@theglitchking/semantic-pages 0.3.2 → 0.4.1

package/dist/{chunk-ZM3YYKVD.js → chunk-7BYJ7MHY.js}

@@ -11,6 +11,7 @@ import { fileURLToPath } from "url";
 var DEFAULT_MODEL = "nomic-ai/nomic-embed-text-v1.5";
 var CACHE_DIR = join(homedir(), ".semantic-pages", "models");
 var DEFAULT_WORKERS = 1;
+var DEFAULT_BATCH_SIZE = 32;
 var ONNX_MODEL_PATHS = {
   "nomic-ai/nomic-embed-text-v1.5": "onnx/model.onnx",
   "sentence-transformers/all-MiniLM-L6-v2": "onnx/model.onnx"
@@ -40,10 +41,12 @@ var Embedder = class {
   runtimeLabel = "wasm";
   initialized = false;
   numWorkers;
+  batchSize;
   modelPath = "";
-  constructor(model = DEFAULT_MODEL, numWorkers = DEFAULT_WORKERS) {
+  constructor(model = DEFAULT_MODEL, numWorkers = DEFAULT_WORKERS, batchSize = DEFAULT_BATCH_SIZE) {
     this.model = model;
     this.numWorkers = numWorkers;
+    this.batchSize = batchSize;
   }
   async init() {
     if (this.initialized) return;
@@ -72,7 +75,7 @@ var Embedder = class {
     const test = await this.embed("test");
     this.dimensions = test.length;
     this.initialized = true;
-    process.stderr.write(`Embedder ready (${label} runtime, ${this.dimensions}d)
+    process.stderr.write(`Embedder ready (${label} runtime, ${this.dimensions}d, batch_size=${this.batchSize})
 `);
   }
   async embed(text) {
@@ -132,14 +135,102 @@ var Embedder = class {
     }
     return result;
   }
+  // Mean pool + L2 normalize the output of a batched ONNX forward pass.
+  // outputData: flat Float32Array of shape [batchSize, seqLen, hiddenSize]
+  // maskData:   flat number[] of shape [batchSize, seqLen]
+  meanPoolAndNormalizeMany(outputData, maskData, batchSize, seqLen, hiddenSize) {
+    const results = [];
+    for (let b = 0; b < batchSize; b++) {
+      const result = new Float32Array(hiddenSize);
+      let maskSum = 0;
+      for (let t = 0; t < seqLen; t++) {
+        const mask = maskData[b * seqLen + t];
+        maskSum += mask;
+        const offset = (b * seqLen + t) * hiddenSize;
+        for (let d = 0; d < hiddenSize; d++) {
+          result[d] += outputData[offset + d] * mask;
+        }
+      }
+      if (maskSum > 0) {
+        for (let d = 0; d < hiddenSize; d++) result[d] /= maskSum;
+      }
+      let norm = 0;
+      for (let d = 0; d < hiddenSize; d++) norm += result[d] * result[d];
+      norm = Math.sqrt(norm);
+      if (norm > 0) {
+        for (let d = 0; d < hiddenSize; d++) result[d] /= norm;
+      }
+      results.push(result);
+    }
+    return results;
+  }
+  // Embed a sub-batch of texts (length <= batchSize) in a single ONNX forward pass.
+  //
+  // Tokenizes each text individually (well-defined output format for all HF versions),
+  // then manually pads to the longest sequence in the batch and builds a [n, seqLen]
+  // tensor for one ONNX call. The speedup is from batching the ONNX inference —
+  // individual tokenization is negligible (<1ms each).
+  async embedSubBatch(texts) {
+    if (!this.session || !this.tokenizer || !this.ort)
+      throw new Error("Embedder not initialized. Call init() first.");
+    const n = texts.length;
+    const encodings = await Promise.all(
+      texts.map(
+        (text) => this.tokenizer(text, {
+          padding: false,
+          truncation: true,
+          max_length: 512,
+          return_tensor: false
+        })
+      )
+    );
+    const tokenized = encodings.map((enc) => ({
+      ids: Array.from(enc.input_ids.data ?? enc.input_ids),
+      mask: Array.from(enc.attention_mask.data ?? enc.attention_mask)
+    }));
+    const seqLen = Math.max(...tokenized.map((t) => t.ids.length));
+    const flatIds = new BigInt64Array(n * seqLen);
+    const flatMask = new BigInt64Array(n * seqLen);
+    const flatMaskNums = new Array(n * seqLen).fill(0);
+    for (let i = 0; i < n; i++) {
+      const { ids, mask } = tokenized[i];
+      for (let j = 0; j < ids.length; j++) {
+        flatIds[i * seqLen + j] = BigInt(ids[j]);
+        flatMask[i * seqLen + j] = BigInt(mask[j]);
+        flatMaskNums[i * seqLen + j] = mask[j];
+      }
+    }
+    const inputIds = new this.ort.Tensor("int64", flatIds, [n, seqLen]);
+    const attentionMask = new this.ort.Tensor("int64", flatMask, [n, seqLen]);
+    const feeds = { input_ids: inputIds, attention_mask: attentionMask };
+    if (this.session.inputNames.includes("token_type_ids")) {
+      feeds.token_type_ids = new this.ort.Tensor(
+        "int64",
+        new BigInt64Array(n * seqLen),
+        [n, seqLen]
+      );
+    }
+    const output = await this.session.run(feeds);
+    const outputTensor = output[this.session.outputNames[0]];
+    const hiddenSize = outputTensor.dims[outputTensor.dims.length - 1];
+    return this.meanPoolAndNormalizeMany(
+      outputTensor.data,
+      flatMaskNums,
+      n,
+      seqLen,
+      hiddenSize
+    );
+  }
   async embedBatch(texts, onProgress) {
     if (this.numWorkers > 1 && texts.length >= this.numWorkers * 2) {
       return this.embedBatchParallel(texts, onProgress);
     }
     const results = [];
-    for (let i = 0; i < texts.length; i++) {
-      results.push(await this.embed(texts[i]));
-      onProgress?.(i + 1, texts.length);
+    for (let i = 0; i < texts.length; i += this.batchSize) {
+      const subBatch = texts.slice(i, i + this.batchSize);
+      const embeddings = await this.embedSubBatch(subBatch);
+      results.push(...embeddings);
+      await onProgress?.(Math.min(i + subBatch.length, texts.length), texts.length, embeddings);
     }
     return results;
   }
@@ -150,13 +241,8 @@ var Embedder = class {
       workerPath = join(thisDir, "core", "embed-worker.js");
     }
     if (!existsSync(workerPath)) {
-      process.stderr.write("Worker script not found, falling back to serial embedding\n");
-      const results = [];
-      for (let i = 0; i < texts.length; i++) {
-        results.push(await this.embed(texts[i]));
-        onProgress?.(i + 1, texts.length);
-      }
-      return results;
+      process.stderr.write("Worker script not found, falling back to batched embedding\n");
+      return this.embedBatch(texts, onProgress);
     }
     const chunkSize = Math.ceil(texts.length / this.numWorkers);
     const chunks = [];
@@ -172,7 +258,8 @@ var Embedder = class {
             modelPath: this.modelPath,
             modelName: this.model,
             cacheDir: CACHE_DIR,
-            runtimeLabel: this.runtimeLabel
+            runtimeLabel: this.runtimeLabel,
+            batchSize: this.batchSize
           }
         });
         worker.on("message", (msg) => {
@@ -793,4 +880,4 @@ export {
   TagManager,
   Watcher
 };
-//# sourceMappingURL=chunk-ZM3YYKVD.js.map
+//# sourceMappingURL=chunk-7BYJ7MHY.js.map

package/dist/chunk-7BYJ7MHY.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/core/embedder.ts","../src/core/graph.ts","../src/core/vector.ts","../src/core/search-text.ts","../src/core/crud.ts","../src/core/frontmatter.ts","../src/core/watcher.ts"],"sourcesContent":["import { AutoTokenizer } from \"@huggingface/transformers\";\nimport { readFile, writeFile, mkdir } from \"node:fs/promises\";\nimport { join, dirname } from \"node:path\";\nimport { existsSync, createWriteStream } from \"node:fs\";\nimport { homedir, cpus } from \"node:os\";\nimport { Readable } from \"node:stream\";\nimport { pipeline as streamPipeline } from \"node:stream/promises\";\nimport { Worker } from \"node:worker_threads\";\nimport { fileURLToPath } from \"node:url\";\n\nconst DEFAULT_MODEL = \"nomic-ai/nomic-embed-text-v1.5\";\nconst CACHE_DIR = join(homedir(), \".semantic-pages\", \"models\");\n// Default to 1 worker (serial). Worker threads only help on memory-rich machines\n// (each worker loads its own ONNX session, ~400 MB each). On typical dev machines\n// with <4 GB free RAM, parallel workers cause swap thrashing and are 3x slower.\n// Enable with --workers N when you have sufficient RAM (N * ~400 MB free).\nconst DEFAULT_WORKERS = 1;\n// Number of texts to embed in a single ONNX forward pass.\n// Transformers process batches nearly as fast as a single sample, so batching\n// reduces 2,853 ONNX calls to ~90 calls (batch_size=32) — ~16x faster.\nconst DEFAULT_BATCH_SIZE = 32;\n\n// ONNX model file paths per known model\nconst ONNX_MODEL_PATHS: Record<string, string> = {\n  \"nomic-ai/nomic-embed-text-v1.5\": \"onnx/model.onnx\",\n  \"sentence-transformers/all-MiniLM-L6-v2\": \"onnx/model.onnx\",\n};\n\ninterface OrtSession {\n  run(feeds: Record<string, unknown>): Promise<Record<string, { data: Float32Array; dims: number[] }>>;\n  inputNames: string[];\n  outputNames: string[];\n}\n\ninterface OrtModule {\n  InferenceSession: {\n    create(path: string, options?: Record<string, unknown>): Promise<OrtSession>;\n  };\n  Tensor: new (type: string, data: ArrayLike<number | bigint>, dims: number[]) => unknown;\n}\n\ntype RuntimeLabel = \"native\" | \"wasm\";\n\nasync function resolveOnnxRuntime(): Promise<{ ort: OrtModule; label: RuntimeLabel }> {\n  try {\n    const ort = await import(\"onnxruntime-node\");\n    return { ort: ort as unknown as OrtModule, label: \"native\" };\n  } catch {\n    const ort = await import(\"onnxruntime-web\");\n    return { ort: ort as unknown as OrtModule, label: \"wasm\" };\n  }\n}\n\nasync function downloadFile(url: string, destPath: string): Promise<void> {\n  const response = await fetch(url);\n  if (!response.ok) throw new Error(`Download failed (${response.status}): ${url}`);\n  if (!response.body) throw new Error(`No response body: ${url}`);\n  const fileStream = createWriteStream(destPath);\n  await streamPipeline(Readable.fromWeb(response.body as never), fileStream);\n}\n\nexport class Embedder {\n  private model: string;\n  private session: OrtSession | null = null;\n  private tokenizer: Awaited<ReturnType<typeof AutoTokenizer.from_pretrained>> | null = null;\n  private ort: OrtModule | null = null;\n  private dimensions = 0;\n  private runtimeLabel: RuntimeLabel = \"wasm\";\n  private initialized = false;\n  private numWorkers: number;\n  private batchSize: number;\n  private modelPath = \"\";\n\n  constructor(\n    model: string = DEFAULT_MODEL,\n    numWorkers: number = DEFAULT_WORKERS,\n    batchSize: number = DEFAULT_BATCH_SIZE\n  ) {\n    this.model = model;\n    this.numWorkers = numWorkers;\n    this.batchSize = batchSize;\n  }\n\n  async init(): Promise<void> {\n    if (this.initialized) return;\n\n    const modelDir = join(CACHE_DIR, this.model.replace(/\\//g, \"--\"));\n    await mkdir(modelDir, { recursive: true });\n\n    // Resolve ONNX runtime (native C++ or WASM fallback)\n    const { ort, label } = await resolveOnnxRuntime();\n    this.ort = ort;\n    this.runtimeLabel = label;\n\n    // Download ONNX model if not cached\n    this.modelPath = join(modelDir, \"model.onnx\");\n    const modelPath = this.modelPath;\n    if (!existsSync(modelPath)) {\n      const onnxSubpath = ONNX_MODEL_PATHS[this.model] ?? \"onnx/model.onnx\";\n      const url = `https://huggingface.co/${this.model}/resolve/main/${onnxSubpath}`;\n      process.stderr.write(`Downloading ONNX model: ${this.model}...\\n`);\n      await downloadFile(url, modelPath);\n      process.stderr.write(`Model downloaded to ${modelDir}\\n`);\n    }\n\n    // Load tokenizer (uses HF transformers tokenizer infrastructure)\n    this.tokenizer = await AutoTokenizer.from_pretrained(this.model, {\n      cache_dir: CACHE_DIR,\n    });\n\n    // Create ONNX inference session\n    this.session = await ort.InferenceSession.create(modelPath, {\n      executionProviders: [label === \"native\" ? \"cpu\" : \"wasm\"],\n    });\n\n    // Determine dimensions from a test embedding\n    const test = await this.embed(\"test\");\n    this.dimensions = test.length;\n    this.initialized = true;\n\n    process.stderr.write(`Embedder ready (${label} runtime, ${this.dimensions}d, batch_size=${this.batchSize})\\n`);\n  }\n\n  async embed(text: string): Promise<Float32Array> {\n    if (!this.session || !this.tokenizer || !this.ort)\n      throw new Error(\"Embedder not initialized. Call init() first.\");\n\n    // Tokenize\n    const encoded = await this.tokenizer(text, {\n      padding: true,\n      truncation: true,\n      max_length: 512,\n      return_tensor: false,\n    });\n\n    const inputIdsRaw: number[] = Array.from(encoded.input_ids.data ?? encoded.input_ids);\n    const attentionMaskRaw: number[] = Array.from(encoded.attention_mask.data ?? encoded.attention_mask);\n    const seqLen = inputIdsRaw.length;\n\n    // Build ONNX input tensors (most models expect int64)\n    const inputIds = new this.ort.Tensor(\n      \"int64\",\n      BigInt64Array.from(inputIdsRaw.map(BigInt)),\n      [1, seqLen]\n    );\n    const attentionMask = new this.ort.Tensor(\n      \"int64\",\n      BigInt64Array.from(attentionMaskRaw.map(BigInt)),\n      [1, seqLen]\n    );\n\n    const feeds: Record<string, unknown> = { input_ids: inputIds, attention_mask: attentionMask };\n\n    // Some models need token_type_ids\n    if (this.session.inputNames.includes(\"token_type_ids\")) {\n      feeds.token_type_ids = new this.ort.Tensor(\n        \"int64\",\n        new BigInt64Array(seqLen),\n        [1, seqLen]\n      );\n    }\n\n    // Run inference\n    const output = await this.session.run(feeds);\n    const outputTensor = output[this.session.outputNames[0]];\n    const hiddenSize = outputTensor.dims[outputTensor.dims.length - 1];\n\n    // Mean pooling with attention mask + L2 normalization\n    return this.meanPoolAndNormalize(outputTensor.data, attentionMaskRaw, seqLen, hiddenSize);\n  }\n\n  private meanPoolAndNormalize(\n    embeddings: Float32Array,\n    attentionMask: number[],\n    seqLen: number,\n    hiddenSize: number\n  ): Float32Array {\n    const result = new Float32Array(hiddenSize);\n    let maskSum = 0;\n\n    for (let t = 0; t < seqLen; t++) {\n      const mask = attentionMask[t];\n      maskSum += mask;\n      const offset = t * hiddenSize;\n      for (let d = 0; d < hiddenSize; d++) {\n        result[d] += embeddings[offset + d] * mask;\n      }\n    }\n\n    if (maskSum > 0) {\n      for (let d = 0; d < hiddenSize; d++) result[d] /= maskSum;\n    }\n\n    // L2 normalize\n    let norm = 0;\n    for (let d = 0; d < hiddenSize; d++) norm += result[d] * result[d];\n    norm = Math.sqrt(norm);\n    if (norm > 0) {\n      for (let d = 0; d < hiddenSize; d++) result[d] /= norm;\n    }\n\n    return result;\n  }\n\n  // Mean pool + L2 normalize the output of a batched ONNX forward pass.\n  // outputData: flat Float32Array of shape [batchSize, seqLen, hiddenSize]\n  // maskData:   flat number[] of shape [batchSize, seqLen]\n  private meanPoolAndNormalizeMany(\n    outputData: Float32Array,\n    maskData: number[],\n    batchSize: number,\n    seqLen: number,\n    hiddenSize: number\n  ): Float32Array[] {\n    const results: Float32Array[] = [];\n    for (let b = 0; b < batchSize; b++) {\n      const result = new Float32Array(hiddenSize);\n      let maskSum = 0;\n      for (let t = 0; t < seqLen; t++) {\n        const mask = maskData[b * seqLen + t];\n        maskSum += mask;\n        const offset = (b * seqLen + t) * hiddenSize;\n        for (let d = 0; d < hiddenSize; d++) {\n          result[d] += outputData[offset + d] * mask;\n        }\n      }\n      if (maskSum > 0) {\n        for (let d = 0; d < hiddenSize; d++) result[d] /= maskSum;\n      }\n      // L2 normalize\n      let norm = 0;\n      for (let d = 0; d < hiddenSize; d++) norm += result[d] * result[d];\n      norm = Math.sqrt(norm);\n      if (norm > 0) {\n        for (let d = 0; d < hiddenSize; d++) result[d] /= norm;\n      }\n      results.push(result);\n    }\n    return results;\n  }\n\n  // Embed a sub-batch of texts (length <= batchSize) in a single ONNX forward pass.\n  //\n  // Tokenizes each text individually (well-defined output format for all HF versions),\n  // then manually pads to the longest sequence in the batch and builds a [n, seqLen]\n  // tensor for one ONNX call. The speedup is from batching the ONNX inference —\n  // individual tokenization is negligible (<1ms each).\n  private async embedSubBatch(texts: string[]): Promise<Float32Array[]> {\n    if (!this.session || !this.tokenizer || !this.ort)\n      throw new Error(\"Embedder not initialized. Call init() first.\");\n\n    const n = texts.length;\n\n    // Tokenize each text individually — avoids ambiguous batch tokenizer output format\n    const encodings = await Promise.all(\n      texts.map((text) =>\n        this.tokenizer!(text, {\n          padding: false,\n          truncation: true,\n          max_length: 512,\n          return_tensor: false,\n        })\n      )\n    );\n\n    // Extract flat token arrays and find max sequence length for this batch\n    const tokenized = encodings.map((enc) => ({\n      ids: Array.from(enc.input_ids.data ?? enc.input_ids) as number[],\n      mask: Array.from(enc.attention_mask.data ?? enc.attention_mask) as number[],\n    }));\n    const seqLen = Math.max(...tokenized.map((t) => t.ids.length));\n\n    // Build flat padded tensors [n * seqLen] — pad with 0 (PAD token, zero attention)\n    const flatIds = new BigInt64Array(n * seqLen);\n    const flatMask = new BigInt64Array(n * seqLen);\n    const flatMaskNums = new Array<number>(n * seqLen).fill(0);\n\n    for (let i = 0; i < n; i++) {\n      const { ids, mask } = tokenized[i];\n      for (let j = 0; j < ids.length; j++) {\n        flatIds[i * seqLen + j] = BigInt(ids[j]);\n        flatMask[i * seqLen + j] = BigInt(mask[j]);\n        flatMaskNums[i * seqLen + j] = mask[j];\n      }\n      // Positions beyond ids.length remain 0 (padding)\n    }\n\n    // Build batched ONNX tensors [n, seqLen]\n    const inputIds = new this.ort.Tensor(\"int64\", flatIds, [n, seqLen]);\n    const attentionMask = new this.ort.Tensor(\"int64\", flatMask, [n, seqLen]);\n\n    const feeds: Record<string, unknown> = { input_ids: inputIds, attention_mask: attentionMask };\n\n    if (this.session.inputNames.includes(\"token_type_ids\")) {\n      feeds.token_type_ids = new this.ort.Tensor(\n        \"int64\",\n        new BigInt64Array(n * seqLen),\n        [n, seqLen]\n      );\n    }\n\n    // Single forward pass → output shape [n, seqLen, hiddenSize]\n    const output = await this.session.run(feeds);\n    const outputTensor = output[this.session.outputNames[0]];\n    const hiddenSize = outputTensor.dims[outputTensor.dims.length - 1];\n\n    return this.meanPoolAndNormalizeMany(\n      outputTensor.data,\n      flatMaskNums,\n      n,\n      seqLen,\n      hiddenSize\n    );\n  }\n\n  async embedBatch(\n    texts: string[],\n    onProgress?: (embedded: number, total: number, subBatch?: Float32Array[]) => Promise<void> | void\n  ): Promise<Float32Array[]> {\n    // Workers path (disabled by default; kept for --workers N users)\n    if (this.numWorkers > 1 && texts.length >= this.numWorkers * 2) {\n      return this.embedBatchParallel(texts, onProgress);\n    }\n\n    // True batched inference: slice into sub-batches and run one ONNX call each\n    const results: Float32Array[] = [];\n    for (let i = 0; i < texts.length; i += this.batchSize) {\n      const subBatch = texts.slice(i, i + this.batchSize);\n      const embeddings = await this.embedSubBatch(subBatch);\n      results.push(...embeddings);\n      await onProgress?.(Math.min(i + subBatch.length, texts.length), texts.length, embeddings);\n    }\n    return results;\n  }\n\n  private async embedBatchParallel(\n    texts: string[],\n    onProgress?: (embedded: number, total: number, subBatch?: Float32Array[]) => Promise<void> | void\n  ): Promise<Float32Array[]> {\n    // Resolve worker script path. With tsup splitting, embedder code may land\n    // in a top-level chunk (dist/chunk-*.js) rather than dist/core/index.js,\n    // so we try two locations: adjacent to this chunk, and dist/core/ relative\n    // to the package root (two levels up from a dist/ chunk file).\n    const thisDir = dirname(fileURLToPath(import.meta.url));\n    let workerPath = join(thisDir, \"embed-worker.js\");\n    if (!existsSync(workerPath)) {\n      // Chunk file at dist/ level — worker is in dist/core/\n      workerPath = join(thisDir, \"core\", \"embed-worker.js\");\n    }\n\n    if (!existsSync(workerPath)) {\n      // Fallback to serial batched if worker script not found\n      process.stderr.write(\"Worker script not found, falling back to batched embedding\\n\");\n      return this.embedBatch(texts, onProgress);\n    }\n\n    // Split texts into chunks for each worker\n    const chunkSize = Math.ceil(texts.length / this.numWorkers);\n    const chunks: { texts: string[]; startIndex: number }[] = [];\n    for (let i = 0; i < texts.length; i += chunkSize) {\n      chunks.push({ texts: texts.slice(i, i + chunkSize), startIndex: i });\n    }\n\n    const allResults = new Array<Float32Array>(texts.length);\n    let totalDone = 0;\n\n    const workerPromises = chunks.map((chunk) => {\n      return new Promise<void>((resolve, reject) => {\n        const worker = new Worker(workerPath, {\n          workerData: {\n            modelPath: this.modelPath,\n            modelName: this.model,\n            cacheDir: CACHE_DIR,\n            runtimeLabel: this.runtimeLabel,\n            batchSize: this.batchSize,\n          },\n        });\n\n        worker.on(\"message\", (msg: any) => {\n          if (msg.type === \"ready\") {\n            worker.postMessage({ type: \"embed\", texts: chunk.texts, startIndex: chunk.startIndex });\n          } else if (msg.type === \"progress\") {\n            totalDone++;\n            onProgress?.(totalDone, texts.length);\n          } else if (msg.type === \"result\") {\n            for (let i = 0; i < msg.embeddings.length; i++) {\n              allResults[chunk.startIndex + i] = new Float32Array(msg.embeddings[i]);\n            }\n            worker.terminate();\n            resolve();\n          } else if (msg.type === \"error\") {\n            worker.terminate();\n            reject(new Error(msg.error));\n          }\n        });\n\n        worker.on(\"error\", (err) => {\n          worker.terminate();\n          reject(err);\n        });\n      });\n    });\n\n    await Promise.all(workerPromises);\n    return allResults;\n  }\n\n  getDimensions(): number {\n    return this.dimensions;\n  }\n\n  getModel(): string {\n    return this.model;\n  }\n\n  getRuntime(): RuntimeLabel {\n    return this.runtimeLabel;\n  }\n\n  async saveEmbeddings(\n    embeddings: Map<string, Float32Array>,\n    indexPath: string\n  ): Promise<void> {\n    const entries: Array<{ key: string; data: number[] }> = [];\n    for (const [key, vec] of embeddings) {\n      entries.push({ key, data: Array.from(vec) });\n    }\n    await writeFile(join(indexPath, \"embeddings.json\"), JSON.stringify(entries));\n  }\n\n  async loadEmbeddings(\n    indexPath: string\n  ): Promise<Map<string, Float32Array>> {\n    const filePath = join(indexPath, \"embeddings.json\");\n    if (!existsSync(filePath)) return new Map();\n\n    const raw = await readFile(filePath, \"utf-8\");\n    const entries: Array<{ key: string; data: number[] }> = JSON.parse(raw);\n    const map = new Map<string, Float32Array>();\n    for (const entry of entries) {\n      map.set(entry.key, new Float32Array(entry.data));\n    }\n    return map;\n  }\n}\n","import Graph from \"graphology\";\nimport { bfsFromNode } from \"graphology-traversal\";\nimport { bidirectional } from \"graphology-shortest-path\";\nimport type { IndexedDocument, GraphNode, GraphEdge, GraphStats } from \"./types.js\";\nimport { readFile, writeFile } from \"node:fs/promises\";\nimport { join } from \"node:path\";\nimport { existsSync } from \"node:fs\";\n\nexport class GraphBuilder {\n  private graph: Graph;\n\n  constructor() {\n    this.graph = new Graph({ type: \"directed\", multi: false });\n  }\n\n  buildFromDocuments(documents: IndexedDocument[]): void {\n    this.graph.clear();\n\n    // Add nodes\n    for (const doc of documents) {\n      this.graph.addNode(doc.path, {\n        title: doc.title,\n        tags: doc.tags,\n      });\n    }\n\n    const pathLookup = new Map<string, string>();\n    for (const doc of documents) {\n      const nameNoExt = doc.path.replace(/\\.md$/, \"\");\n      const basename = nameNoExt.split(\"/\").pop()!;\n      pathLookup.set(basename.toLowerCase(), doc.path);\n      pathLookup.set(nameNoExt.toLowerCase(), doc.path);\n    }\n\n    // Add wikilink edges\n    for (const doc of documents) {\n      for (const link of doc.wikilinks) {\n        const target = pathLookup.get(link.toLowerCase());\n        if (target && target !== doc.path && !this.graph.hasEdge(doc.path, target)) {\n          this.graph.addEdge(doc.path, target, { type: \"wikilink\", weight: 1.0 });\n        }\n      }\n    }\n\n    // Add tag-based edges\n    const tagToNotes = new Map<string, string[]>();\n    for (const doc of documents) {\n      for (const tag of doc.tags) {\n        const notes = tagToNotes.get(tag) || [];\n        notes.push(doc.path);\n        tagToNotes.set(tag, notes);\n      }\n    }\n\n    for (const [, notes] of tagToNotes) {\n      for (let i = 0; i < notes.length; i++) {\n        for (let j = i + 1; j < notes.length; j++) {\n          if (!this.graph.hasEdge(notes[i], notes[j])) {\n            this.graph.addEdge(notes[i], notes[j], { type: \"tag\", weight: 0.5 });\n          }\n          if (!this.graph.hasEdge(notes[j], notes[i])) {\n            this.graph.addEdge(notes[j], notes[i], { type: \"tag\", weight: 0.5 });\n          }\n        }\n      }\n    }\n  }\n\n  backlinks(notePath: string): GraphNode[] {\n    if (!this.graph.hasNode(notePath)) return [];\n    return this.graph.inNeighbors(notePath).map((n) => this.nodeToGraphNode(n));\n  }\n\n  forwardlinks(notePath: string): GraphNode[] {\n    if (!this.graph.hasNode(notePath)) return [];\n    return this.graph.outNeighbors(notePath).map((n) => this.nodeToGraphNode(n));\n  }\n\n  findPath(from: string, to: string): string[] | null {\n    if (!this.graph.hasNode(from) || !this.graph.hasNode(to)) return null;\n    const path = bidirectional(this.graph, from, to);\n    return path;\n  }\n\n  searchGraph(concept: string, maxDepth = 2): GraphNode[] {\n    const startNodes = this.graph\n      .nodes()\n      .filter((n) => {\n        const attrs = this.graph.getNodeAttributes(n);\n        return (\n          n.toLowerCase().includes(concept.toLowerCase()) ||\n          attrs.title?.toLowerCase().includes(concept.toLowerCase()) ||\n          attrs.tags?.some((t: string) => t.toLowerCase().includes(concept.toLowerCase()))\n        );\n      });\n\n    const visited = new Set<string>();\n    for (const start of startNodes) {\n      let depth = 0;\n      bfsFromNode(this.graph, start, (node) => {\n        visited.add(node);\n        depth++;\n        return depth > maxDepth;\n      });\n    }\n\n    return [...visited].map((n) => this.nodeToGraphNode(n));\n  }\n\n  statistics(): GraphStats {\n    const nodes = this.graph.order;\n    const edges = this.graph.size;\n    const orphans = this.graph.nodes().filter(\n      (n) => this.graph.degree(n) === 0\n    );\n\n    const connections = this.graph.nodes().map((n) => ({\n      path: n,\n      connections: this.graph.degree(n),\n    }));\n    connections.sort((a, b) => b.connections - a.connections);\n\n    const maxPossibleEdges = nodes * (nodes - 1);\n    const density = maxPossibleEdges > 0 ? edges / maxPossibleEdges : 0;\n\n    return {\n      totalNodes: nodes,\n      totalEdges: edges,\n      orphanCount: orphans.length,\n      mostConnected: connections.slice(0, 10),\n      density,\n    };\n  }\n\n  private nodeToGraphNode(nodePath: string): GraphNode {\n    const attrs = this.graph.getNodeAttributes(nodePath);\n    return {\n      path: nodePath,\n      title: attrs.title || nodePath,\n      tags: attrs.tags || [],\n      linkCount: this.graph.outDegree(nodePath),\n      backlinkCount: this.graph.inDegree(nodePath),\n    };\n  }\n\n  async save(indexPath: string): Promise<void> {\n    const data = this.graph.export();\n    await writeFile(join(indexPath, \"graph.json\"), JSON.stringify(data));\n  }\n\n  async load(indexPath: string): Promise<boolean> {\n    const filePath = join(indexPath, \"graph.json\");\n    if (!existsSync(filePath)) return false;\n\n    const raw = await readFile(filePath, \"utf-8\");\n    const data = JSON.parse(raw);\n    this.graph.import(data);\n    return true;\n  }\n\n  getGraph(): Graph {\n    return this.graph;\n  }\n}\n","import hnswlib from \"hnswlib-node\";\nconst { HierarchicalNSW } = hnswlib;\nimport { readFile, writeFile } from \"node:fs/promises\";\nimport { join } from \"node:path\";\nimport { existsSync } from \"node:fs\";\nimport type { SearchResult } from \"./types.js\";\n\ninterface ChunkMeta {\n  docPath: string;\n  chunkIndex: number;\n  text: string;\n}\n\nexport class VectorIndex {\n  private index: InstanceType<typeof HierarchicalNSW> | null = null;\n  private dimensions: number;\n  private chunkMeta: ChunkMeta[] = [];\n\n  constructor(dimensions: number) {\n    this.dimensions = dimensions;\n  }\n\n  build(\n    embeddings: Float32Array[],\n    meta: ChunkMeta[]\n  ): void {\n    if (embeddings.length === 0) {\n      this.index = null;\n      this.chunkMeta = [];\n      return;\n    }\n\n    this.index = new HierarchicalNSW(\"cosine\", this.dimensions);\n    this.index.initIndex(embeddings.length);\n\n    for (let i = 0; i < embeddings.length; i++) {\n      this.index.addPoint(Array.from(embeddings[i]), i);\n    }\n\n    this.chunkMeta = meta;\n  }\n\n  search(queryEmbedding: Float32Array, k: number = 10): SearchResult[] {\n    if (!this.index || this.chunkMeta.length === 0) return [];\n\n    const numResults = Math.min(k, this.chunkMeta.length);\n    const result = this.index.searchKnn(Array.from(queryEmbedding), numResults);\n\n    const seen = new Set<string>();\n    const results: SearchResult[] = [];\n\n    for (let i = 0; i < result.neighbors.length; i++) {\n      const idx = result.neighbors[i];\n      const meta = this.chunkMeta[idx];\n      if (!meta || seen.has(meta.docPath)) continue;\n      seen.add(meta.docPath);\n\n      results.push({\n        path: meta.docPath,\n        title: meta.docPath,\n        score: 1 - result.distances[i],\n        snippet: meta.text.slice(0, 200),\n        matchedChunk: meta.text,\n      });\n    }\n\n    return results;\n  }\n\n  async save(indexPath: string): Promise<void> {\n    if (!this.index) return;\n\n    this.index.writeIndexSync(join(indexPath, \"hnsw.bin\"));\n    await writeFile(\n      join(indexPath, \"hnsw-meta.json\"),\n      JSON.stringify(this.chunkMeta)\n    );\n  }\n\n  async load(indexPath: string): Promise<boolean> {\n    const hnswPath = join(indexPath, \"hnsw.bin\");\n    const metaPath = join(indexPath, \"hnsw-meta.json\");\n\n    if (!existsSync(hnswPath) || !existsSync(metaPath)) return false;\n\n    const raw = await readFile(metaPath, \"utf-8\");\n    this.chunkMeta = JSON.parse(raw);\n\n    this.index = new HierarchicalNSW(\"cosine\", this.dimensions);\n    this.index.initIndex(this.chunkMeta.length);\n    this.index.readIndexSync(hnswPath);\n\n    return true;\n  }\n\n  getChunkMeta(): ChunkMeta[] {\n    return this.chunkMeta;\n  }\n}\n","import type { IndexedDocument, SearchResult, SearchTextOptions } from \"./types.js\";\nimport { minimatch } from \"minimatch\";\n\nexport class TextSearch {\n  private documents: IndexedDocument[] = [];\n\n  setDocuments(documents: IndexedDocument[]): void {\n    this.documents = documents;\n  }\n\n  search(options: SearchTextOptions): SearchResult[] {\n    const { pattern, regex, caseSensitive, pathGlob, tagFilter, limit = 20 } = options;\n\n    let matcher: (text: string) => { matched: boolean; index: number };\n\n    if (regex) {\n      const flags = caseSensitive ? \"g\" : \"gi\";\n      const re = new RegExp(pattern, flags);\n      matcher = (text) => {\n        re.lastIndex = 0;\n        const m = re.exec(text);\n        return { matched: !!m, index: m?.index ?? -1 };\n      };\n    } else {\n      const needle = caseSensitive ? pattern : pattern.toLowerCase();\n      matcher = (text) => {\n        const haystack = caseSensitive ? text : text.toLowerCase();\n        const idx = haystack.indexOf(needle);\n        return { matched: idx >= 0, index: idx };\n      };\n    }\n\n    const results: SearchResult[] = [];\n\n    for (const doc of this.documents) {\n      // Path filter\n      if (pathGlob && !minimatch(doc.path, pathGlob)) continue;\n\n      // Tag filter\n      if (tagFilter?.length) {\n        const hasTag = tagFilter.some((t) => doc.tags.includes(t));\n        if (!hasTag) continue;\n      }\n\n      const { matched, index } = matcher(doc.content);\n      if (!matched) continue;\n\n      const snippetStart = Math.max(0, index - 80);\n      const snippetEnd = Math.min(doc.content.length, index + 120);\n      const snippet = doc.content.slice(snippetStart, snippetEnd).trim();\n\n      results.push({\n        path: doc.path,\n        title: doc.title,\n        score: 1.0,\n        snippet: (snippetStart > 0 ? \"...\" : \"\") + snippet + (snippetEnd < doc.content.length ? \"...\" : \"\"),\n      });\n\n      if (results.length >= limit) break;\n    }\n\n    return results;\n  }\n}\n","import { readFile, writeFile, unlink, rename, mkdir } from \"node:fs/promises\";\nimport { dirname, join, relative } from \"node:path\";\nimport { existsSync } from \"node:fs\";\nimport { glob } from \"glob\";\nimport matter from \"gray-matter\";\nimport type { UpdateNoteOptions } from \"./types.js\";\n\nexport class NoteCrud {\n  private notesPath: string;\n\n  constructor(notesPath: string) {\n    this.notesPath = notesPath;\n  }\n\n  async create(\n    relativePath: string,\n    content: string,\n    frontmatter?: Record<string, unknown>\n  ): Promise<string> {\n    const absPath = join(this.notesPath, relativePath);\n    if (existsSync(absPath)) {\n      throw new Error(`Note already exists: ${relativePath}`);\n    }\n\n    await mkdir(dirname(absPath), { recursive: true });\n\n    let fileContent: string;\n    if (frontmatter && Object.keys(frontmatter).length > 0) {\n      fileContent = matter.stringify(content, frontmatter);\n    } else {\n      fileContent = content;\n    }\n\n    await writeFile(absPath, fileContent, \"utf-8\");\n    return relativePath;\n  }\n\n  async read(relativePath: string): Promise<string> {\n    const absPath = join(this.notesPath, relativePath);\n    return readFile(absPath, \"utf-8\");\n  }\n\n  async readMultiple(paths: string[]): Promise<Map<string, string>> {\n    const results = new Map<string, string>();\n    await Promise.all(\n      paths.map(async (p) => {\n        try {\n          const content = await this.read(p);\n          results.set(p, content);\n        } catch {\n          results.set(p, `[Error: could not read ${p}]`);\n        }\n      })\n    );\n    return results;\n  }\n\n  async update(\n    relativePath: string,\n    content: string,\n    options: UpdateNoteOptions\n  ): Promise<void> {\n    const absPath = join(this.notesPath, relativePath);\n    if (!existsSync(absPath)) {\n      throw new Error(`Note does not exist: ${relativePath}`);\n    }\n\n    const existing = await readFile(absPath, \"utf-8\");\n\n    let updated: string;\n\n    switch (options.mode) {\n      case \"overwrite\":\n        updated = content;\n        break;\n\n      case \"append\":\n        updated = existing + \"\\n\" + content;\n        break;\n\n      case \"prepend\": {\n        const { data, content: body } = matter(existing);\n        const newBody = content + \"\\n\" + body;\n        updated = Object.keys(data).length > 0 ? matter.stringify(newBody, data) : newBody;\n        break;\n      }\n\n      case \"patch-by-heading\": {\n        if (!options.heading) throw new Error(\"patch-by-heading requires a heading\");\n        updated = this.patchByHeading(existing, options.heading, content);\n        break;\n      }\n    }\n\n    await writeFile(absPath, updated, \"utf-8\");\n  }\n\n  async delete(relativePath: string): Promise<void> {\n    const absPath = join(this.notesPath, relativePath);\n    if (!existsSync(absPath)) {\n      throw new Error(`Note does not exist: ${relativePath}`);\n    }\n    await unlink(absPath);\n  }\n\n  async move(fromPath: string, toPath: string): Promise<void> {\n    const absFrom = join(this.notesPath, fromPath);\n    const absTo = join(this.notesPath, toPath);\n\n    if (!existsSync(absFrom)) {\n      throw new Error(`Note does not exist: ${fromPath}`);\n    }\n    if (existsSync(absTo)) {\n      throw new Error(`Destination already exists: ${toPath}`);\n    }\n\n    await mkdir(dirname(absTo), { recursive: true });\n    await rename(absFrom, absTo);\n\n    // Update wikilinks in other files that reference the old path\n    await this.updateWikilinksAfterMove(fromPath, toPath);\n  }\n\n  private async updateWikilinksAfterMove(\n    oldPath: string,\n    newPath: string\n  ): Promise<void> {\n    const oldName = oldPath.replace(/\\.md$/, \"\").split(\"/\").pop()!;\n    const newName = newPath.replace(/\\.md$/, \"\").split(\"/\").pop()!;\n\n    if (oldName === newName) return;\n\n    const files = await glob(\"**/*.md\", { cwd: this.notesPath });\n\n    for (const file of files) {\n      const absPath = join(this.notesPath, file);\n      const content = await readFile(absPath, \"utf-8\");\n\n      const pattern = new RegExp(`\\\\[\\\\[${escapeRegex(oldName)}(\\\\|[^\\\\]]*)?\\\\]\\\\]`, \"g\");\n      if (!pattern.test(content)) continue;\n\n      const updated = content.replace(pattern, `[[${newName}$1]]`);\n      await writeFile(absPath, updated, \"utf-8\");\n    }\n  }\n\n  private patchByHeading(\n    content: string,\n    heading: string,\n    newContent: string\n  ): string {\n    const lines = content.split(\"\\n\");\n    const headingPattern = new RegExp(`^#{1,6}\\\\s+${escapeRegex(heading)}\\\\s*$`, \"i\");\n\n    let headingIndex = -1;\n    let headingLevel = 0;\n\n    for (let i = 0; i < lines.length; i++) {\n      if (headingPattern.test(lines[i])) {\n        headingIndex = i;\n        const match = lines[i].match(/^(#{1,6})\\s+/);\n        headingLevel = match ? match[1].length : 1;\n        break;\n      }\n    }\n\n    if (headingIndex === -1) {\n      throw new Error(`Heading not found: ${heading}`);\n    }\n\n    // Find the end of this section (next heading of same or higher level)\n    let endIndex = lines.length;\n    for (let i = headingIndex + 1; i < lines.length; i++) {\n      const match = lines[i].match(/^(#{1,6})\\s+/);\n      if (match && match[1].length <= headingLevel) {\n        endIndex = i;\n        break;\n      }\n    }\n\n    const before = lines.slice(0, headingIndex + 1);\n    const after = lines.slice(endIndex);\n\n    return [...before, \"\", newContent, \"\", ...after].join(\"\\n\");\n  }\n}\n\nfunction escapeRegex(str: string): string {\n  return str.replace(/[.*+?^${}()|[\\]\\\\]/g, \"\\\\$&\");\n}\n","import { readFile, writeFile } from \"node:fs/promises\";\nimport { join } from \"node:path\";\nimport { glob } from \"glob\";\nimport matter from \"gray-matter\";\n\nexport class FrontmatterManager {\n  private notesPath: string;\n\n  constructor(notesPath: string) {\n    this.notesPath = notesPath;\n  }\n\n  async get(relativePath: string): Promise<Record<string, unknown>> {\n    const absPath = join(this.notesPath, relativePath);\n    const raw = await readFile(absPath, \"utf-8\");\n    const { data } = matter(raw);\n    return data;\n  }\n\n  async update(\n    relativePath: string,\n    fields: Record<string, unknown>\n  ): Promise<void> {\n    const absPath = join(this.notesPath, relativePath);\n    const raw = await readFile(absPath, \"utf-8\");\n    const { data, content } = matter(raw);\n\n    for (const [key, value] of Object.entries(fields)) {\n      if (value === null || value === undefined) {\n        delete data[key];\n      } else {\n        data[key] = value;\n      }\n    }\n\n    const updated = matter.stringify(content, data);\n    await writeFile(absPath, updated, \"utf-8\");\n  }\n}\n\nexport class TagManager {\n  private notesPath: string;\n\n  constructor(notesPath: string) {\n    this.notesPath = notesPath;\n  }\n\n  async list(relativePath: string): Promise<string[]> {\n    const absPath = join(this.notesPath, relativePath);\n    const raw = await readFile(absPath, \"utf-8\");\n    const { data, content } = matter(raw);\n\n    const fmTags = Array.isArray(data.tags) ? (data.tags as string[]) : [];\n    const inlineTags = [...content.matchAll(/(?:^|\\s)#([a-zA-Z][\\w-/]*)/g)].map(\n      (m) => m[1]\n    );\n\n    return [...new Set([...fmTags, ...inlineTags])];\n  }\n\n  async add(relativePath: string, tags: string[]): Promise<void> {\n    const absPath = join(this.notesPath, relativePath);\n    const raw = await readFile(absPath, \"utf-8\");\n    const { data, content } = matter(raw);\n\n    const existing = Array.isArray(data.tags) ? (data.tags as string[]) : [];\n    const merged = [...new Set([...existing, ...tags])];\n    data.tags = merged;\n\n    const updated = matter.stringify(content, data);\n    await writeFile(absPath, updated, \"utf-8\");\n  }\n\n  async remove(relativePath: string, tags: string[]): Promise<void> {\n    const absPath = join(this.notesPath, relativePath);\n    const raw = await readFile(absPath, \"utf-8\");\n    const { data, content } = matter(raw);\n\n    // Remove from frontmatter\n    if (Array.isArray(data.tags)) {\n      data.tags = (data.tags as string[]).filter((t) => !tags.includes(t));\n    }\n\n    // Remove inline tags\n    let updatedContent = content;\n    for (const tag of tags) {\n      const pattern = new RegExp(`(^|\\\\s)#${escapeRegex(tag)}(?=\\\\s|$)`, \"g\");\n      updatedContent = updatedContent.replace(pattern, \"$1\");\n    }\n\n    const updated = matter.stringify(updatedContent, data);\n    await writeFile(absPath, updated, \"utf-8\");\n  }\n\n  async renameVaultWide(oldTag: string, newTag: string): Promise<number> {\n    const files = await glob(\"**/*.md\", { cwd: this.notesPath });\n    let count = 0;\n\n    for (const file of files) {\n      const absPath = join(this.notesPath, file);\n      const raw = await readFile(absPath, \"utf-8\");\n      const { data, content } = matter(raw);\n      let changed = false;\n\n      // Rename in frontmatter\n      if (Array.isArray(data.tags)) {\n        const idx = (data.tags as string[]).indexOf(oldTag);\n        if (idx >= 0) {\n          (data.tags as string[])[idx] = newTag;\n          changed = true;\n        }\n      }\n\n      // Rename inline tags\n      const pattern = new RegExp(`(^|\\\\s)#${escapeRegex(oldTag)}(?=\\\\s|$)`, \"g\");\n      const updatedContent = content.replace(pattern, `$1#${newTag}`);\n      if (updatedContent !== content) changed = true;\n\n      if (changed) {\n        const updated = matter.stringify(updatedContent, data);\n        await writeFile(absPath, updated, \"utf-8\");\n        count++;\n      }\n    }\n\n    return count;\n  }\n}\n\nfunction escapeRegex(str: string): string {\n  return str.replace(/[.*+?^${}()|[\\]\\\\]/g, \"\\\\$&\");\n}\n","import { watch, type FSWatcher } from \"chokidar\";\nimport { EventEmitter } from \"node:events\";\n\nexport interface WatcherEvents {\n  changed: (paths: string[]) => void;\n  error: (error: Error) => void;\n}\n\nexport class Watcher extends EventEmitter {\n  private notesPath: string;\n  private fsWatcher: FSWatcher | null = null;\n  private debounceMs: number;\n  private pendingChanges = new Set<string>();\n  private debounceTimer: ReturnType<typeof setTimeout> | null = null;\n  private readyPromise: Promise<void> | null = null;\n  private usePolling: boolean;\n\n  constructor(notesPath: string, debounceMs: number = 500, usePolling: boolean = false) {\n    super();\n    this.notesPath = notesPath;\n    this.debounceMs = debounceMs;\n    this.usePolling = usePolling;\n  }\n\n  start(): void {\n    if (this.fsWatcher) return;\n\n    this.fsWatcher = watch(\"**/*.md\", {\n      cwd: this.notesPath,\n      ignoreInitial: true,\n      followSymlinks: true,\n      ignored: [\n        \"**/node_modules/**\",\n        \"**/.semantic-pages-index/**\",\n        \"**/.git/**\",\n      ],\n      ...(this.usePolling ? { usePolling: true, interval: 100 } : {}),\n    });\n\n    this.readyPromise = new Promise<void>((resolve) => {\n      this.fsWatcher!.on(\"ready\", resolve);\n    });\n\n    this.fsWatcher.on(\"add\", (path) => this.enqueue(path));\n    this.fsWatcher.on(\"change\", (path) => this.enqueue(path));\n    this.fsWatcher.on(\"unlink\", (path) => this.enqueue(path));\n    this.fsWatcher.on(\"error\", (err) => this.emit(\"error\", err));\n  }\n\n  async ready(): Promise<void> {\n    if (this.readyPromise) await this.readyPromise;\n  }\n\n  stop(): void {\n    if (this.debounceTimer) clearTimeout(this.debounceTimer);\n    this.fsWatcher?.close();\n    this.fsWatcher = null;\n    this.pendingChanges.clear();\n  }\n\n  private enqueue(path: string): void {\n    this.pendingChanges.add(path);\n\n    if (this.debounceTimer) clearTimeout(this.debounceTimer);\n    this.debounceTimer = setTimeout(() => {\n      const paths = [...this.pendingChanges];\n      this.pendingChanges.clear();\n      this.emit(\"changed\", paths);\n    }, this.debounceMs);\n  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package/dist/cli/index.js

@@ -199,7 +199,7 @@ function printToolDetail(name) {
 }
 program.name("semantic-pages").description(
   "Semantic search + knowledge graph MCP server for markdown files\n\n  Start MCP server:  semantic-pages --notes ./vault\n  Show vault stats:  semantic-pages --notes ./vault --stats\n  Force reindex:     semantic-pages --notes ./vault --reindex\n  List MCP tools:    semantic-pages tools\n  Tool details:      semantic-pages tools search_semantic"
-).version("0.1.3");
+).version("0.4.1");
 program.command("tools [name]").description("List all MCP tools, or show details for a specific tool").action((name) => {
   if (name) {
     printToolDetail(name);
@@ -208,7 +208,7 @@ program.command("tools [name]").description("List all MCP tools, or show details
   }
   process.exit(0);
 });
-program.command("serve", { isDefault: true }).description("Start the MCP server (default command)").requiredOption("--notes <path>", "Path to markdown notes directory").option("--reindex", "Force full reindex and exit").option("--stats", "Show vault statistics and exit").option("--model <name>", "Embedding model to use", "nomic-ai/nomic-embed-text-v1.5").option("--workers <n>", "Number of worker threads for parallel embedding", parseInt).option("--no-watch", "Disable file watcher").action(async (opts) => {
+program.command("serve", { isDefault: true }).description("Start the MCP server (default command)").requiredOption("--notes <path>", "Path to markdown notes directory").option("--reindex", "Force full reindex and exit").option("--stats", "Show vault statistics and exit").option("--model <name>", "Embedding model to use", "nomic-ai/nomic-embed-text-v1.5").option("--workers <n>", "Number of worker threads for parallel embedding", parseInt).option("--batch-size <n>", "Texts per ONNX forward pass (default: 32)", parseInt).option("--no-watch", "Disable file watcher").action(async (opts) => {
   const notesPath = resolve(opts.notes);
   if (!existsSync(notesPath)) {
     console.error(`Error: notes directory not found: ${notesPath}`);
@@ -231,6 +231,7 @@ program.command("serve", { isDefault: true }).description("Start the MCP server
       waitForReady: true,
       model: opts.model,
       workers: opts.workers,
+      batchSize: opts.batchSize,
       onProgress: (embedded, total) => {
         process.stderr.write(`\rEmbedding ${embedded}/${total} chunks...`);
       }
@@ -240,7 +241,7 @@ program.command("serve", { isDefault: true }).description("Start the MCP server
     process.exit(0);
   }
   const { startServer } = await import("../mcp/server.js");
-  await startServer(notesPath, { watch: opts.watch, model: opts.model, workers: opts.workers });
+  await startServer(notesPath, { watch: opts.watch, model: opts.model, workers: opts.workers, batchSize: opts.batchSize });
 });
 program.parse();
 //# sourceMappingURL=index.js.map

package/dist/cli/index.js.map

@@ -1 +1 @@
-{"version":3,"sources":["../../src/cli/index.ts"],"sourcesContent":["#!/usr/bin/env node\n\nimport { program } from \"commander\";\nimport { resolve } from \"node:path\";\nimport { existsSync } from \"node:fs\";\n\nconst TOOL_HELP: Record<string, { description: string; args: string; examples: string[] }> = {\n  // Search\n  search_semantic: {\n    description: \"Vector similarity search — find notes by meaning, not just keywords\",\n    args: '{ \"query\": \"string\", \"limit?\": 10 }',\n    examples: [\n      '{ \"query\": \"microservices architecture\", \"limit\": 5 }',\n      '{ \"query\": \"how to deploy to production\" }',\n    ],\n  },\n  search_text: {\n    description: \"Full-text keyword or regex search with optional filters\",\n    args: '{ \"pattern\": \"string\", \"regex?\": false, \"caseSensitive?\": false, \"pathGlob?\": \"string\", \"tagFilter?\": [\"string\"], \"limit?\": 20 }',\n    examples: [\n      '{ \"pattern\": \"RabbitMQ\" }',\n      '{ \"pattern\": \"OAuth\\\\\\\\d\", \"regex\": true }',\n      '{ \"pattern\": \"deploy\", \"pathGlob\": \"devops/**\", \"tagFilter\": [\"kubernetes\"] }',\n    ],\n  },\n  search_graph: {\n    description: \"Graph traversal — find notes connected to a concept via wikilinks and tags\",\n    args: '{ \"concept\": \"string\", \"maxDepth?\": 2 }',\n    examples: [\n      '{ \"concept\": \"microservices\" }',\n      '{ \"concept\": \"auth\", \"maxDepth\": 3 }',\n    ],\n  },\n  search_hybrid: {\n    description: \"Combined semantic + graph search — vector results re-ranked by graph proximity\",\n    args: '{ \"query\": \"string\", \"limit?\": 10 }',\n    examples: [\n      '{ \"query\": \"event driven architecture\", \"limit\": 5 }',\n    ],\n  },\n\n  // Read\n  read_note: {\n    description: \"Read the full content of a specific note by path\",\n    args: '{ \"path\": \"string\" }',\n    examples: [\n      '{ \"path\": \"project-overview.md\" }',\n      '{ \"path\": \"notes/meeting-2024-01-15.md\" }',\n    ],\n  },\n  read_multiple_notes: {\n    description: \"Batch read multiple notes in one call\",\n    args: '{ \"paths\": [\"string\"] }',\n    examples: [\n      '{ \"paths\": [\"overview.md\", \"architecture.md\", \"deployment.md\"] }',\n    ],\n  },\n  list_notes: {\n    description: \"List all indexed notes with metadata (title, tags, link count)\",\n    args: \"{}\",\n    examples: [\"{}\"],\n  },\n\n  // Write\n  create_note: {\n    description: \"Create a new markdown note with optional YAML frontmatter\",\n    args: '{ \"path\": \"string\", \"content\": \"string\", \"frontmatter?\": {} }',\n    examples: [\n      '{ \"path\": \"new-guide.md\", \"content\": \"# Guide\\\\n\\\\nContent here.\" }',\n      '{ \"path\": \"tagged.md\", \"content\": \"Content.\", \"frontmatter\": { \"title\": \"Tagged Note\", \"tags\": [\"test\"] } }',\n    ],\n  },\n  update_note: {\n    description: \"Edit note content — overwrite, append, prepend, or patch by heading\",\n    args: '{ \"path\": \"string\", \"content\": \"string\", \"mode\": \"overwrite|append|prepend|patch-by-heading\", \"heading?\": \"string\" }',\n    examples: [\n      '{ \"path\": \"guide.md\", \"content\": \"New content.\", \"mode\": \"overwrite\" }',\n      '{ \"path\": \"guide.md\", \"content\": \"\\\\n## Appendix\\\\nExtra info.\", \"mode\": \"append\" }',\n      '{ \"path\": \"guide.md\", \"content\": \"Updated architecture section.\", \"mode\": \"patch-by-heading\", \"heading\": \"Architecture\" }',\n    ],\n  },\n  delete_note: {\n    description: \"Delete a note permanently (requires confirm=true)\",\n    args: '{ \"path\": \"string\", \"confirm\": true }',\n    examples: [\n      '{ \"path\": \"old-note.md\", \"confirm\": true }',\n      '{ \"path\": \"old-note.md\", \"confirm\": false }  // returns warning, does not delete',\n    ],\n  },\n  move_note: {\n    description: \"Move or rename a note — automatically updates wikilinks across the vault\",\n    args: '{ \"from\": \"string\", \"to\": \"string\" }',\n    examples: [\n      '{ \"from\": \"user-service.md\", \"to\": \"auth-service.md\" }',\n      '{ \"from\": \"old/note.md\", \"to\": \"new/location/note.md\" }',\n    ],\n  },\n\n  // Metadata\n  get_frontmatter: {\n    description: \"Read parsed YAML frontmatter from a note as JSON\",\n    args: '{ \"path\": \"string\" }',\n    examples: ['{ \"path\": \"project-overview.md\" }'],\n  },\n  update_frontmatter: {\n    description: \"Set or delete YAML frontmatter keys — pass null to delete a key\",\n    args: '{ \"path\": \"string\", \"fields\": {} }',\n    examples: [\n      '{ \"path\": \"note.md\", \"fields\": { \"status\": \"active\", \"priority\": 1 } }',\n      '{ \"path\": \"note.md\", \"fields\": { \"deprecated_field\": null } }  // deletes the key',\n    ],\n  },\n  manage_tags: {\n    description: \"Add, remove, or list tags on a note (frontmatter and inline)\",\n    args: '{ \"path\": \"string\", \"action\": \"add|remove|list\", \"tags?\": [\"string\"] }',\n    examples: [\n      '{ \"path\": \"note.md\", \"action\": \"list\" }',\n      '{ \"path\": \"note.md\", \"action\": \"add\", \"tags\": [\"important\", \"reviewed\"] }',\n      '{ \"path\": \"note.md\", \"action\": \"remove\", \"tags\": [\"draft\"] }',\n    ],\n  },\n  rename_tag: {\n    description: \"Rename a tag across all notes in the vault (frontmatter + inline)\",\n    args: '{ \"oldTag\": \"string\", \"newTag\": \"string\" }',\n    examples: ['{ \"oldTag\": \"architecture\", \"newTag\": \"arch\" }'],\n  },\n\n  // Graph\n  backlinks: {\n    description: \"Find all notes that link TO a given note via [[wikilinks]]\",\n    args: '{ \"path\": \"string\" }',\n    examples: ['{ \"path\": \"microservices.md\" }'],\n  },\n  forwardlinks: {\n    description: \"Find all notes linked FROM a given note\",\n    args: '{ \"path\": \"string\" }',\n    examples: ['{ \"path\": \"project-overview.md\" }'],\n  },\n  graph_path: {\n    description: \"Find the shortest path between two notes in the knowledge graph\",\n    args: '{ \"from\": \"string\", \"to\": \"string\" }',\n    examples: ['{ \"from\": \"project-overview.md\", \"to\": \"user-service.md\" }'],\n  },\n  graph_statistics: {\n    description: \"Knowledge graph stats — most connected nodes, orphans, density\",\n    args: \"{}\",\n    examples: [\"{}\"],\n  },\n\n  // System\n  get_stats: {\n    description: \"Vault and index statistics — note count, chunks, embeddings, graph density\",\n    args: \"{}\",\n    examples: [\"{}\"],\n  },\n  reindex: {\n    description: \"Force a full reindex of the vault\",\n    args: \"{}\",\n    examples: [\"{}\"],\n  },\n};\n\nconst TOOL_CATEGORIES: Record<string, string[]> = {\n  Search: [\"search_semantic\", \"search_text\", \"search_graph\", \"search_hybrid\"],\n  Read: [\"read_note\", \"read_multiple_notes\", \"list_notes\"],\n  Write: [\"create_note\", \"update_note\", \"delete_note\", \"move_note\"],\n  Metadata: [\"get_frontmatter\", \"update_frontmatter\", \"manage_tags\", \"rename_tag\"],\n  Graph: [\"backlinks\", \"forwardlinks\", \"graph_path\", \"graph_statistics\"],\n  System: [\"get_stats\", \"reindex\"],\n};\n\nfunction printToolList() {\n  console.log(\"\\nSemantic Pages — 21 MCP Tools\\n\");\n  console.log(\"Usage: These tools are available via MCP when the server is running.\");\n  console.log(\"       Run `semantic-pages tools <name>` for details on a specific tool.\\n\");\n\n  for (const [category, tools] of Object.entries(TOOL_CATEGORIES)) {\n    console.log(`  ${category}:`);\n    for (const name of tools) {\n      const tool = TOOL_HELP[name];\n      console.log(`    ${name.padEnd(24)} ${tool.description}`);\n    }\n    console.log();\n  }\n\n  console.log(\"Run `semantic-pages tools <tool-name>` for arguments and examples.\");\n}\n\nfunction printToolDetail(name: string) {\n  const tool = TOOL_HELP[name];\n  if (!tool) {\n    console.error(`Unknown tool: ${name}`);\n    console.error(`Run \\`semantic-pages tools\\` to see all available tools.`);\n    process.exit(1);\n  }\n\n  console.log(`\\n  ${name}`);\n  console.log(`  ${\"─\".repeat(name.length)}`);\n  console.log(`  ${tool.description}\\n`);\n  console.log(`  Arguments:`);\n  console.log(`    ${tool.args}\\n`);\n  console.log(`  Examples:`);\n  for (const ex of tool.examples) {\n    console.log(`    ${ex}`);\n  }\n  console.log();\n}\n\nprogram\n  .name(\"semantic-pages\")\n  .description(\n    \"Semantic search + knowledge graph MCP server for markdown files\\n\\n\" +\n    \"  Start MCP server:  semantic-pages --notes ./vault\\n\" +\n    \"  Show vault stats:  semantic-pages --notes ./vault --stats\\n\" +\n    \"  Force reindex:     semantic-pages --notes ./vault --reindex\\n\" +\n    \"  List MCP tools:    semantic-pages tools\\n\" +\n    \"  Tool details:      semantic-pages tools search_semantic\"\n  )\n  .version(\"0.1.3\");\n\nprogram\n  .command(\"tools [name]\")\n  .description(\"List all MCP tools, or show details for a specific tool\")\n  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import(\"../core/indexer.js\");\n      const indexer = new Indexer(notesPath);\n      const docs = await indexer.indexAll();\n      console.log(`Notes: ${docs.length}`);\n      console.log(`Chunks: ${docs.reduce((n: number, d: any) => n + d.chunks.length, 0)}`);\n      console.log(`Wikilinks: ${docs.reduce((n: number, d: any) => n + d.wikilinks.length, 0)}`);\n      console.log(`Tags: ${new Set(docs.flatMap((d: any) => d.tags)).size} unique`);\n      process.exit(0);\n    }\n\n    if (opts.reindex) {\n      const { createServer } = await import(\"../mcp/server.js\");\n      await createServer(notesPath, {\n        watch: false,\n        waitForReady: true,\n        model: opts.model,\n        workers: opts.workers,\n        onProgress: (embedded, total) => {\n          process.stderr.write(`\\rEmbedding ${embedded}/${total} chunks...`);\n        },\n      });\n      process.stderr.write(\"\\n\");\n      console.log(\"Reindex complete.\");\n      process.exit(0);\n    }\n\n    // 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+{"version":3,"sources":["../../src/cli/index.ts"],"sourcesContent":["#!/usr/bin/env node\n\nimport { program } from \"commander\";\nimport { resolve } from \"node:path\";\nimport { existsSync } from \"node:fs\";\n\nconst TOOL_HELP: Record<string, { description: string; args: string; examples: string[] }> = {\n  // Search\n  search_semantic: {\n    description: \"Vector similarity search — find notes by meaning, not just keywords\",\n    args: '{ \"query\": \"string\", \"limit?\": 10 }',\n    examples: [\n      '{ \"query\": \"microservices architecture\", \"limit\": 5 }',\n      '{ \"query\": \"how to deploy to production\" }',\n    ],\n  },\n  search_text: {\n    description: \"Full-text keyword or regex search with optional filters\",\n    args: '{ \"pattern\": \"string\", \"regex?\": false, \"caseSensitive?\": false, \"pathGlob?\": \"string\", \"tagFilter?\": [\"string\"], \"limit?\": 20 }',\n    examples: [\n      '{ \"pattern\": \"RabbitMQ\" }',\n      '{ \"pattern\": 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knowledge graph\",\n    args: '{ \"from\": \"string\", \"to\": \"string\" }',\n    examples: ['{ \"from\": \"project-overview.md\", \"to\": \"user-service.md\" }'],\n  },\n  graph_statistics: {\n    description: \"Knowledge graph stats — most connected nodes, orphans, density\",\n    args: \"{}\",\n    examples: [\"{}\"],\n  },\n\n  // System\n  get_stats: {\n    description: \"Vault and index statistics — note count, chunks, embeddings, graph density\",\n    args: \"{}\",\n    examples: [\"{}\"],\n  },\n  reindex: {\n    description: \"Force a full reindex of the vault\",\n    args: \"{}\",\n    examples: [\"{}\"],\n  },\n};\n\nconst TOOL_CATEGORIES: Record<string, string[]> = {\n  Search: [\"search_semantic\", \"search_text\", \"search_graph\", \"search_hybrid\"],\n  Read: [\"read_note\", \"read_multiple_notes\", \"list_notes\"],\n  Write: [\"create_note\", \"update_note\", \"delete_note\", \"move_note\"],\n  Metadata: [\"get_frontmatter\", \"update_frontmatter\", \"manage_tags\", \"rename_tag\"],\n  Graph: [\"backlinks\", \"forwardlinks\", \"graph_path\", \"graph_statistics\"],\n  System: [\"get_stats\", \"reindex\"],\n};\n\nfunction printToolList() {\n  console.log(\"\\nSemantic Pages — 21 MCP Tools\\n\");\n  console.log(\"Usage: These tools are available via MCP when the server is running.\");\n  console.log(\"       Run `semantic-pages tools <name>` for details on a specific tool.\\n\");\n\n  for (const [category, tools] of Object.entries(TOOL_CATEGORIES)) {\n    console.log(`  ${category}:`);\n    for (const name of tools) {\n      const tool = TOOL_HELP[name];\n      console.log(`    ${name.padEnd(24)} ${tool.description}`);\n    }\n    console.log();\n  }\n\n  console.log(\"Run `semantic-pages tools <tool-name>` for arguments and examples.\");\n}\n\nfunction printToolDetail(name: string) {\n  const tool = TOOL_HELP[name];\n  if (!tool) {\n    console.error(`Unknown tool: ${name}`);\n    console.error(`Run \\`semantic-pages tools\\` to see all available tools.`);\n    process.exit(1);\n  }\n\n  console.log(`\\n  ${name}`);\n  console.log(`  ${\"─\".repeat(name.length)}`);\n  console.log(`  ${tool.description}\\n`);\n  console.log(`  Arguments:`);\n  console.log(`    ${tool.args}\\n`);\n  console.log(`  Examples:`);\n  for (const ex of tool.examples) {\n    console.log(`    ${ex}`);\n  }\n  console.log();\n}\n\nprogram\n  .name(\"semantic-pages\")\n  .description(\n    \"Semantic search + knowledge graph MCP server for markdown files\\n\\n\" +\n    \"  Start MCP server:  semantic-pages --notes ./vault\\n\" +\n    \"  Show vault stats:  semantic-pages --notes ./vault --stats\\n\" +\n    \"  Force reindex:     semantic-pages --notes ./vault --reindex\\n\" +\n    \"  List MCP tools:    semantic-pages tools\\n\" +\n    \"  Tool details:      semantic-pages tools search_semantic\"\n  )\n  .version(\"0.4.1\");\n\nprogram\n  .command(\"tools [name]\")\n  .description(\"List all MCP tools, or show details for a specific tool\")\n  .action((name?: string) => {\n    if (name) {\n      printToolDetail(name);\n    } else {\n      printToolList();\n    }\n    process.exit(0);\n  });\n\nprogram\n  .command(\"serve\", { isDefault: true })\n  .description(\"Start the MCP server (default command)\")\n  .requiredOption(\"--notes <path>\", \"Path to markdown notes directory\")\n  .option(\"--reindex\", \"Force full reindex and exit\")\n  .option(\"--stats\", \"Show vault statistics and exit\")\n  .option(\"--model <name>\", \"Embedding model to use\", \"nomic-ai/nomic-embed-text-v1.5\")\n  .option(\"--workers <n>\", \"Number of worker threads for parallel embedding\", parseInt)\n  .option(\"--batch-size <n>\", \"Texts per ONNX forward pass (default: 32)\", parseInt)\n  .option(\"--no-watch\", \"Disable file watcher\")\n  .action(async (opts) => {\n    const notesPath = resolve(opts.notes);\n\n    if (!existsSync(notesPath)) {\n      console.error(`Error: notes directory not found: ${notesPath}`);\n      process.exit(1);\n    }\n\n    if (opts.stats) {\n      const { Indexer } = await import(\"../core/indexer.js\");\n      const indexer = new Indexer(notesPath);\n      const docs = await indexer.indexAll();\n      console.log(`Notes: ${docs.length}`);\n      console.log(`Chunks: ${docs.reduce((n: number, d: any) => n + d.chunks.length, 0)}`);\n      console.log(`Wikilinks: ${docs.reduce((n: number, d: any) => n + d.wikilinks.length, 0)}`);\n      console.log(`Tags: ${new Set(docs.flatMap((d: any) => d.tags)).size} unique`);\n      process.exit(0);\n    }\n\n    if (opts.reindex) {\n      const { createServer } = await import(\"../mcp/server.js\");\n      await createServer(notesPath, {\n        watch: false,\n        waitForReady: true,\n        model: opts.model,\n        workers: opts.workers,\n        batchSize: opts.batchSize,\n        onProgress: (embedded, total) => {\n          process.stderr.write(`\\rEmbedding ${embedded}/${total} chunks...`);\n        },\n      });\n      process.stderr.write(\"\\n\");\n      console.log(\"Reindex complete.\");\n      process.exit(0);\n    }\n\n    // Default: start MCP server on stdio\n    const { startServer } = await import(\"../mcp/server.js\");\n    await startServer(notesPath, { watch: opts.watch, model: opts.model, workers: opts.workers, batchSize: opts.batchSize });\n  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package/dist/core/embed-worker.js

@@ -1,7 +1,33 @@
 // src/core/embed-worker.ts
 import { parentPort, workerData } from "worker_threads";
 import { AutoTokenizer } from "@huggingface/transformers";
-var { modelPath, modelName, cacheDir, runtimeLabel } = workerData;
+var { modelPath, modelName, cacheDir, runtimeLabel, batchSize = 32 } = workerData;
+function meanPoolAndNormalizeMany(outputData, maskData, batchSize2, seqLen, hiddenSize) {
+  const results = [];
+  for (let b = 0; b < batchSize2; b++) {
+    const result = new Float32Array(hiddenSize);
+    let maskSum = 0;
+    for (let t = 0; t < seqLen; t++) {
+      const mask = maskData[b * seqLen + t];
+      maskSum += mask;
+      const offset = (b * seqLen + t) * hiddenSize;
+      for (let d = 0; d < hiddenSize; d++) {
+        result[d] += outputData[offset + d] * mask;
+      }
+    }
+    if (maskSum > 0) {
+      for (let d = 0; d < hiddenSize; d++) result[d] /= maskSum;
+    }
+    let norm = 0;
+    for (let d = 0; d < hiddenSize; d++) norm += result[d] * result[d];
+    norm = Math.sqrt(norm);
+    if (norm > 0) {
+      for (let d = 0; d < hiddenSize; d++) result[d] /= norm;
+    }
+    results.push(result);
+  }
+  return results;
+}
 async function init() {
   let ort;
   try {
@@ -24,51 +50,57 @@ async function init() {
     if (msg.type !== "embed") return;
     try {
       const embeddings = [];
-      for (let i = 0; i < msg.texts.length; i++) {
-        const encoded = await tokenizer(msg.texts[i], {
-          padding: true,
-          truncation: true,
-          max_length: 512,
-          return_tensor: false
-        });
-        const inputIdsRaw = Array.from(encoded.input_ids.data ?? encoded.input_ids);
-        const attentionMaskRaw = Array.from(encoded.attention_mask.data ?? encoded.attention_mask);
-        const seqLen = inputIdsRaw.length;
-        const inputIds = new ort.Tensor("int64", BigInt64Array.from(inputIdsRaw.map(BigInt)), [1, seqLen]);
-        const attentionMask = new ort.Tensor("int64", BigInt64Array.from(attentionMaskRaw.map(BigInt)), [1, seqLen]);
+      let totalDone = 0;
+      for (let i = 0; i < msg.texts.length; i += batchSize) {
+        const subBatch = msg.texts.slice(i, i + batchSize);
+        const n = subBatch.length;
+        const encodings = await Promise.all(
+          subBatch.map(
+            (text) => tokenizer(text, { padding: false, truncation: true, max_length: 512, return_tensor: false })
+          )
+        );
+        const tokenized = encodings.map((enc) => ({
+          ids: Array.from(enc.input_ids.data ?? enc.input_ids),
+          mask: Array.from(enc.attention_mask.data ?? enc.attention_mask)
+        }));
+        const seqLen = Math.max(...tokenized.map((t) => t.ids.length));
+        const flatIds = new BigInt64Array(n * seqLen);
+        const flatMask = new BigInt64Array(n * seqLen);
+        const flatMaskNums = new Array(n * seqLen).fill(0);
+        for (let b = 0; b < n; b++) {
+          const { ids, mask } = tokenized[b];
+          for (let j = 0; j < ids.length; j++) {
+            flatIds[b * seqLen + j] = BigInt(ids[j]);
+            flatMask[b * seqLen + j] = BigInt(mask[j]);
+            flatMaskNums[b * seqLen + j] = mask[j];
+          }
+        }
+        const inputIds = new ort.Tensor("int64", flatIds, [n, seqLen]);
+        const attentionMask = new ort.Tensor("int64", flatMask, [n, seqLen]);
         const feeds = { input_ids: inputIds, attention_mask: attentionMask };
         if (needsTokenTypeIds) {
-          feeds.token_type_ids = new ort.Tensor("int64", new BigInt64Array(seqLen), [1, seqLen]);
+          feeds.token_type_ids = new ort.Tensor("int64", new BigInt64Array(n * seqLen), [n, seqLen]);
         }
         const output = await session.run(feeds);
         const outputTensor = output[outputName];
         const hiddenSize = outputTensor.dims[outputTensor.dims.length - 1];
-        const result = new Float32Array(hiddenSize);
-        let maskSum = 0;
-        for (let t = 0; t < seqLen; t++) {
-          const mask = attentionMaskRaw[t];
-          maskSum += mask;
-          const offset = t * hiddenSize;
-          for (let d = 0; d < hiddenSize; d++) {
-            result[d] += outputTensor.data[offset + d] * mask;
-          }
-        }
-        if (maskSum > 0) {
-          for (let d = 0; d < hiddenSize; d++) result[d] /= maskSum;
-        }
-        let norm = 0;
-        for (let d = 0; d < hiddenSize; d++) norm += result[d] * result[d];
-        norm = Math.sqrt(norm);
-        if (norm > 0) {
-          for (let d = 0; d < hiddenSize; d++) result[d] /= norm;
+        const batchEmbeddings = meanPoolAndNormalizeMany(
+          outputTensor.data,
+          flatMaskNums,
+          n,
+          seqLen,
+          hiddenSize
+        );
+        for (const emb of batchEmbeddings) {
+          embeddings.push(emb);
+          totalDone++;
+          parentPort.postMessage({
+            type: "progress",
+            done: totalDone,
+            total: msg.texts.length,
+            startIndex: msg.startIndex
+          });
         }
-        embeddings.push(result);
-        parentPort.postMessage({
-          type: "progress",
-          done: i + 1,
-          total: msg.texts.length,
-          startIndex: msg.startIndex
-        });
       }
       parentPort.postMessage({
         type: "result",

package/dist/core/embed-worker.js.map

@@ -1 +1 @@
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