0; j < chunkIds.length; j++) {\n                    const buf = Buffer.from(embeddings[j].buffer);\n                    insertVec.run(chunkIds[j], buf);\n                    this._hnsw.add(embeddings[j], chunkIds[j]);\n                    this._vecCache.set(chunkIds[j], embeddings[j]);\n                }\n            });\n\n            indexed++;\n            totalChunks += chunks.length;\n        }\n\n        return { indexed, skipped, chunks: totalChunks };\n    }\n\n    /**\n     * Remove all indexed data for a collection.\n     */\n    removeCollection(collection: string): void {\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    /**\n     * Split document into chunks at natural markdown boundaries.\n     * Uses heading-aware scoring like qmd.\n     */\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\n        let chunkStart = 0;  // char position\n        let lineStart = 0;   // line index\n\n        while (chunkStart < text.length) {\n            const remaining = text.length - chunkStart;\n            if (remaining <= TARGET_CHARS + WINDOW_CHARS) {\n                // Last chunk — take everything\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                    // Merge with previous chunk\n                    chunks[chunks.length - 1].text += '\\n' + lastText;\n                } else {\n                    chunks.push({ text: lastText, pos: chunkStart });\n                }\n                break;\n            }\n\n            // Find best break point in window\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                // Score decay: prefer closer break points\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            const chunkText = text.slice(chunkStart, bestBreak).trim();\n            if (chunkText.length >= MIN_CHUNK_CHARS) {\n                chunks.push({ text: chunkText, pos: chunkStart });\n            }\n\n            chunkStart = bestBreak;\n        }\n\n        return chunks;\n    }\n\n    /**\n     * Find all potential break points in the document with scores.\n     */\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            // Track code fences\n            if (line.trimStart().startsWith('```')) {\n                inCodeBlock = !inCodeBlock;\n                if (!inCodeBlock) {\n                    // End of code block is a good break point\n                    points.push({ pos: charPos + line.length + 1, score: 80 });\n                }\n                charPos += line.length + 1;\n                continue;\n            }\n\n            // Skip break points inside code blocks\n            if (inCodeBlock) {\n                charPos += line.length + 1;\n                continue;\n            }\n\n            // Score this line as a potential break point\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    /**\n     * Extract document title from first heading or filename.\n     */\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 — 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 { BrainBankModule, ModuleContext } from './types.ts';\nimport type { HNSWIndex } from '../vector/hnsw.ts';\nimport type { Database } from '../storage/database.ts';\nimport type { EmbeddingProvider, DocumentCollection, SearchResult } from '../types.ts';\nimport { DocIndexer } from '../indexers/doc-indexer.ts';\n\nexport interface DocsModuleOptions {}\n\nclass DocsModuleImpl implements BrainBankModule {\n    readonly name = 'docs';\n    hnsw!: HNSWIndex;\n    indexer!: DocIndexer;\n    vecCache = new Map<number, Float32Array>();\n    private _db!: Database;\n    private _embedding!: EmbeddingProvider;\n\n    constructor(private opts: DocsModuleOptions = {}) {}\n\n    async initialize(ctx: ModuleContext): Promise<void> {\n        this._db = ctx.db;\n        this._embedding = ctx.embedding;\n        this.hnsw = await ctx.createHnsw();\n        ctx.loadVectors('doc_vectors', 'chunk_id', this.hnsw, this.vecCache);\n        this.indexer = new DocIndexer(ctx.db, ctx.embedding, this.hnsw, this.vecCache);\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 only. */\n    async search(query: string, options?: {\n        collection?: string;\n        k?: number;\n        minScore?: number;\n    }): Promise<SearchResult[]> {\n        const k = options?.k ?? 8;\n        const queryVec = await this._embedding.embed(query);\n        const hits = this.hnsw.search(queryVec, k);\n\n        const results: SearchResult[] = [];\n        for (const hit of hits) {\n            if (options?.minScore && hit.score < options.minScore) continue;\n\n            const chunk = this._db.prepare(\n                'SELECT * FROM doc_chunks WHERE id = ?'\n            ).get(hit.id) as any;\n\n            if (!chunk) continue;\n            if (options?.collection && chunk.collection !== options.collection) continue;\n\n            const ctx = this._getDocContext(chunk.collection, chunk.file_path);\n\n            results.push({\n                type: 'document',\n                score: hit.score,\n                filePath: chunk.file_path,\n                content: chunk.content,\n                context: ctx,\n                metadata: {\n                    collection: chunk.collection,\n                    title: chunk.title,\n                    seq: chunk.seq,\n                },\n            });\n        }\n\n        return results;\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    /** 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._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._db.prepare(\n            'SELECT context FROM collections WHERE name = ?'\n        ).get(collection) as any;\n        return coll?.context ?? undefined;\n    }\n}\n\n/** Create a document collections module. */\nexport function docs(opts?: DocsModuleOptions): BrainBankModule {\n    return new 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