@theglitchking/semantic-memory 1.5.1 → 1.5.3

package/.claude-plugin/marketplace.json

@@ -6,13 +6,13 @@
   },
   "metadata": {
     "description": "Single-plugin marketplace for semantic-memory — the unified memory-layer plugin. v1.1.0 absorbs brain's strengths: AGENTS.md contract artifact, hard-gated verification sessions, multi-agent skill bundler (codex/copilot/pi), and SessionStart drift detection. v1.3 adds confidence decay — age-aware retrieval ranking with verify_note to reset the clock. All backwards-compatible with v1.0.x via deprecation shims.",
-    "version": "1.5.1"
+    "version": "1.5.3"
   },
   "plugins": [
     {
       "name": "semantic-memory",
       "description": "Unified memory-layer plugin for Claude Code. One MCP server, 44 tools across multi-corpus search/read/write/graph/lint/sessions/contract. v1.1.0 adds: AGENTS.md contract artifact, hard-gated verification sessions (session_start/run/finish/status), proposal-mode synthesize_note + synthesize_promote, multi-agent skill bundler (codex/copilot/pi via the new `skills` CLI), and SessionStart drift detection. v1.2 completes the hygiene line: `/healthcheck --fix` auto-remediation, `lint_vault({checks:['code_symbols']})` code-path drift, and a fresh-install CI smoke gate. v1.3 adds confidence decay: age-aware search ranking (0.5^(age/half-life), type-aware, floored, composes with load_priority), a `decay` block surfaced on decayed results, `verify_note` to reset the clock, `evergreen` opt-out, and `decay-config`/`decay-trace` CLI introspection. v1.3.1 adds local-only selection-logging telemetry (which note each search result actually got used), the `decay_candidates` lint, and a `selection-stats` CLI. v1.4.0 is the resident-expert bridge: a learned human→artifact lexicon (`manage_lexicon`) with propose-and-confirm alias capture, verbatim symptom capture + symptom-keyed indexing (terse symptom queries match the note), Tier-1 lexicon query expansion in the hook, archive path-class down-weight, injection hygiene (score-gate + dedup + top-3 + compact instructions), section-targeted `read_note`, and opt-in conditional tool registration. v1.5.0 is the expert-character layer: entity dossiers (`manage_dossier`) — per-component living notes (purpose / failure modes / knobs / incident log / current state) that accrete in place, with two-hop retrieval (utterance→entity→dossier injected first); usage-feedback ranking that boosts repeatedly-cited notes (capped, composes with decay/path-class) plus a `decoys` lint for retrieved-but-never-cited notes (surfaced, never auto-down-ranked); session paging (Stop drafts a durable session digest as a proposal, SessionStart pages in a curated digest instead of a broad sweep); and a speaker profile (`manage_profile`) that models how the human communicates — severity calibration, chronic omissions, verbosity, shorthand — injected at SessionStart. Backwards-compatible with v1.0.x — every previous tool name remains callable through deprecation shims (removed in v2.0.0).",
-      "version": "1.5.1",
+      "version": "1.5.3",
       "author": {
         "name": "TheGlitchKing"
       },

package/.claude-plugin/plugin.json

@@ -1,7 +1,7 @@
 {
   "name": "semantic-memory",
   "description": "Unified memory-layer plugin for Claude Code. One MCP server, multiple typed corpora (vault / code / plans / docs / research / project-map), unified cross-corpus knowledge graph, conditional tool registration, in-process drift detection, and human↔code translation. Rebrand of `semantic-sidekick` at v1.0.0 — see CHANGELOG for migration.",
-  "version": "1.5.1",
+  "version": "1.5.3",
   "author": {
     "name": "TheGlitchKing",
     "email": "theglitchking@users.noreply.github.com"

package/CHANGELOG.md

@@ -2,6 +2,49 @@
 
 All notable changes to semantic-memory (formerly semantic-sidekick) will be documented here.
 
+## [1.5.3] - 2026-10-24 — Secret redaction
+
+Patch release. Until now nothing stopped an API key, token or password that passed through the plugin from being written to disk in the clear — and vault notes are usually committed to git. Every write point now masks secrets first, and `lint_vault` can find the ones already there.
+
+### Security
+
+- **Redaction at every write point** (`src/core/redact.ts`), two layers: the exact values of secret-named env vars on the machine (process env + `~/.claude/settings.json` `env`), then patterns — PEM private keys, `user:pass@` URL credentials, `Bearer`/`Basic` headers, secret-named `name=value` / `name: value` / JSON pairs, `--token VALUE` flags, vendor key prefixes (`sk-`/`pk-`/`rk-`, `ghp_`, `github_pat_`, `glpat-`, `xox*-`, `GOCSPX-`, `hvs.`, `AKIA`/`ASIA`, `AIza`, `whsec_`, `re_`, `hf_`, `npm_`), JWTs.
+  - **Notes** (create/update, `apply_patch`, synthesize, ingest, promote, `update_frontmatter`, dossiers, speaker profile, lexicon aliases, `log.md`) use a *precise* set tuned so ordinary content survives: commit SHAs, UUIDs, hashes, paths, `pk_customer_orders`, `max_tokens`, `monkey: …`, code such as `api_key = os.getenv` (a name=value only counts when the value looks random: a digit, or 16+ letters) and placeholders (`<your-key>`, `${API_TOKEN}`, `process.env.X`, `changeme`, `xxxx`) are untouched. `update_note` redacts only the incoming text.
+  - **Logs and state** (search queries in `selection.jsonl`, `session.json` task / `session_run` command and output tail, the hook's capture-pending excerpt) also mask long base64 and letter-and-digit tokens.
+  - The hook imports the redactor from `dist/core/redact.js`; if it cannot load, the capture excerpt is withheld rather than stored raw.
+  - Tool results say how many secrets were redacted (`… (2 secrets redacted)`, or `redacted: N` in JSON results), never which.
+- **`lint_vault({ checks: ["secrets"] })`** — opt-in check that reports notes already containing a secret: path, line and kind, never the value; nothing is rewritten. A secret that was ever committed must be **rotated**: redaction cannot remove it from git history.
+- Known limit: a secret written as plain prose ("the password is hunter2") is not caught.
+
+### Changed
+
+- `NoteCrud.create()` returns `{ path, redacted }` instead of the path string; `NoteCrud.update()` returns the same shape (was `void`). Only affects code using `@theglitchking/semantic-memory` as a library.
+
+### Tests
+
+- Full suite **516 green** (440 in 1.5.2). One integration test per write point through the real MCP tools (all fail without the change), a sweep of the whole vault for the fake values, false-positive cases for ordinary note content, linear-time checks on 1 MB pathological inputs.
+
+## [1.5.2] - 2026-10-24 — Docs index freshness (issue #29)
+
+Patch release. In the standard two-server setup (`semantic-vault` → `.claude/.vault`, `semantic-sidekick` → `.documentation --read-only`) the docs index went stale after it was first built and the hooks never searched the docs. Fixes for every cause found, plus the dependency audit.
+
+### Fixed
+
+- **Stale cached index is rebuilt at startup.** A cache whose `meta.totalChunks` no longer matches the notes on disk loaded as `"stale"` and was served forever; startup only reindexed when the cache failed to load. It now rebuilds in the background and serves the stale index meanwhile.
+- **File watcher works under chokidar 5.** `watch("**/*.md")` is a literal path since chokidar 4 dropped globs, so no event ever fired and edits during a session were never reindexed. The watcher now watches the notes folder and filters (`node_modules`, `.semantic-sidekick-index`, `.git`, non-markdown).
+- **One bad doc no longer fails the whole index.** `indexAll()` rejected if any file failed, so a single doc with invalid YAML frontmatter (e.g. an unquoted colon in `purpose:`) left the entire corpus unindexed. Invalid frontmatter now indexes the body with empty frontmatter; any other per-file error skips that file. Both are reported on stderr.
+- **Hooks search every `semantic-*` notes path.** The prompt hook and the SessionStart search used only the first `.mcp.json` entry, normally an (often empty) vault. They now search every entry's `--notes` path in parallel and merge hits by score; with more than one corpus each hit is labelled with its server. Writes (log events, dossiers, session digests, speaker profile) stay on one path: the first entry without `--read-only`. `SIDEKICK_VAULT_PATH` still means a single path. Hook latency on a two-server project: ~670 ms → ~800 ms.
+- **Capture prompts stay in their own session.** `capture-pending.json` is per project, so a cue typed in one session showed up in another concurrent session's Stop prompt, and any SessionStart or Stop wiped every session's items. Items now carry `session_id`; each session asks about and clears only its own. Items from before 1.5.2 go to whichever session reads them first; other sessions' items older than a week are pruned.
+- **Watcher tests can fail again.** They treated their own timeout as "filesystem events not available" and passed while the watcher was dead.
+
+### Changed
+
+- **Dependency audit:** 30 findings (1 critical, 19 high; 22 in production) → 3 (1 in production). `overrides` re-pinned to current patches (several 1.5.1 pins had become the vulnerable versions); in-range updates including `@modelcontextprotocol/sdk` 1.32.2, `@huggingface/transformers` 4.3.1, `onnxruntime-node` 1.30.0, `vitest` 4.1.12. Still open, breaking-only fixes: `zod` (every 3.x is affected; the fix is zod 4, which changes the MCP tool schemas) and dev-only `esbuild` (low).
+
+### Tests
+
+- Full suite **440 green** (was 418); build and lint clean; golden retrieval eval unchanged (recall@1 86%, MRR 0.929). Each fix has a test that fails on 1.5.1.
+
 ## [1.5.1] - 2026-07-12 — Dependency audit hardening (supply chain)
 
 Patch release: clears the transitive `npm audit` findings surfaced after upgrading from the 1.2.x line, with **no runtime or API change**. Every advisory was unreachable in practice — this is a local **stdio** MCP server plus hook scripts processing the user's **own** files: the `hono`/`express-rate-limit`/`ip-address`/`qs`/`fast-uri` cluster is the MCP SDK's HTTP-server transport, which this plugin never instantiates (stdio only); `protobufjs`/`@xmldom/xmldom` are the local embedding runtime; `js-yaml`/`brace-expansion` parse your own notes/globs.

package/README.md

@@ -78,6 +78,10 @@ System (2): `get_stats`, `reindex`
 
 See the originating design discussion in `.planning/semantic-sidekick/` for rationale and phase-by-phase build plan.
 
+## Privacy and secrets
+
+Everything stays on your machine (local embedding model, no network telemetry). Since v1.5.3 every write masks API keys, tokens, passwords and private keys before they reach disk, and `lint_vault({ checks: ["secrets"] })` finds ones already in notes. Details and limits: [SECURITY.md](SECURITY.md#secret-redaction-v153).
+
 ## Development
 
 ```bash

package/dist/{chunk-25EIQWXL.js → chunk-44BQDRXD.js}

@@ -124,8 +124,8 @@ var Embedder = class {
       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 inputIdsRaw = Array.from(encoded.input_ids);
+    const attentionMaskRaw = Array.from(encoded.attention_mask);
     const seqLen = inputIdsRaw.length;
     const inputIds = new this.ort.Tensor(
       "int64",
@@ -222,8 +222,8 @@ var Embedder = class {
       )
     );
     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)
+      ids: Array.from(enc.input_ids),
+      mask: Array.from(enc.attention_mask)
     }));
     const seqLen = Math.max(...tokenized.map((t) => t.ids.length));
     const flatIds = new BigInt64Array(n * seqLen);
@@ -648,4 +648,4 @@ export {
   VectorIndex,
   TextSearch
 };
-//# sourceMappingURL=chunk-25EIQWXL.js.map
+//# sourceMappingURL=chunk-44BQDRXD.js.map

package/dist/chunk-44BQDRXD.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"],"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-sidekick\", \"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-sidekick 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);\n    const attentionMaskRaw: number[] = Array.from(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) as number[],\n      mask: Array.from(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  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package/dist/{chunk-2EELGTLX.js → chunk-D5QLNNA4.js}

@@ -1,6 +1,6 @@
 import {
   lintVault
-} from "./chunk-FM26NFTR.js";
+} from "./chunk-OFXQXVG5.js";
 
 // src/core/healthcheck.ts
 import { readFile, writeFile, mkdir } from "fs/promises";
@@ -338,4 +338,4 @@ export {
   filterToDrift,
   formatDriftBanner
 };
-//# sourceMappingURL=chunk-2EELGTLX.js.map
+//# sourceMappingURL=chunk-D5QLNNA4.js.map

package/dist/{chunk-A3KYHKB5.js → chunk-FTRXH2WC.js}

@@ -1,9 +1,12 @@
 import {
   listDossiers
-} from "./chunk-WSU4QIPB.js";
+} from "./chunk-XAXK7NM4.js";
 import {
   deriveSessionDir
-} from "./chunk-S4KW7VH4.js";
+} from "./chunk-LGQPP5FQ.js";
+import {
+  redactDeep
+} from "./chunk-OEF5U5GV.js";
 
 // src/core/lexicon.ts
 import { readFile, writeFile, mkdir, unlink } from "fs/promises";
@@ -88,7 +91,8 @@ function expandQuery(aliases, query) {
   const additions = [...new Set(matched.map((a) => a.canonical))].join(" ");
   return { expanded: `${query} ${additions}`, matched };
 }
-async function writeAliasNote(vaultPath, rel, entry) {
+async function writeAliasNote(vaultPath, rel, raw) {
+  const entry = redactDeep(raw, "precise").value;
   const fm = {
     type: "alias",
     canonical: entry.canonical,
@@ -173,4 +177,4 @@ export {
   findAliasConflicts,
   removeAlias
 };
-//# sourceMappingURL=chunk-A3KYHKB5.js.map
+//# sourceMappingURL=chunk-FTRXH2WC.js.map

package/dist/chunk-FTRXH2WC.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/core/lexicon.ts"],"sourcesContent":["import { readFile, writeFile, mkdir, unlink } from \"node:fs/promises\";\nimport { existsSync } from \"node:fs\";\nimport { join, dirname } from \"node:path\";\nimport { glob } from \"glob\";\nimport matter from \"gray-matter\";\nimport { redactDeep } from \"./redact.js\";\nimport { deriveSessionDir } from \"./session.js\";\nimport { listDossiers } from \"./dossier.js\";\n\n/**\n * Lexicon corpus (v1.4 Phase 3) — the learned human→artifact vocabulary.\n *\n * The heart of the human→LLM bridge: maps the human's own phrasing (\"the flaky\n * thing\", \"the deploy dance\") to concrete artifacts (paths / code symbols).\n * Canonical storage is markdown notes of type `alias` under <vault>/lexicon/;\n * a derived JSON cache under .claude/.semantic-memory/ is what the hot-path hook\n * reads for deterministic query expansion.\n */\n\nexport type Confidence = \"low\" | \"medium\" | \"high\";\n\nexport interface AliasEntry {\n  /** The concrete target: a note path or a code symbol/path. */\n  canonical: string;\n  /** The human's actual words that refer to it (verbatim). */\n  phrases: string[];\n  confidence: Confidence;\n  evidence_count: number;\n  last_used?: string;\n  source: \"learned\" | \"authored\";\n  /** The lexicon note path this entry came from. */\n  path: string;\n}\n\nconst CACHE_FILE = \"lexicon-cache.json\";\nconst LEXICON_DIR = \"lexicon\";\n\nexport function normalizePhrase(s: string): string {\n  return s.toLowerCase().trim().replace(/\\s+/g, \" \");\n}\n\nexport function slugify(s: string): string {\n  return s.toLowerCase().replace(/[^a-z0-9]+/g, \"-\").replace(/^-+|-+$/g, \"\").slice(0, 60) || \"alias\";\n}\n\nfunction confidenceFor(evidenceCount: number): Confidence {\n  return evidenceCount >= 3 ? \"high\" : evidenceCount >= 2 ? \"medium\" : \"low\";\n}\n\n/** Read every lexicon note into entries and write the derived cache. */\nexport async function compileLexicon(vaultPath: string): Promise<AliasEntry[]> {\n  const files = await glob(`${LEXICON_DIR}/**/*.md`, { cwd: vaultPath });\n  const entries: AliasEntry[] = [];\n  for (const rel of files) {\n    try {\n      const { data } = matter(await readFile(join(vaultPath, rel), \"utf-8\"));\n      if (data.type !== \"alias\" || typeof data.canonical !== \"string\") continue;\n      const phrases = Array.isArray(data.phrases) ? data.phrases.map(String).map((p) => p.trim()).filter(Boolean) : [];\n      entries.push({\n        canonical: data.canonical,\n        phrases,\n        confidence: ([\"low\", \"medium\", \"high\"] as const).includes(data.confidence) ? data.confidence : confidenceFor(1),\n        evidence_count: typeof data.evidence_count === \"number\" ? data.evidence_count : phrases.length ? 1 : 0,\n        last_used: typeof data.last_used === \"string\" ? data.last_used : undefined,\n        source: data.source === \"authored\" ? \"authored\" : \"learned\",\n        path: rel,\n      });\n    } catch {\n      /* skip unreadable note */\n    }\n  }\n  // Fold in dossier aliases (v1.5 Phase 8): a dossier's `aliases:` are the human's\n  // phrases for that entity, so they become query-expansion bindings pointing at the\n  // dossier note. Authored, not learned — the human named the entity deliberately.\n  // A lexicon note for the same canonical wins (it carries real evidence_count).\n  try {\n    const dossiers = await listDossiers(vaultPath);\n    for (const d of dossiers) {\n      if (d.aliases.length === 0) continue;\n      if (entries.some((e) => e.canonical === d.path)) continue;\n      entries.push({\n        canonical: d.path,\n        phrases: d.aliases,\n        confidence: \"high\",\n        evidence_count: d.aliases.length,\n        source: \"authored\",\n        path: d.path,\n      });\n    }\n  } catch {\n    /* dossiers optional — lexicon compiles fine without them */\n  }\n  try {\n    const dir = deriveSessionDir(vaultPath);\n    await mkdir(dir, { recursive: true });\n    await writeFile(join(dir, CACHE_FILE), JSON.stringify({ compiledAt: new Date().toISOString(), aliases: entries }, null, 2), \"utf-8\");\n  } catch {\n    /* cache write is best-effort */\n  }\n  return entries;\n}\n\n/** Fast read for the hook: use the cache if present, else compile. */\nexport async function loadLexiconCache(vaultPath: string): Promise<AliasEntry[]> {\n  const cachePath = join(deriveSessionDir(vaultPath), CACHE_FILE);\n  if (existsSync(cachePath)) {\n    try {\n      const data = JSON.parse(await readFile(cachePath, \"utf-8\"));\n      if (Array.isArray(data?.aliases)) return data.aliases as AliasEntry[];\n    } catch {\n      /* fall through to recompile */\n    }\n  }\n  return compileLexicon(vaultPath);\n}\n\nexport function lookupPhrase(aliases: AliasEntry[], phrase: string): AliasEntry[] {\n  const n = normalizePhrase(phrase);\n  return aliases.filter((a) => a.phrases.some((p) => normalizePhrase(p) === n));\n}\n\n/**\n * Expand a query by appending the canonical targets of any alias phrases that\n * appear in it. Deterministic, no LLM — this is the Tier-1 hook-time expansion.\n */\nexport function expandQuery(aliases: AliasEntry[], query: string): { expanded: string; matched: AliasEntry[] } {\n  const nq = normalizePhrase(query);\n  const matched = aliases.filter((a) => a.phrases.some((p) => p && nq.includes(normalizePhrase(p))));\n  if (matched.length === 0) return { expanded: query, matched: [] };\n  const additions = [...new Set(matched.map((a) => a.canonical))].join(\" \");\n  return { expanded: `${query} ${additions}`, matched };\n}\n\nasync function writeAliasNote(vaultPath: string, rel: string, raw: Omit<AliasEntry, \"path\">): Promise<void> {\n  // phrases are captured from user utterances\n  const entry = redactDeep(raw, \"precise\").value;\n  const fm = {\n    type: \"alias\",\n    canonical: entry.canonical,\n    phrases: entry.phrases,\n    confidence: entry.confidence,\n    evidence_count: entry.evidence_count,\n    last_used: entry.last_used,\n    source: entry.source,\n  };\n  const body = `# Alias: ${entry.canonical}\\n\\nHuman phrases that refer to \\`${entry.canonical}\\`.\\n`;\n  const abs = join(vaultPath, rel);\n  await mkdir(dirname(abs), { recursive: true });\n  await writeFile(abs, matter.stringify(body, fm), \"utf-8\");\n}\n\n/**\n * Upsert an alias. New canonical → new note (evidence 1). Existing canonical →\n * merge phrases, bump evidence_count, recompute confidence. Recompiles the cache.\n */\nexport async function addAlias(\n  vaultPath: string,\n  input: { canonical: string; phrases: string[]; source?: \"learned\" | \"authored\"; today?: string }\n): Promise<{ path: string; created: boolean; evidence_count: number; confidence: Confidence }> {\n  const existing = await compileLexicon(vaultPath);\n  const match = existing.find((a) => a.canonical === input.canonical);\n  const today = input.today ?? new Date().toISOString().slice(0, 10);\n  const cleanPhrases = input.phrases.map((p) => p.trim()).filter(Boolean);\n\n  if (match) {\n    const phrases = [...new Set([...match.phrases, ...cleanPhrases])];\n    const evidence_count = match.evidence_count + 1;\n    const confidence = confidenceFor(evidence_count);\n    await writeAliasNote(vaultPath, match.path, { ...match, phrases, evidence_count, confidence, last_used: today });\n    await compileLexicon(vaultPath);\n    return { path: match.path, created: false, evidence_count, confidence };\n  }\n\n  const rel = join(LEXICON_DIR, `${slugify(input.canonical)}.md`);\n  const evidence_count = 1;\n  const confidence = confidenceFor(evidence_count);\n  await writeAliasNote(vaultPath, rel, {\n    canonical: input.canonical,\n    phrases: cleanPhrases,\n    confidence,\n    evidence_count,\n    last_used: today,\n    source: input.source ?? \"learned\",\n  });\n  await compileLexicon(vaultPath);\n  return { path: rel, created: true, evidence_count, confidence };\n}\n\nexport interface AliasConflict {\n  phrase: string;\n  canonicals: string[];\n}\n\n/**\n * Find conflicting bindings: the same (normalized) phrase mapping to more than one\n * canonical target. A wrong alias silently misroutes every future query with that\n * phrase, so conflicts are surfaced (never auto-resolved) for a human to fix.\n */\nexport function findAliasConflicts(aliases: AliasEntry[]): AliasConflict[] {\n  const byPhrase = new Map<string, Set<string>>();\n  for (const a of aliases) {\n    for (const p of a.phrases) {\n      const n = normalizePhrase(p);\n      if (!n) continue;\n      if (!byPhrase.has(n)) byPhrase.set(n, new Set());\n      byPhrase.get(n)!.add(a.canonical);\n    }\n  }\n  const conflicts: AliasConflict[] = [];\n  for (const [phrase, canonicals] of byPhrase) {\n    if (canonicals.size > 1) conflicts.push({ phrase, canonicals: [...canonicals].sort() });\n  }\n  return conflicts.sort((a, b) => a.phrase.localeCompare(b.phrase));\n}\n\n/** Remove an alias note by canonical. 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package/dist/{chunk-OWZWMB4P.js → chunk-FURCIJBO.js}

@@ -245,4 +245,4 @@ export {
   installDefaultSchema,
   validateNote
 };
-//# sourceMappingURL=chunk-OWZWMB4P.js.map
+//# sourceMappingURL=chunk-FURCIJBO.js.map

package/dist/chunk-FURCIJBO.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/core/schema.ts","../src/core/schema-default.ts"],"sourcesContent":["import { readFile, writeFile, access } from \"node:fs/promises\";\nimport { constants } from \"node:fs\";\nimport { join } from \"node:path\";\nimport { parse as parseYaml } from \"yaml\";\nimport matter from \"gray-matter\";\nimport { DEFAULT_SCHEMA_YAML } from \"./schema-default.js\";\n\nexport interface VaultSchema {\n  version: number;\n  provenance_fields: string[];\n  status_enum: string[];\n  confidence_enum: string[];\n  severity_enum: string[];\n  types: Record<string, { description?: string; required: string[] }>;\n  lint: {\n    missing_provenance: { applies_to: string[]; severity: \"warn\" | \"error\" };\n    stale: { max_age_days: number; severity: \"warn\" | \"error\" };\n    schema_violations: { severity: \"warn\" | \"error\" };\n  };\n}\n\nexport type Severity = \"warn\" | \"error\";\n\nexport interface LintFinding {\n  path: string;\n  rule: \"missing_provenance\" | \"stale\" | \"schema_violations\" | \"broken_links\" | \"code_symbols\" | \"decay_candidates\" | \"alias_conflicts\" | \"decoys\" | \"secrets\";\n  severity: Severity;\n  message: string;\n}\n\nexport async function loadSchema(vaultPath: string): Promise<VaultSchema> {\n  const schemaPath = join(vaultPath, \"vault.schema.yml\");\n  let raw: string;\n  try {\n    await access(schemaPath, constants.R_OK);\n    raw = await readFile(schemaPath, \"utf-8\");\n  } catch {\n    raw = DEFAULT_SCHEMA_YAML;\n  }\n  const parsed = parseYaml(raw) as VaultSchema;\n  return parsed;\n}\n\n/**\n * Bootstrap the schema file in a vault by writing the default if none exists.\n * Used by the `--install-schema` CLI flag. 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Down-weights search results by time since last_verified.\n# Composes multiplicatively with load_priority — it never removes notes, only ranks\n# them lower (floored). Set enabled: false for byte-identical pre-v1.3 ranking.\ndecay:\n  enabled: true\n  default_half_life_days: 365   # multiplier = 0.5 ^ (age_days / half_life)\n  per_type:\n    decision: 365\n    note: 365\n    gotcha: 180\n    source: null                # null = never decays\n    proposal: 14\n  floor: 0.1                     # notes never drop below this multiplier\n  hotness_boost:\n    enabled: false              # extend half-life for heavily-backlinked notes (opt-in)\n    cap: 2.0\n\n# Path-class ranking (v1.4). Down-weights whole regions of the vault by path glob\n# (composes multiplicatively with decay + load_priority). First matching rule wins.\n# The default down-weights archived notes so retired docs stop dominating results.\npath_class:\n  enabled: true\n  rules:\n    - glob: \"archive/**\"\n      multiplier: 0.3\n\n# Usage-feedback ranking (v1.5). Boosts notes that get CITED after retrieval (per\n# the local selection log) so load-bearing knowledge floats up. Bounded by cap to\n# stop a feedback runaway; composes multiplicatively with decay + path_class +\n# load_priority. A no-op until the selection log has citations. The complementary\n# signal (retrieved-but-never-cited \"decoys\") is surfaced by lint_vault, NEVER\n# auto-down-ranked. Set enabled: false for byte-identical pre-v1.5 ranking.\nusage_boost:\n  enabled: true\n  cap: 1.5            # max multiplier a note can earn from citations\n  per_citation: 0.1   # multiplier += per_citation × citation_count, then capped\n\n# Token-frugal tool surface (v1.4). When enabled, the server registers a reduced\n# tool set in modes that don't need the full surface (outage-silence → search/read\n# only). DEFAULT OFF — mid-session mode switches don't re-register, so opt in and\n# dogfood before relying on it.\ntools:\n  conditional: false\n\n# Selection-logging telemetry (v1.3.1). Records what search returned and which\n# note the answer used, to a LOCAL append-only JSONL at\n# .claude/.semantic-memory/selection.jsonl (gitignored). Never leaves the machine.\n# Feeds the decay_candidates lint and (later) usage-feedback ranking. 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package/dist/{chunk-V45NJIHI.js → chunk-IGHCVAAL.js}

@@ -9,6 +9,15 @@ import { existsSync } from "fs";
 import { basename, join } from "path";
 var DOCS_CACHE_FILE = "docs.cache.json";
 var CHUNK_TARGET_CHARS = 2e3;
+function parseFrontmatter(raw, file) {
+  try {
+    return matter(raw);
+  } catch (err) {
+    process.stderr.write(`Invalid frontmatter in ${file}, indexing body only: ${err?.message?.split("\n")[0] ?? err}
+`);
+    return { data: {}, content: raw.replace(/^---\r?\n[\s\S]*?\r?\n---[^\S\r\n]*(\r?\n|$)/, "") };
+  }
+}
 var Indexer = class {
   notesPath;
   processor;
@@ -19,9 +28,15 @@ var Indexer = class {
   async indexAll() {
     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))
+      files.map(
+        (file) => this.indexFile(join(this.notesPath, file), file).catch((err) => {
+          process.stderr.write(`Skipping ${file}: ${err?.message ?? err}
+`);
+          return null;
+        })
+      )
     );
-    return docs;
+    return docs.filter((d) => d !== null);
   }
   /**
    * Load parsed-doc cache from disk. Returns null if missing or unreadable.
@@ -51,7 +66,7 @@ var Indexer = class {
       readFile(absolutePath, "utf-8"),
       stat(absolutePath)
     ]);
-    const { data: frontmatter, content } = matter(raw);
+    const { data: frontmatter, content } = parseFrontmatter(raw, relativePath);
     const tree = this.processor.parse(content);
     const wikilinks = this.extractWikilinks(tree);
     const tags = this.extractTags(content, frontmatter);
@@ -168,4 +183,4 @@ var Indexer = class {
 export {
   Indexer
 };
-//# sourceMappingURL=chunk-V45NJIHI.js.map
+//# sourceMappingURL=chunk-IGHCVAAL.js.map

package/dist/chunk-IGHCVAAL.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, writeFile, stat } from \"node:fs/promises\";\nimport { existsSync } from \"node:fs\";\nimport { basename, join, relative } from \"node:path\";\nimport type { IndexedDocument } from \"./types.js\";\n\nconst DOCS_CACHE_FILE = \"docs.cache.json\";\n\nconst CHUNK_TARGET_CHARS = 2000; // ~512 tokens\n\n// Invalid YAML (e.g. an unquoted colon in a value) keeps the body searchable with empty frontmatter\nfunction parseFrontmatter(raw: string, file: string): { data: Record<string, unknown>; content: string } {\n  try {\n    return matter(raw);\n  } catch (err: any) {\n    process.stderr.write(`Invalid frontmatter in ${file}, indexing body only: ${err?.message?.split(\"\\n\")[0] ?? err}\\n`);\n    return { data: {}, content: raw.replace(/^---\\r?\\n[\\s\\S]*?\\r?\\n---[^\\S\\r\\n]*(\\r?\\n|$)/, \"\") };\n  }\n}\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    // One unreadable file must not take the whole corpus down with it\n    const docs = await Promise.all(\n      files.map((file) =>\n        this.indexFile(join(this.notesPath, file), file).catch((err) => {\n          process.stderr.write(`Skipping ${file}: ${err?.message ?? err}\\n`);\n          return null;\n        })\n      )\n    );\n    return docs.filter((d): d is IndexedDocument => d !== null);\n  }\n\n  /**\n   * Load parsed-doc cache from disk. Returns null if missing or unreadable.\n   * The cache is a verbatim JSON dump of a prior indexAll() result, written by\n   * saveDocsCache. Consumers (search CLI / hook path) prefer this over re-parsing\n   * 500+ markdown files; the tradeoff is that cache may be stale if the vault\n   * changed since the last reindex — same staleness window as the vector cache.\n   */\n  async loadDocsCache(indexPath: string): Promise<IndexedDocument[] | null> {\n    const p = join(indexPath, DOCS_CACHE_FILE);\n    if (!existsSync(p)) return null;\n    try {\n      const raw = await readFile(p, \"utf-8\");\n      const parsed = JSON.parse(raw);\n      if (!Array.isArray(parsed)) return null;\n      return parsed as IndexedDocument[];\n    } catch {\n      return null;\n    }\n  }\n\n  async saveDocsCache(indexPath: string, docs: IndexedDocument[]): Promise<void> {\n    const p = join(indexPath, DOCS_CACHE_FILE);\n    await writeFile(p, JSON.stringify(docs), \"utf-8\");\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 } = parseFrontmatter(raw, relativePath);\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    // Symptom-keyed indexing (v1.4 Phase 5). Each verbatim `symptoms:` phrase is\n    // added as its own chunk, so a terse symptom query (\"it hangs after reindex\")\n    // matches the note directly — the fix for asymmetric retrieval (query-shaped\n    // keys stored alongside document-shaped content). Synthetic child chunks point\n    // at the same note path; no index-format change.\n    const symptoms = Array.isArray(frontmatter.symptoms)\n      ? (frontmatter.symptoms as unknown[]).filter((s): s is string => typeof s === \"string\" && s.trim().length > 0).map((s) => s.trim())\n      : [];\n    const allChunks = symptoms.length > 0 ? [...chunks, ...symptoms] : chunks;\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: allChunks,\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/{chunk-S4KW7VH4.js → chunk-LGQPP5FQ.js}

@@ -1,3 +1,7 @@
+import {
+  redact
+} from "./chunk-OEF5U5GV.js";
+
 // src/core/session.ts
 import { mkdir, readFile, writeFile, rm } from "fs/promises";
 import { existsSync } from "fs";
@@ -34,7 +38,7 @@ var SessionManager = class {
     const id = `ses_${now.replace(/[:.]/g, "-")}`;
     const state = {
       id,
-      task: task.trim(),
+      task: redact(task.trim(), "broad").text,
       started_at: now,
       last_activity_at: now,
       verifications: [],
@@ -59,7 +63,8 @@ var SessionManager = class {
       return { ok: false, error: "session_run requires a non-empty command." };
     }
     const start = Date.now();
-    const record = await this.spawnAndCapture(cmd, timeoutMs ?? DEFAULT_TIMEOUT_MS);
+    const raw = await this.spawnAndCapture(cmd, timeoutMs ?? DEFAULT_TIMEOUT_MS);
+    const record = { ...raw, cmd: redact(raw.cmd, "broad").text, tail: redact(raw.tail, "broad").text };
     record.duration_ms = Date.now() - start;
     state.verifications.push(record);
     state.last_activity_at = (/* @__PURE__ */ new Date()).toISOString();
@@ -200,4 +205,4 @@ export {
   deriveProjectRoot,
   deriveSessionDir
 };
-//# sourceMappingURL=chunk-S4KW7VH4.js.map
+//# sourceMappingURL=chunk-LGQPP5FQ.js.map

package/dist/chunk-LGQPP5FQ.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/core/session.ts"],"sourcesContent":["import { mkdir, readFile, writeFile, rm } from \"node:fs/promises\";\nimport { redact } from \"./redact.js\";\nimport { existsSync } from \"node:fs\";\nimport { join } from \"node:path\";\nimport { spawn } from \"node:child_process\";\n\nexport interface VerificationRecord {\n  cmd: string;\n  exit: number | null;\n  signal: string | null;\n  duration_ms: number;\n  tail: string;\n  at: string;\n}\n\nexport interface SessionState {\n  id: string;\n  task: string;\n  started_at: string;\n  last_activity_at: string;\n  verifications: VerificationRecord[];\n  notes_touched: string[];\n  closed_at?: string;\n  closed_summary?: string;\n  closed_verified_waived?: boolean;\n  closed_waiver_reason?: string;\n}\n\nexport type SessionStatus =\n  | { state: \"no_session\" }\n  | (SessionState & { state: \"active\" | \"stale\" });\n\nexport interface SessionStartOptions {\n  /** When true and a session for the same task is already open, return the existing id rather than failing. Defaults to true. */\n  reuseSameTask?: boolean;\n}\n\nexport interface SessionFinishInput {\n  summary: string;\n  /**\n   * When false, the caller is explicitly waiving verification (e.g. for doc-only edits).\n   * Requires a non-empty `reason`. When true (default) and no verifications have been\n   * recorded, the call is refused.\n   */\n  verified?: boolean;\n  reason?: string;\n}\n\nconst STALE_THRESHOLD_MS = 24 * 60 * 60 * 1000;\nconst DEFAULT_TIMEOUT_MS = 5 * 60 * 1000;\nconst TAIL_BYTES = 4096;\n\n/**\n * SessionManager owns a single session.json file at `<sessionDir>/session.json`.\n *\n * State is durable across MCP server restarts (the file persists). At most one session\n * is active per project at a time — concurrent sessions are explicitly out of scope\n * for v1.1; brain has the same constraint.\n *\n * Hard gates:\n *  - session_finish refuses without verifications unless verified=false + reason\n *  - session_run refuses without an open session\n *  - session_start refuses if another session is open with a different task\n *\n * Stale detection: a session whose last_activity_at is >24h old is reported as\n * state:\"stale\" by status(). Stale sessions can still be finished or extended; the\n * label is informational so callers can decide whether to abandon (rm + start new) or\n * resume.\n */\nexport class SessionManager {\n  constructor(private sessionDir: string) {}\n\n  get sessionPath(): string {\n    return join(this.sessionDir, \"session.json\");\n  }\n\n  async start(task: string, opts: SessionStartOptions = {}): Promise<{ ok: true; id: string; reused?: boolean } | { ok: false; error: string }> {\n    if (!task || task.trim().length === 0) {\n      return { ok: false, error: \"session_start requires a non-empty task.\" };\n    }\n    await mkdir(this.sessionDir, { recursive: true });\n    const existing = await this.read();\n    if (existing && !existing.closed_at) {\n      const reuseSameTask = opts.reuseSameTask !== false;\n      if (reuseSameTask && existing.task === task) {\n        return { ok: true, id: existing.id, reused: true };\n      }\n      return {\n        ok: false,\n        error: `Session already open: id=${existing.id}, task=${JSON.stringify(existing.task)}. Close it with session_finish first.`,\n      };\n    }\n    const now = new Date().toISOString();\n    const id = `ses_${now.replace(/[:.]/g, \"-\")}`;\n    const state: SessionState = {\n      id,\n      task: redact(task.trim(), \"broad\").text,\n      started_at: now,\n      last_activity_at: now,\n      verifications: [],\n      notes_touched: [],\n    };\n    await writeFile(this.sessionPath, JSON.stringify(state, null, 2), \"utf-8\");\n    return { ok: true, id };\n  }\n\n  async status(): Promise<SessionStatus> {\n    const state = await this.read();\n    if (!state || state.closed_at) return { state: \"no_session\" };\n    const age = Date.now() - new Date(state.last_activity_at).getTime();\n    const label: \"active\" | \"stale\" = age > STALE_THRESHOLD_MS ? \"stale\" : \"active\";\n    return { ...state, state: label };\n  }\n\n  async run(cmd: string, timeoutMs?: number): Promise<{ ok: true; record: VerificationRecord } | { ok: false; error: string }> {\n    const state = await this.read();\n    if (!state || state.closed_at) {\n      return { ok: false, error: \"No active session. Run session_start first.\" };\n    }\n    if (!cmd || cmd.trim().length === 0) {\n      return { ok: false, error: \"session_run requires a non-empty command.\" };\n    }\n    const start = Date.now();\n    const raw = await this.spawnAndCapture(cmd, timeoutMs ?? DEFAULT_TIMEOUT_MS);\n    // session.json keeps the command and its output tail: either can carry a token\n    const record = { ...raw, cmd: redact(raw.cmd, \"broad\").text, tail: redact(raw.tail, \"broad\").text };\n    record.duration_ms = Date.now() - start;\n    state.verifications.push(record);\n    state.last_activity_at = new Date().toISOString();\n    await writeFile(this.sessionPath, JSON.stringify(state, null, 2), \"utf-8\");\n    return { ok: true, record };\n  }\n\n  async finish(input: SessionFinishInput): Promise<{ ok: true; closed: SessionState } | { ok: false; error: string }> {\n    const state = await this.read();\n    if (!state || state.closed_at) {\n      return { ok: false, error: \"No active session to finish.\" };\n    }\n    const explicitWaiver = input.verified === false;\n    if (!explicitWaiver && state.verifications.length === 0) {\n      return {\n        ok: false,\n        error:\n          \"session_finish refused: no verification commands recorded. Run session_run with a real verification command (tests, lint, etc.) first, OR pass verified=false with a reason to waive verification (e.g. for doc-only edits).\",\n      };\n    }\n    if (explicitWaiver && (!input.reason || input.reason.trim().length === 0)) {\n      return {\n        ok: false,\n        error: \"session_finish refused: verified=false requires a non-empty `reason` explaining why verification is not applicable to this task.\",\n      };\n    }\n    if (!input.summary || input.summary.trim().length === 0) {\n      return { ok: false, error: \"session_finish requires a non-empty `summary`.\" };\n    }\n    const closed: SessionState = {\n      ...state,\n      closed_at: new Date().toISOString(),\n      closed_summary: input.summary.trim(),\n      ...(explicitWaiver && {\n        closed_verified_waived: true,\n        closed_waiver_reason: input.reason!.trim(),\n      }),\n    };\n    // Sessions are ephemeral runtime state — finished sessions are removed from disk.\n    // Durable artifacts (synthesize_note proposals, log entries) capture what mattered.\n    await rm(this.sessionPath, { force: true });\n    return { ok: true, closed };\n  }\n\n  /**\n   * Append paths to notes_touched on the active session, deduplicating. No-op when no\n   * session is active. Used by patch tools to record what the session edited.\n   */\n  async recordNotesTouched(paths: string[]): Promise<void> {\n    if (paths.length === 0) return;\n    const state = await this.read();\n    if (!state || state.closed_at) return;\n    const set = new Set(state.notes_touched);\n    for (const p of paths) set.add(p);\n    state.notes_touched = Array.from(set);\n    state.last_activity_at = new Date().toISOString();\n    await writeFile(this.sessionPath, JSON.stringify(state, null, 2), \"utf-8\");\n  }\n\n  /**\n   * Read the active session WITHOUT computing the stale label. Returns null when no\n   * session is active or when the file is unparseable.\n   */\n  async readActive(): Promise<SessionState | null> {\n    const state = await this.read();\n    if (!state || state.closed_at) return null;\n    return state;\n  }\n\n  private async read(): Promise<SessionState | null> {\n    if (!existsSync(this.sessionPath)) return null;\n    try {\n      const raw = await readFile(this.sessionPath, \"utf-8\");\n      const parsed = JSON.parse(raw);\n      if (typeof parsed?.id !== \"string\") return null;\n      return parsed as SessionState;\n    } catch {\n      return null;\n    }\n  }\n\n  private spawnAndCapture(cmd: string, timeoutMs: number): Promise<VerificationRecord> {\n    return new Promise((resolve) => {\n      const proc = spawn(cmd, { shell: true });\n      let buf = \"\";\n      let killedByTimeout = false;\n      const timer = setTimeout(() => {\n        killedByTimeout = true;\n        proc.kill(\"SIGTERM\");\n        setTimeout(() => {\n          try { proc.kill(\"SIGKILL\"); } catch { /* already gone */ }\n        }, 1000).unref();\n      }, timeoutMs);\n\n      const onData = (chunk: Buffer) => {\n        buf += chunk.toString(\"utf-8\");\n        if (buf.length > TAIL_BYTES * 4) {\n          buf = buf.slice(buf.length - TAIL_BYTES * 2);\n        }\n      };\n      proc.stdout?.on(\"data\", onData);\n      proc.stderr?.on(\"data\", onData);\n\n      proc.on(\"close\", (code, signal) => {\n        clearTimeout(timer);\n        const tail = buf.slice(-TAIL_BYTES);\n        resolve({\n          cmd,\n          exit: killedByTimeout ? null : code,\n          signal: killedByTimeout ? \"SIGTERM (timeout)\" : (signal ?? null),\n          duration_ms: 0,\n          tail,\n          at: new Date().toISOString(),\n        });\n      });\n\n      proc.on(\"error\", (err) => {\n        clearTimeout(timer);\n        const tail = buf + `\\n[spawn error: ${err.message}]`;\n        resolve({\n          cmd,\n          exit: null,\n          signal: null,\n          duration_ms: 0,\n          tail: tail.slice(-TAIL_BYTES),\n          at: new Date().toISOString(),\n        });\n      });\n    });\n  }\n}\n\n/**\n * Heuristic: derive the project root from the vault path. If the vault path ends in\n * `.claude/.vault`, the project root is two levels up. Otherwise the vault path is\n * treated as the project root.\n */\nexport function deriveProjectRoot(notesPath: string): string {\n  const norm = notesPath.replace(/[\\\\/]+$/, \"\");\n  if (norm.endsWith(\"/.claude/.vault\") || norm.endsWith(\"\\\\.claude\\\\.vault\")) {\n    return norm.slice(0, -\".claude/.vault\".length).replace(/[\\\\/]+$/, \"\");\n  }\n  return norm;\n}\n\nexport function deriveSessionDir(notesPath: string): string {\n  return join(deriveProjectRoot(notesPath), \".claude\", 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package/dist/{chunk-NTYYS53O.js → chunk-NBY4TRP7.js}

@@ -1,6 +1,9 @@
 import {
   deriveSessionDir
-} from "./chunk-S4KW7VH4.js";
+} from "./chunk-LGQPP5FQ.js";
+import {
+  redact
+} from "./chunk-OEF5U5GV.js";
 
 // src/core/telemetry.ts
 import { appendFile, readFile, mkdir } from "fs/promises";
@@ -28,7 +31,8 @@ async function appendEvent(vaultPath, event, nowIso) {
     if (!telemetryEnabled(vaultPath)) return;
     const dir = deriveSessionDir(vaultPath);
     await mkdir(dir, { recursive: true });
-    const line = JSON.stringify({ ts: nowIso ?? (/* @__PURE__ */ new Date()).toISOString(), ...event });
+    const safe = event.kind === "search" ? { ...event, query: redact(event.query, "broad").text } : event;
+    const line = JSON.stringify({ ts: nowIso ?? (/* @__PURE__ */ new Date()).toISOString(), ...safe });
     await appendFile(selectionLogPath(vaultPath), line + "\n", "utf-8");
   } catch {
   }
@@ -88,4 +92,4 @@ export {
   readSelectionLog,
   computeSelectionStats
 };
-//# sourceMappingURL=chunk-NTYYS53O.js.map
+//# sourceMappingURL=chunk-NBY4TRP7.js.map

package/dist/chunk-NBY4TRP7.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/core/telemetry.ts"],"sourcesContent":["import { appendFile, readFile, mkdir } from \"node:fs/promises\";\nimport { existsSync, readFileSync } from \"node:fs\";\nimport { join } from \"node:path\";\nimport { redact } from \"./redact.js\";\nimport { parse as parseYaml } from \"yaml\";\nimport { deriveSessionDir } from \"./session.js\";\n\n/**\n * Selection-logging telemetry (v1.3.1).\n *\n * Records what retrieval actually returned and which note the answer used, so a\n * later release (v1.4 usage-feedback ranking) can learn which knowledge is\n * load-bearing. Strictly local, append-only JSONL, fire-and-forget, opt-out.\n *\n * NO NETWORK: this module performs local filesystem I/O only, and never opens a\n * socket or issues a remote request — a unit test greps this file to keep it that way.\n */\n\nconst LOG_FILE = \"selection.jsonl\";\nconst CORRELATION_WINDOW_MS = 60_000;\n\nexport interface SearchEvent {\n  kind: \"search\";\n  tool: string;\n  query: string;\n  results: { path: string; score: number; decay?: number }[];\n}\n\nexport interface SelectionEvent {\n  kind: \"selection\";\n  note_path: string;\n  via: string;\n  /** True when this selection followed a recent search that returned this path. */\n  correlated?: boolean;\n}\n\nexport type TelemetryEvent = (SearchEvent | SelectionEvent) & { ts?: string };\n\n/** Absolute path to the selection log for a given vault. */\nexport function selectionLogPath(vaultPath: string): string {\n  return join(deriveSessionDir(vaultPath), LOG_FILE);\n}\n\n/**\n * Whether telemetry is enabled. Reads `telemetry.enabled` from vault.schema.yml;\n * defaults true (opt-out, not opt-in). Fails open to enabled only if the schema\n * is unreadable — a missing `telemetry` block means \"use the default (true)\".\n */\nexport function telemetryEnabled(vaultPath: string): boolean {\n  try {\n    const schemaPath = join(vaultPath, \"vault.schema.yml\");\n    if (!existsSync(schemaPath)) return true;\n    const parsed = parseYaml(readFileSync(schemaPath, \"utf-8\")) as { telemetry?: { enabled?: boolean } } | null;\n    const e = parsed?.telemetry?.enabled;\n    return typeof e === \"boolean\" ? e : true;\n  } catch {\n    return true;\n  }\n}\n\n/**\n * Append one event. Fire-and-forget: respects the opt-out and NEVER throws — a\n * telemetry failure must not affect the tool call that triggered it.\n */\nexport async function appendEvent(vaultPath: string, event: TelemetryEvent, nowIso?: string): Promise<void> {\n  try {\n    if (!telemetryEnabled(vaultPath)) return;\n    const dir = deriveSessionDir(vaultPath);\n    await mkdir(dir, { recursive: true });\n    // only the free-text query: note_path feeds usage-boost citation counts and must stay intact\n    const safe = event.kind === \"search\" ? { ...event, query: redact(event.query, \"broad\").text } : event;\n    const line = JSON.stringify({ ts: nowIso ?? new Date().toISOString(), ...safe });\n    await appendFile(selectionLogPath(vaultPath), line + \"\\n\", \"utf-8\");\n  } catch {\n    // fire-and-forget\n  }\n}\n\n// --- In-process correlation ring ---\n// Remembers the most recent search's top-k paths per vault so a subsequent\n// read/synthesize can be attributed to it (best-effort, time-bounded).\n\nconst recentSearch = new Map<string, { paths: Set<string>; atMs: number }>();\n\nexport function recordSearchForCorrelation(vaultPath: string, paths: string[], nowMs?: number): void {\n  recentSearch.set(vaultPath, { paths: new Set(paths), atMs: nowMs ?? 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