@theglitchking/semantic-pages 0.6.1 → 0.6.2

package/.claude-plugin/marketplace.json

@@ -6,13 +6,13 @@
   },
   "metadata": {
     "description": "Official marketplace for semantic-pages - Semantic search + knowledge graph MCP server with auto-wiring for .claude/.vault and hit-em-with-the-docs companion",
-    "version": "0.6.1"
+    "version": "0.6.2"
   },
   "plugins": [
     {
       "name": "semantic-pages",
       "description": "Semantic search + knowledge graph MCP server for markdown vaults. Auto-wires a read/write vault at .claude/.vault, and a read-only docs index at .documentation when hit-em-with-the-docs is also installed.",
-      "version": "0.6.1",
+      "version": "0.6.2",
       "author": {
         "name": "TheGlitchKing"
       },

package/.claude-plugin/plugin.json

@@ -1,7 +1,7 @@
 {
   "name": "semantic-pages",
   "description": "Semantic search + knowledge graph MCP server for markdown vaults. Auto-wires a read/write vault at .claude/.vault, and a read-only docs index at .documentation when hit-em-with-the-docs is also installed.",
-  "version": "0.6.1",
+  "version": "0.6.2",
   "author": {
     "name": "TheGlitchKing",
     "email": "theglitchking@users.noreply.github.com"

package/dist/{chunk-P7BHYKVE.js → chunk-BJPL3RYK.js}

@@ -1,6 +1,6 @@
 // src/core/embedder.ts
 import { AutoTokenizer } from "@huggingface/transformers";
-import { readFile, writeFile, mkdir } from "fs/promises";
+import { readFile, writeFile, mkdir, rename, unlink } from "fs/promises";
 import { join, dirname } from "path";
 import { existsSync, createWriteStream } from "fs";
 import { homedir } from "os";
@@ -34,8 +34,18 @@ async function downloadFile(url, destPath) {
   const response = await fetch(url);
   if (!response.ok) throw new Error(`Download failed (${response.status}): ${url}`);
   if (!response.body) throw new Error(`No response body: ${url}`);
-  const fileStream = createWriteStream(destPath);
-  await streamPipeline(Readable.fromWeb(response.body), fileStream);
+  const tempPath = `${destPath}.${process.pid}.${Date.now()}.tmp`;
+  try {
+    const fileStream = createWriteStream(tempPath);
+    await streamPipeline(Readable.fromWeb(response.body), fileStream);
+    await rename(tempPath, destPath);
+  } catch (err) {
+    try {
+      await unlink(tempPath);
+    } catch {
+    }
+    throw err;
+  }
 }
 var Embedder = class {
   model;
@@ -633,7 +643,7 @@ var TextSearch = class {
 };
 
 // src/core/crud.ts
-import { readFile as readFile4, writeFile as writeFile4, unlink, rename, mkdir as mkdir2 } from "fs/promises";
+import { readFile as readFile4, writeFile as writeFile4, unlink as unlink2, rename as rename2, mkdir as mkdir2 } from "fs/promises";
 import { dirname as dirname2, join as join4 } from "path";
 import { existsSync as existsSync4 } from "fs";
 import { glob } from "glob";
@@ -709,7 +719,7 @@ var NoteCrud = class {
     if (!existsSync4(absPath)) {
       throw new Error(`Note does not exist: ${relativePath}`);
     }
-    await unlink(absPath);
+    await unlink2(absPath);
   }
   async move(fromPath, toPath) {
     const absFrom = join4(this.notesPath, fromPath);
@@ -721,7 +731,7 @@ var NoteCrud = class {
       throw new Error(`Destination already exists: ${toPath}`);
     }
     await mkdir2(dirname2(absTo), { recursive: true });
-    await rename(absFrom, absTo);
+    await rename2(absFrom, absTo);
     await this.updateWikilinksAfterMove(fromPath, toPath);
   }
   async updateWikilinksAfterMove(oldPath, newPath) {
@@ -951,4 +961,4 @@ export {
   TagManager,
   Watcher
 };
-//# sourceMappingURL=chunk-P7BHYKVE.js.map
+//# sourceMappingURL=chunk-BJPL3RYK.js.map

package/dist/chunk-BJPL3RYK.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, rename, unlink } from \"node:fs/promises\";\nimport { join, dirname } from \"node:path\";\nimport { existsSync, createWriteStream } from \"node:fs\";\nimport { homedir } 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\n// MiniLM-L6-v2 is the default: ~3 min to index 2,853 chunks on CPU vs ~16 min for nomic.\n// nomic-embed-text-v1.5 gives higher quality embeddings but is much slower on CPU.\nconst DEFAULT_MODEL = \"sentence-transformers/all-MiniLM-L6-v2\";\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). On typical dev machines\n// with <4 GB free RAM, parallel workers cause swap thrashing and are slower.\n// Enable with --workers N when you have sufficient RAM.\nconst DEFAULT_WORKERS = 1;\n// batch=16 is optimal for MiniLM on CPU (short sequences, low padding waste).\n// For larger models (nomic 768d), batch=1 is faster due to padding overhead.\nconst DEFAULT_BATCH_SIZE = 16;\n// Quantized ONNX: faster on CPU but not all models have a quantized variant.\n// MiniLM fp32 is already fast enough; nomic benefits from quantized.\n// Falls back to fp32 automatically if quantized file is not available.\nconst DEFAULT_QUANTIZED = false;\n\n// Full-precision ONNX model subpaths\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\n// Quantized (int8) ONNX model subpaths — faster on CPU, ~same quality\nconst ONNX_QUANTIZED_MODEL_PATHS: Record<string, string> = {\n  \"nomic-ai/nomic-embed-text-v1.5\": \"onnx/model_quantized.onnx\",\n  \"sentence-transformers/all-MiniLM-L6-v2\": \"onnx/model_quantized.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\n// Download to a process-unique temp file, then atomically rename onto the\n// final path. Two concurrent downloaders won't corrupt each other's partial\n// writes — the worst case is one wasted download (rename is last-writer-wins\n// but each rename installs a complete, valid file). Without this, multiple\n// processes calling Embedder.init() against the same cache (e.g. parallel\n// vitest workers, or multiple semantic-pages servers on a fresh install) race\n// on a single shared writeStream and produce a corrupt ONNX file that fails\n// Protobuf parsing on load.\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: ${url}`);\n  const tempPath = `${destPath}.${process.pid}.${Date.now()}.tmp`;\n  try {\n    const fileStream = createWriteStream(tempPath);\n    await streamPipeline(Readable.fromWeb(response.body as never), fileStream);\n    await rename(tempPath, destPath);\n  } catch (err) {\n    try { await unlink(tempPath); } catch { /* temp may not exist */ }\n    throw err;\n  }\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 quantized: boolean;\n  private modelPath = \"\";\n\n  constructor(\n    model: string = DEFAULT_MODEL,\n    numWorkers: number = DEFAULT_WORKERS,\n    batchSize: number = DEFAULT_BATCH_SIZE,\n    quantized: boolean = DEFAULT_QUANTIZED\n  ) {\n    this.model = model;\n    this.numWorkers = numWorkers;\n    this.batchSize = batchSize;\n    this.quantized = quantized;\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. Tries quantized first if requested,\n    // falls back to fp32 if the quantized file is not available for this model.\n    let useQuantized = this.quantized;\n    const modelFileName = useQuantized ? \"model_quantized.onnx\" : \"model.onnx\";\n    this.modelPath = join(modelDir, modelFileName);\n    const modelPath = this.modelPath;\n    if (!existsSync(modelPath)) {\n      const pathMap = useQuantized ? ONNX_QUANTIZED_MODEL_PATHS : ONNX_MODEL_PATHS;\n      const onnxSubpath = pathMap[this.model] ?? (useQuantized ? \"onnx/model_quantized.onnx\" : \"onnx/model.onnx\");\n      const url = `https://huggingface.co/${this.model}/resolve/main/${onnxSubpath}`;\n      process.stderr.write(`Downloading ONNX model: ${this.model} (${useQuantized ? \"quantized\" : \"fp32\"})...\\n`);\n      try {\n        await downloadFile(url, modelPath);\n      } catch (err: any) {\n        if (useQuantized && err?.message?.includes(\"404\")) {\n          // Quantized not available for this model — fall back to fp32\n          process.stderr.write(`Quantized model not available, falling back to fp32\\n`);\n          useQuantized = false;\n          this.modelPath = join(modelDir, \"model.onnx\");\n          const fp32Subpath = ONNX_MODEL_PATHS[this.model] ?? \"onnx/model.onnx\";\n          const fp32Url = `https://huggingface.co/${this.model}/resolve/main/${fp32Subpath}`;\n          process.stderr.write(`Downloading ONNX model: ${this.model} (fp32)...\\n`);\n          await downloadFile(fp32Url, this.modelPath);\n        } else {\n          throw err;\n        }\n      }\n      process.stderr.write(`Model downloaded to ${modelDir}\\n`);\n    }\n    // Load tokenizer (uses HF transformers tokenizer infrastructure)\n    this.tokenizer = await AutoTokenizer.from_pretrained(this.model, {\n      cache_dir: CACHE_DIR,\n    });\n\n    // Create ONNX inference session (use this.modelPath — may have been updated by fallback)\n    this.session = await ort.InferenceSession.create(this.modelPath, {\n      executionProviders: [label === \"native\" ? \"cpu\" : \"wasm\"],\n    });\n\n    // Determine dimensions from a test embedding\n    const test = await this.embed(\"test\");\n    this.dimensions = test.length;\n    this.initialized = true;\n\n    const modelShort = this.model.split(\"/\").pop() ?? this.model;\n    process.stderr.write(`Embedder ready (${modelShort}, ${label}, ${this.dimensions}d, batch=${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\n/**\n * Tags shared by more than this many docs are too generic to be meaningful\n * graph edges (e.g. \"api\", \"testing\"). Only specific/rare tags create edges.\n * Docs without frontmatter are unaffected — their inline #tags still participate\n * but only if those tags are specific enough to pass this threshold.\n */\nconst TAG_EDGE_MAX_DOCS = 15;\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 — store optional metadata fields when present\n    for (const doc of documents) {\n      this.graph.addNode(doc.path, {\n        title: doc.title,\n        tags: doc.tags,\n        ...(doc.status !== undefined && { status: doc.status }),\n        ...(doc.loadPriority !== undefined && { loadPriority: doc.loadPriority }),\n      });\n    }\n\n    const pathLookup = new Map<string, string>();\n    for (const doc of documents) {\n      const nameNoExt = doc.path.replace(/\\.md$/, \"\");\n      const basename = nameNoExt.split(\"/\").pop()!;\n      pathLookup.set(basename.toLowerCase(), doc.path);\n      pathLookup.set(nameNoExt.toLowerCase(), doc.path);\n    }\n\n    // Add wikilink edges (weight 1.0)\n    for (const doc of documents) {\n      for (const link of doc.wikilinks) {\n        const target = pathLookup.get(link.toLowerCase());\n        if (target && target !== doc.path && !this.graph.hasEdge(doc.path, target)) {\n          this.graph.addEdge(doc.path, target, { type: \"wikilink\", weight: 1.0 });\n        }\n      }\n    }\n\n    // Add related_docs edges (weight 1.0) — only present when frontmatter has related_docs\n    // Falls back gracefully: docs without this field are simply skipped\n    for (const doc of documents) {\n      if (!doc.relatedDocs?.length) continue;\n      for (const ref of doc.relatedDocs) {\n        // Try full normalized path first, then basename — same strategy as wikilinks\n        const normalized = ref.replace(/\\.md$/, \"\").toLowerCase();\n        const base = normalized.split(\"/\").pop()!;\n        const target = pathLookup.get(normalized) ?? pathLookup.get(base);\n        if (target && target !== doc.path && !this.graph.hasEdge(doc.path, target)) {\n          this.graph.addEdge(doc.path, target, { type: \"related\", weight: 1.0 });\n        }\n      }\n    }\n\n    // Add tag-based edges (weight 0.5) — capped at TAG_EDGE_MAX_DOCS per tag.\n    // Generic tags shared by many docs (e.g. \"api\", \"testing\") create noise;\n    // only specific tags (e.g. \"qdrant\", \"celery\") create meaningful connections.\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      if (notes.length >= TAG_EDGE_MAX_DOCS) continue; // too generic — skip\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, limit = 20): GraphNode[] {\n    const lc = concept.toLowerCase();\n\n    const directMatches = new Set<string>(\n      this.graph.nodes().filter((n) => {\n        const attrs = this.graph.getNodeAttributes(n);\n        const title = typeof attrs.title === \"string\" ? attrs.title : String(attrs.title ?? \"\");\n        return (\n          n.toLowerCase().includes(lc) ||\n          title.toLowerCase().includes(lc) ||\n          (attrs.tags as string[] | undefined)?.some((t) => t.toLowerCase().includes(lc))\n        );\n      })\n    );\n\n    const visited = new Set<string>();\n    for (const start of directMatches) {\n      bfsFromNode(this.graph, start, (_node, _attr, depth) => {\n        if (visited.size >= limit * 3) return true; // gather 3x limit before ranking\n        visited.add(_node);\n        return depth >= maxDepth;\n      });\n    }\n\n    // Sort: direct matches first, then by loadPriority desc, then by degree desc\n    // deprecated/archived nodes sort to the end\n    const ranked = [...visited].sort((a, b) => {\n      const aAttrs = this.graph.getNodeAttributes(a);\n      const bAttrs = this.graph.getNodeAttributes(b);\n      const aDeprecated = aAttrs.status === \"deprecated\" || aAttrs.status === \"archived\" ? 1 : 0;\n      const bDeprecated = bAttrs.status === \"deprecated\" || bAttrs.status === \"archived\" ? 1 : 0;\n      if (aDeprecated !== bDeprecated) return aDeprecated - bDeprecated;\n      const aDirect = directMatches.has(a) ? 0 : 1;\n      const bDirect = directMatches.has(b) ? 0 : 1;\n      if (aDirect !== bDirect) return aDirect - bDirect;\n      const aPriority = (aAttrs.loadPriority as number | undefined) ?? 5;\n      const bPriority = (bAttrs.loadPriority as number | undefined) ?? 5;\n      if (aPriority !== bPriority) return bPriority - aPriority;\n      return this.graph.degree(b) - this.graph.degree(a);\n    });\n\n    return ranked.slice(0, limit).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: typeof attrs.title === \"string\" ? attrs.title : nodePath,\n      tags: (attrs.tags as string[]) || [],\n      linkCount: this.graph.outDegree(nodePath),\n      backlinkCount: this.graph.inDegree(nodePath),\n      ...(attrs.loadPriority !== undefined && { loadPriority: attrs.loadPriority as number }),\n      ...(attrs.status !== undefined && { status: attrs.status as string }),\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    // Merge auto-stamps with caller-supplied frontmatter (caller wins on conflicts)\n    const stamps = computeStamps(content);\n    const merged = { ...stamps, ...(frontmatter ?? {}) };\n    const fileContent = matter.stringify(content, merged);\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    // Re-parse the final content and inject updated stamps\n    // (preserves all existing frontmatter, only overwrites the three auto fields)\n    const { data: existingFm, content: body } = matter(updated);\n    const stamps = computeStamps(body);\n    const newFm = { ...existingFm, ...stamps };\n    await writeFile(absPath, matter.stringify(body, newFm), \"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\n/**\n * Compute the three auto-stamp fields from note body text.\n * These are always factual/computable — no editorial judgment required.\n * - last_updated: today's date (YYYY-MM-DD)\n * - word_count: whitespace-separated token count\n * - estimated_read_time: assumes ~200 wpm average reading speed\n */\nfunction computeStamps(body: string): Record<string, unknown> {\n  const today = new Date().toISOString().slice(0, 10); // YYYY-MM-DD\n  const wordCount = body.trim() ? body.trim().split(/\\s+/).length : 0;\n  const minutes = Math.max(1, Math.ceil(wordCount / 200));\n  return {\n    last_updated: today,\n    word_count: wordCount,\n    estimated_read_time: `${minutes} min read`,\n  };\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 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package/dist/{chunk-XNEE7Z2S.js → chunk-UCATYEVZ.js}

@@ -21,7 +21,7 @@ var Indexer = class {
     this.processor = unified().use(remarkParse).use(remarkWikiLink);
   }
   async indexAll() {
-    const files = await glob("**/*.md", { cwd: this.notesPath });
+    const files = await glob("**/*.md", { cwd: this.notesPath, follow: true });
     const docs = await Promise.all(
       files.map((file) => this.indexFile(join(this.notesPath, file), file))
     );
@@ -148,4 +148,4 @@ export {
   __export,
   Indexer
 };
-//# sourceMappingURL=chunk-XNEE7Z2S.js.map
+//# sourceMappingURL=chunk-UCATYEVZ.js.map

package/dist/chunk-UCATYEVZ.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/core/indexer.ts"],"sourcesContent":["import { unified } from \"unified\";\nimport remarkParse from \"remark-parse\";\nimport remarkWikiLink from \"remark-wiki-link\";\nimport matter from \"gray-matter\";\nimport { glob } from \"glob\";\nimport { readFile, stat } from \"node:fs/promises\";\nimport { basename, join, relative } from \"node:path\";\nimport type { IndexedDocument } from \"./types.js\";\n\nconst CHUNK_TARGET_CHARS = 2000; // ~512 tokens\n\nexport class Indexer {\n  private notesPath: string;\n  private processor: any;\n\n  constructor(notesPath: string) {\n    this.notesPath = notesPath;\n    this.processor = unified().use(remarkParse).use(remarkWikiLink);\n  }\n\n  async indexAll(): Promise<IndexedDocument[]> {\n    // follow: true descends into symlinked directories. Without this, users\n    // who symlink an external folder into their vault (a common pattern for\n    // sharing notes across projects) get silently empty indexing for the\n    // symlinked content. glob does cycle detection via visited inodes so\n    // circular symlinks are handled safely.\n    const files = await glob(\"**/*.md\", { cwd: this.notesPath, follow: true });\n    const docs = await Promise.all(\n      files.map((file) => this.indexFile(join(this.notesPath, file), file))\n    );\n    return docs;\n  }\n\n  async indexFile(\n    absolutePath: string,\n    relativePath: string\n  ): Promise<IndexedDocument> {\n    const [raw, fileStat] = await Promise.all([\n      readFile(absolutePath, \"utf-8\"),\n      stat(absolutePath),\n    ]);\n    const { data: frontmatter, content } = matter(raw);\n    const tree = this.processor.parse(content);\n\n    const wikilinks = this.extractWikilinks(tree);\n    const tags = this.extractTags(content, frontmatter);\n    const headers = this.extractHeaders(tree);\n    const plainText = this.stripMarkdown(content);\n    const chunks = this.chunkText(plainText);\n\n    const title =\n      (frontmatter.title as string) ||\n      headers[0] ||\n      basename(relativePath, \".md\");\n\n    // Resolve modification time: prefer frontmatter date fields over fs.stat\n    // Supports hit-em-with-the-docs (last_updated) and common alternatives\n    const mtime = this.resolveMtime(frontmatter, fileStat.mtime);\n\n    // Optional hit-em-with-the-docs fields (only populated when present)\n    const loadPriority =\n      typeof frontmatter.load_priority === \"number\"\n        ? Math.min(10, Math.max(1, frontmatter.load_priority))\n        : undefined;\n    const status =\n      typeof frontmatter.status === \"string\" ? frontmatter.status : undefined;\n    const tier =\n      typeof frontmatter.tier === \"string\" ? frontmatter.tier : undefined;\n    const domains = Array.isArray(frontmatter.domains)\n      ? (frontmatter.domains as string[])\n      : undefined;\n    const purpose =\n      typeof frontmatter.purpose === \"string\" ? frontmatter.purpose : undefined;\n    const relatedDocs = Array.isArray(frontmatter.related_docs)\n      ? (frontmatter.related_docs as string[]).filter((v) => typeof v === \"string\")\n      : undefined;\n\n    return {\n      path: relativePath,\n      title,\n      content: plainText,\n      frontmatter,\n      wikilinks,\n      tags,\n      headers,\n      chunks,\n      mtime,\n      ...(loadPriority !== undefined && { loadPriority }),\n      ...(status !== undefined && { status }),\n      ...(tier !== undefined && { tier }),\n      ...(domains !== undefined && { domains }),\n      ...(purpose !== undefined && { purpose }),\n      ...(relatedDocs !== undefined && { relatedDocs }),\n    };\n  }\n\n  /**\n   * Resolve the best available modification date for a document.\n   * Priority: last_updated → updated → date → lastmod → fs.stat mtime\n   * Accepts YYYY-MM-DD strings or full ISO timestamps.\n   */\n  private resolveMtime(\n    frontmatter: Record<string, unknown>,\n    statMtime: Date\n  ): string {\n    const candidates = [\n      frontmatter.last_updated,\n      frontmatter.updated,\n      frontmatter.date,\n      frontmatter.lastmod,\n    ];\n    for (const val of candidates) {\n      if (!val) continue;\n      const str = val instanceof Date ? val.toISOString() : String(val);\n      const parsed = new Date(str);\n      if (!isNaN(parsed.getTime())) return parsed.toISOString();\n    }\n    return statMtime.toISOString();\n  }\n\n  private extractWikilinks(tree: any): string[] {\n    const links: string[] = [];\n    const walk = (node: any) => {\n      if (node.type === \"wikiLink\") {\n        links.push(node.value || node.data?.alias || \"\");\n      }\n      if (node.children) {\n        for (const child of node.children) walk(child);\n      }\n    };\n    walk(tree);\n    return [...new Set(links.filter(Boolean))];\n  }\n\n  private extractTags(content: string, frontmatter: Record<string, unknown>): string[] {\n    const inlineTags = [...content.matchAll(/(?:^|\\s)#([a-zA-Z][\\w-/]*)/g)].map(\n      (m) => m[1]\n    );\n\n    const fmTags = Array.isArray(frontmatter.tags)\n      ? (frontmatter.tags as string[])\n      : [];\n\n    return [...new Set([...fmTags, ...inlineTags])];\n  }\n\n  private extractHeaders(tree: any): string[] {\n    const headers: string[] = [];\n    const walk = (node: any) => {\n      if (node.type === \"heading\") {\n        const text = this.nodeToText(node);\n        if (text) headers.push(text);\n      }\n      if (node.children) {\n        for (const child of node.children) walk(child);\n      }\n    };\n    walk(tree);\n    return headers;\n  }\n\n  private nodeToText(node: any): string {\n    if (node.type === \"text\") return node.value;\n    if (node.children) return node.children.map((c: any) => this.nodeToText(c)).join(\"\");\n    return \"\";\n  }\n\n  private stripMarkdown(content: string): string {\n    return content\n      .replace(/```[\\s\\S]*?```/g, \"\")\n      .replace(/`[^`]+`/g, \"\")\n      .replace(/!\\[.*?\\]\\(.*?\\)/g, \"\")\n      .replace(/\\[([^\\]]+)\\]\\(.*?\\)/g, \"$1\")\n      .replace(/#{1,6}\\s+/g, 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package/dist/cli/index.js

@@ -208,14 +208,14 @@ 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("--read-only", "Suppress write tools (create_note, update_note, delete_note, move_note, update_frontmatter, manage_tags, rename_tag) \u2014 use for shared docs vaults owned by another tool").option("--model <name>", "Embedding model to use (default: all-MiniLM-L6-v2, fast; use nomic-ai/nomic-embed-text-v1.5 for higher quality)").option("--workers <n>", "Number of worker threads for parallel embedding", parseInt).option("--batch-size <n>", "Texts per ONNX forward pass (default: 8)", parseInt).option("--no-quantized", "Use full-precision model instead of quantized (slower, slightly higher quality)").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("--wait-for-ready", "Block startup until index is fully built before serving (default: index in background; tools return 'Indexing in progress' until ready)").option("--read-only", "Suppress write tools (create_note, update_note, delete_note, move_note, update_frontmatter, manage_tags, rename_tag) \u2014 use for shared docs vaults owned by another tool").option("--model <name>", "Embedding model to use (default: all-MiniLM-L6-v2, fast; use nomic-ai/nomic-embed-text-v1.5 for higher quality)").option("--workers <n>", "Number of worker threads for parallel embedding", parseInt).option("--batch-size <n>", "Texts per ONNX forward pass (default: 8)", parseInt).option("--no-quantized", "Use full-precision model instead of quantized (slower, slightly higher quality)").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}`);
     process.exit(1);
   }
   if (opts.stats) {
-    const { Indexer } = await import("../indexer-UEYFOOER.js");
+    const { Indexer } = await import("../indexer-6QLY6KBC.js");
     const indexer = new Indexer(notesPath);
     const docs = await indexer.indexAll();
     console.log(`Notes: ${docs.length}`);
@@ -244,6 +244,7 @@ program.command("serve", { isDefault: true }).description("Start the MCP server
   const { startServer } = await import("../mcp/server.js");
   await startServer(notesPath, {
     watch: opts.watch,
+    waitForReady: opts.waitForReady,
     model: opts.model,
     workers: opts.workers,
     batchSize: opts.batchSize,

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(\"0.4.3\");\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(\"--read-only\", \"Suppress write tools (create_note, update_note, delete_note, move_note, update_frontmatter, manage_tags, rename_tag) — use for shared docs vaults owned by another tool\")\n  .option(\"--model <name>\", \"Embedding model to use (default: all-MiniLM-L6-v2, fast; use nomic-ai/nomic-embed-text-v1.5 for higher quality)\")\n  .option(\"--workers <n>\", \"Number of worker threads for parallel embedding\", parseInt)\n  .option(\"--batch-size <n>\", \"Texts per ONNX forward pass (default: 8)\", parseInt)\n  .option(\"--no-quantized\", \"Use full-precision model instead of quantized (slower, slightly higher quality)\")\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        quantized: opts.quantized,\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, {\n      watch: opts.watch,\n      model: opts.model,\n      workers: opts.workers,\n      batchSize: opts.batchSize,\n      quantized: opts.quantized,\n      readOnly: opts.readOnly,\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\": \"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 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\"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   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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(\"0.4.3\");\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(\"--wait-for-ready\", \"Block startup until index is fully built before serving (default: index in background; tools return 'Indexing in progress' until ready)\")\n  .option(\"--read-only\", \"Suppress write tools (create_note, update_note, delete_note, move_note, update_frontmatter, manage_tags, rename_tag) — use for shared docs vaults owned by another tool\")\n  .option(\"--model <name>\", \"Embedding model to use (default: all-MiniLM-L6-v2, fast; use nomic-ai/nomic-embed-text-v1.5 for higher quality)\")\n  .option(\"--workers <n>\", \"Number of worker threads for parallel embedding\", parseInt)\n  .option(\"--batch-size <n>\", \"Texts per ONNX forward pass (default: 8)\", parseInt)\n  .option(\"--no-quantized\", \"Use full-precision model instead of quantized (slower, slightly higher quality)\")\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        quantized: opts.quantized,\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, {\n      watch: opts.watch,\n      waitForReady: opts.waitForReady,\n      model: opts.model,\n      workers: opts.workers,\n      batchSize: opts.batchSize,\n      quantized: opts.quantized,\n      readOnly: opts.readOnly,\n    });\n  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package/dist/core/index.js

@@ -7,10 +7,10 @@ import {
   TextSearch,
   VectorIndex,
   Watcher
-} from "../chunk-P7BHYKVE.js";
+} from "../chunk-BJPL3RYK.js";
 import {
   Indexer
-} from "../chunk-XNEE7Z2S.js";
+} from "../chunk-UCATYEVZ.js";
 export {
   Embedder,
   FrontmatterManager,

package/dist/indexer-6QLY6KBC.js

@@ -0,0 +1,7 @@
+import {
+  Indexer
+} from "./chunk-UCATYEVZ.js";
+export {
+  Indexer
+};
+//# sourceMappingURL=indexer-6QLY6KBC.js.map

package/dist/mcp/server.js

@@ -7,11 +7,11 @@ import {
   TextSearch,
   VectorIndex,
   Watcher
-} from "../chunk-P7BHYKVE.js";
+} from "../chunk-BJPL3RYK.js";
 import {
   Indexer,
   __export
-} from "../chunk-XNEE7Z2S.js";
+} from "../chunk-UCATYEVZ.js";
 
 // src/mcp/server.ts
 import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
@@ -4083,12 +4083,17 @@ async function createServer(notesPath, options = {}) {
       indexState = "loading";
       await embedder.init();
       const metaPath = join(indexPath, "meta.json");
+      let meta = null;
       if (existsSync(metaPath)) {
-        const meta = JSON.parse(await readFile(metaPath, "utf-8"));
-        if (meta.model && meta.model !== embedder.getModel()) {
-          process.stderr.write(`Model changed (${meta.model} \u2192 ${embedder.getModel()}), forcing reindex
+        try {
+          meta = JSON.parse(await readFile(metaPath, "utf-8"));
+          if (meta?.model && meta.model !== embedder.getModel()) {
+            process.stderr.write(`Model changed (${meta.model} \u2192 ${embedder.getModel()}), forcing reindex
 `);
-          return false;
+            return false;
+          }
+        } catch {
+          meta = null;
         }
       }
       const tempVector = new VectorIndex(embedder.getDimensions());
@@ -4102,7 +4107,9 @@ async function createServer(notesPath, options = {}) {
       docByPath = new Map(documents.map((d) => [d.path, d]));
       textSearch.setDocuments(documents);
       vectorIndex = tempVector;
-      indexState = "stale";
+      const currentChunks = documents.reduce((n, d) => n + d.chunks.length, 0);
+      const fresh = meta?.totalChunks !== void 0 && meta.totalChunks === currentChunks;
+      indexState = fresh ? "ready" : "stale";
       return true;
     } catch {
       return false;