@theglitchking/semantic-memory 1.5.1 → 1.5.3

package/dist/{profile-LXUEF7TX.js → profile-UE4YVTDC.js}

@@ -5,9 +5,10 @@ import {
   readSpeakerProfile,
   speakerProfileTemplate,
   updateProfileSection
-} from "./chunk-7M3JZOYH.js";
-import "./chunk-WSU4QIPB.js";
-import "./chunk-S4KW7VH4.js";
+} from "./chunk-WZEKIUYG.js";
+import "./chunk-XAXK7NM4.js";
+import "./chunk-LGQPP5FQ.js";
+import "./chunk-OEF5U5GV.js";
 import "./chunk-PZ5AY32C.js";
 export {
   PROFILE_SECTIONS,
@@ -17,4 +18,4 @@ export {
   speakerProfileTemplate,
   updateProfileSection
 };
-//# sourceMappingURL=profile-LXUEF7TX.js.map
+//# sourceMappingURL=profile-UE4YVTDC.js.map

package/dist/{schema-ATFCLC6Y.js → schema-LY6533NJ.js}

@@ -2,11 +2,11 @@ import {
   installDefaultSchema,
   loadSchema,
   validateNote
-} from "./chunk-OWZWMB4P.js";
+} from "./chunk-FURCIJBO.js";
 import "./chunk-PZ5AY32C.js";
 export {
   installDefaultSchema,
   loadSchema,
   validateNote
 };
-//# sourceMappingURL=schema-ATFCLC6Y.js.map
+//# sourceMappingURL=schema-LY6533NJ.js.map

package/dist/{search-AHKEFI2B.js → search-ZS6OW74K.js}

@@ -3,10 +3,10 @@ import {
   GraphBuilder,
   TextSearch,
   VectorIndex
-} from "./chunk-25EIQWXL.js";
+} from "./chunk-44BQDRXD.js";
 import {
   Indexer
-} from "./chunk-V45NJIHI.js";
+} from "./chunk-IGHCVAAL.js";
 import "./chunk-PZ5AY32C.js";
 
 // src/cli/search.ts
@@ -199,4 +199,4 @@ function extractKeywords(query) {
 export {
   runSearch
 };
-//# sourceMappingURL=search-AHKEFI2B.js.map
+//# sourceMappingURL=search-ZS6OW74K.js.map

package/dist/{telemetry-GB2TEHVE.js → telemetry-B4KP3UVE.js}

@@ -6,8 +6,9 @@ import {
   selectionLogPath,
   telemetryEnabled,
   wasRecentlySearched
-} from "./chunk-NTYYS53O.js";
-import "./chunk-S4KW7VH4.js";
+} from "./chunk-NBY4TRP7.js";
+import "./chunk-LGQPP5FQ.js";
+import "./chunk-OEF5U5GV.js";
 import "./chunk-PZ5AY32C.js";
 export {
   appendEvent,
@@ -18,4 +19,4 @@ export {
   telemetryEnabled,
   wasRecentlySearched
 };
-//# sourceMappingURL=telemetry-GB2TEHVE.js.map
+//# sourceMappingURL=telemetry-B4KP3UVE.js.map

package/dist/telemetry-B4KP3UVE.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":[],"sourcesContent":[],"mappings":"","names":[]}

package/hooks/vault-context.js

@@ -10,12 +10,14 @@
 //
 // Fails open: any error logs to stderr and emits an empty additionalContext.
 
-import { spawnSync } from "node:child_process";
+import { spawnSync, execFile } from "node:child_process";
+import { promisify } from "node:util";
 import { existsSync, readFileSync, writeFileSync, mkdirSync, readdirSync, statSync } from "node:fs";
 import { join, resolve, basename, dirname } from "node:path";
 import { createHash } from "node:crypto";
 import { fileURLToPath } from "node:url";
 
+const execFileAsync = promisify(execFile);
 const DEBUG = process.env.SIDEKICK_DEBUG === "1";
 function debug(msg) {
   if (DEBUG) process.stderr.write(`[vault-context] ${msg}\n`);
@@ -39,13 +41,16 @@ function emit(eventName, additionalContext) {
   process.stdout.write(JSON.stringify(out) + "\n");
 }
 
-function findVaultPath(projectRoot) {
-  // 1. Explicit env override (useful for tests)
+// Every notes path the hook searches: [{ name, path, readOnly }], in .mcp.json order.
+// The standard setup has two (semantic-vault → .claude/.vault, semantic-sidekick → .documentation --read-only).
+function findNotesSources(projectRoot) {
+  // 1. Explicit env override (useful for tests) — a single path, replaces the lookup
   if (process.env.SIDEKICK_VAULT_PATH) {
     const p = resolve(process.env.SIDEKICK_VAULT_PATH);
-    return existsSync(p) ? p : null;
+    return existsSync(p) ? [{ name: "vault", path: p, readOnly: false }] : [];
   }
-  // 2. Read .mcp.json → mcpServers.semantic-vault.args[--notes ...]
+  // 2. Read .mcp.json → mcpServers.semantic-{vault,sidekick,memory}.args[--notes ...]
+  const sources = [];
   const mcpPath = join(projectRoot, ".mcp.json");
   if (existsSync(mcpPath)) {
     try {
@@ -58,16 +63,24 @@ function findVaultPath(projectRoot) {
         const i = args.indexOf("--notes");
         if (i >= 0 && i + 1 < args.length) {
           const p = resolve(projectRoot, args[i + 1]);
-          if (existsSync(p)) return p;
+          if (existsSync(p) && !sources.some((s) => s.path === p)) {
+            sources.push({ name, path: p, readOnly: args.includes("--read-only") });
+          }
         }
       }
     } catch (e) {
       debug(`.mcp.json parse failed: ${e.message}`);
     }
   }
+  if (sources.length > 0) return sources;
   // 3. Default
   const def = join(projectRoot, ".claude", ".vault");
-  return existsSync(def) ? def : null;
+  return existsSync(def) ? [{ name: "vault", path: def, readOnly: false }] : [];
+}
+
+// The one path the hook writes to (log events, dossiers, digests, profile): never a read-only docs server
+function pickVaultPath(sources) {
+  return (sources.find((s) => !s.readOnly) ?? sources[0])?.path ?? null;
 }
 
 function findCliBin(projectRoot) {
@@ -86,23 +99,31 @@ function findCliBin(projectRoot) {
   return null;
 }
 
-function runSearchCli(cliBin, args, timeoutMs) {
-  const r = spawnSync("node", [cliBin, "search", ...args], {
-    stdio: ["ignore", "pipe", "pipe"],
-    timeout: timeoutMs,
-  });
-  if (r.status !== 0) {
-    debug(`search exited ${r.status}: ${r.stderr?.toString().trim()}`);
-    return null;
-  }
+async function runSearchCli(cliBin, args, timeoutMs) {
   try {
-    return JSON.parse(r.stdout.toString());
+    const { stdout } = await execFileAsync("node", [cliBin, "search", ...args], {
+      timeout: timeoutMs,
+      maxBuffer: 16 * 1024 * 1024,
+    });
+    return JSON.parse(stdout);
   } catch (e) {
-    debug(`search output parse failed: ${e.message}`);
+    debug(`search failed: ${e.stderr?.toString().trim() || e.message}`);
     return null;
   }
 }
 
+// Search every source in parallel (one CLI spawn each) and merge by score. Hits carry
+// `source` only when more than one corpus was searched, so single-corpus output is unchanged.
+async function searchSources(cliBin, sources, limit, query) {
+  const results = await Promise.all(
+    sources.map((s) => runSearchCli(cliBin, ["--notes", s.path, "--limit", String(limit), query], 30_000))
+  );
+  const multi = sources.length > 1;
+  return results
+    .flatMap((hits, i) => (Array.isArray(hits) ? hits : []).map((h) => (multi ? { ...h, source: sources[i].name } : h)))
+    .sort((a, b) => (b.score ?? 0) - (a.score ?? 0));
+}
+
 // Fire-and-forget structured log event via CLI. Hooks don't import core modules;
 // the CLI is the shared log-writing surface so both MCP and hook code land in
 // the same log.md with the same format.
@@ -148,7 +169,8 @@ function dedupeByBasename(hits) {
   const seen = new Set();
   const out = [];
   for (const h of hits) {
-    const base = String(h.path || "").split("/").pop();
+    // per corpus: the same basename in the vault and in the docs is two different notes
+    const base = `${h.source ?? ""}:${String(h.path || "").split("/").pop()}`;
     if (seen.has(base)) continue;
     seen.add(base);
     out.push(h);
@@ -169,7 +191,8 @@ export function formatContextBlock(source, query, hits) {
   lines.push("");
   for (const h of shown) {
     const score = typeof h.score === "number" ? h.score.toFixed(2) : "";
-    lines.push(`- \`${h.path}\`${score ? ` (score: ${score})` : ""}`);
+    const meta = [h.source, score ? `score: ${score}` : ""].filter(Boolean).join(", ");
+    lines.push(`- \`${h.path}\`${meta ? ` (${meta})` : ""}`);
     if (h.snippet) {
       const snip = h.snippet.replace(/\s+/g, " ").slice(0, 240);
       lines.push(`  > ${snip}`);
@@ -532,40 +555,69 @@ function detectCaptureCue(prompt) {
   return null;
 }
 
-function addCapturePending(projectRoot, prompt, cueSource) {
+// The pending file is per project, but items are keyed by session_id so concurrent sessions
+// never see (or clear) each other's cues. An item without one (pre-1.5.2 file) belongs to
+// whichever session reads it first; a hook input without session_id sees everything, as before.
+const PENDING_MAX_AGE_MS = 7 * 24 * 60 * 60 * 1000;
+const ownsPendingItem = (item, sessionId) => !sessionId || !item.session_id || item.session_id === sessionId;
+
+function readAllCapturePending(projectRoot) {
   try {
-    const { resolvedRead, writePath } = statePath(projectRoot, "capture-pending");
+    const path = statePath(projectRoot, "capture-pending").resolvedRead;
+    const state = JSON.parse(readFileSync(path, "utf8"));
+    return Array.isArray(state.items) ? state.items : [];
+  } catch {
+    return [];
+  }
+}
+
+// The redactor ships in the built package next to this hook (dist/core/redact.js: fs/os/path only).
+// If it can't be loaded, the excerpt is withheld rather than written to disk unredacted.
+const WITHHELD = "[excerpt withheld: redactor unavailable]";
+async function redactExcerpt(prompt) {
+  try {
+    const { redact } = await import(new URL("../dist/core/redact.js", import.meta.url).href);
+    // redact the whole prompt before cutting, so a secret split at the cut is still caught
+    return redact(prompt, "broad").text.slice(0, 200);
+  } catch (e) {
+    debug(`redactor unavailable: ${e.message}`);
+    return WITHHELD;
+  }
+}
+
+function addCapturePending(projectRoot, excerpt, cueSource, sessionId) {
+  try {
+    const { writePath } = statePath(projectRoot, "capture-pending");
     ensureStateDir(writePath);
-    let state = { items: [] };
-    try { state = JSON.parse(readFileSync(resolvedRead, "utf8")); } catch {}
-    if (!Array.isArray(state.items)) state.items = [];
-    state.items.push({
+    const items = readAllCapturePending(projectRoot);
+    items.push({
       ts: new Date().toISOString(),
       cue: cueSource,
-      excerpt: prompt.slice(0, 200),
+      excerpt,
+      ...(sessionId ? { session_id: sessionId } : {}),
     });
-    writeFileSync(writePath, JSON.stringify(state));
+    writeFileSync(writePath, JSON.stringify({ items }));
   } catch (e) {
     debug(`capture pending write failed: ${e.message}`);
   }
 }
 
-function resetCapturePending(projectRoot) {
+// Clears this session's items; other sessions' items stay unless older than a week (a session
+// that died without a Stop never clears its own).
+function resetCapturePending(projectRoot, sessionId) {
   try {
     const { writePath } = statePath(projectRoot, "capture-pending");
     ensureStateDir(writePath);
-    writeFileSync(writePath, JSON.stringify({ items: [] }));
+    const now = Date.now();
+    const items = readAllCapturePending(projectRoot).filter(
+      (i) => !ownsPendingItem(i, sessionId) && now - Date.parse(i.ts) < PENDING_MAX_AGE_MS
+    );
+    writeFileSync(writePath, JSON.stringify({ items }));
   } catch {}
 }
 
-function readCapturePending(projectRoot) {
-  try {
-    const path = statePath(projectRoot, "capture-pending").resolvedRead;
-    const state = JSON.parse(readFileSync(path, "utf8"));
-    return Array.isArray(state.items) ? state.items : [];
-  } catch {
-    return [];
-  }
+function readCapturePending(projectRoot, sessionId) {
+  return readAllCapturePending(projectRoot).filter((i) => ownsPendingItem(i, sessionId));
 }
 
 function normalizeFingerprint(prompt) {
@@ -594,12 +646,12 @@ function saveFingerprints(projectRoot, state) {
   }
 }
 
-async function handleSessionStart(projectRoot, vaultPath, cliBin) {
+async function handleSessionStart(projectRoot, vaultPath, cliBin, sources, sessionId) {
   // Capture the previous mode (if any) before we reset — so future-Claude
   // can tell, from log.md, that we rolled back from research/outage without
   // being shown the postmortem prompt (which is the lossy case).
   const priorMode = readMode(projectRoot);
-  resetCapturePending(projectRoot);
+  resetCapturePending(projectRoot, sessionId);
   writeMode(projectRoot, "vault-first");
   if (priorMode !== "vault-first") {
     logMaybeModeChange(cliBin, vaultPath, priorMode, "vault-first");
@@ -613,8 +665,8 @@ async function handleSessionStart(projectRoot, vaultPath, cliBin) {
   if (!digestBlock) {
     const query = sessionSeedQuery(projectRoot);
     debug(`sessionstart seed query: "${query}"`);
-    const hits = runSearchCli(cliBin, ["--notes", vaultPath, "--limit", "6", query], 30_000);
-    searchBlock = hits && hits.length > 0 ? formatContextBlock("sessionstart", query, hits) : "";
+    const hits = await searchSources(cliBin, sources, 6, query);
+    searchBlock = hits.length > 0 ? formatContextBlock("sessionstart", query, hits) : "";
   } else {
     debug("sessionstart: paging in curated digest (skipping broad search)");
   }
@@ -790,11 +842,11 @@ function readActiveSession(projectRoot) {
   }
 }
 
-async function handleStop(projectRoot) {
+async function handleStop(projectRoot, sessionId) {
   const stopHookActive = process.env.CLAUDE_STOP_HOOK_ACTIVE === "1";
   if (stopHookActive) {
     // Already blocking — Claude is mid-response to our nudge. Clear and yield.
-    resetCapturePending(projectRoot);
+    resetCapturePending(projectRoot, sessionId);
     emitStop("", false);
     return;
   }
@@ -823,12 +875,12 @@ async function handleStop(projectRoot) {
     }
     lines.push(formatSessionDigestPrompt(session));
     lines.push(`</vault-session-close>`);
-    resetCapturePending(projectRoot);
+    resetCapturePending(projectRoot, sessionId);
     emitStop(lines.join("\n"), true);
     return;
   }
 
-  const pending = readCapturePending(projectRoot);
+  const pending = readCapturePending(projectRoot, sessionId);
   const mode = readMode(projectRoot);
 
   // Mode-specific transition-capture. research-mode and outage-silence each
@@ -846,7 +898,7 @@ async function handleStop(projectRoot) {
     lines.push("");
     lines.push(`Mandatory before Stop: call \`mcp__semantic-vault__synthesize_note\` with dry_run=true to preview a research-synthesis note (derived_from the session's filed sources). Review with the user, then apply. A research session that ends without synthesis is lost work.`);
     lines.push(`</vault-transition-capture>`);
-    resetCapturePending(projectRoot);
+    resetCapturePending(projectRoot, sessionId);
     emitStop(lines.join("\n"), true);
     return;
   }
@@ -857,7 +909,7 @@ async function handleStop(projectRoot) {
       `Outage session ending. Before closing: draft a postmortem via \`mcp__semantic-vault__synthesize_note\` with \`type: gotcha\` (or \`decision\` if architectural). Include timeline, root cause, fix, preventive actions. Dry-run first, confirm with the user, then apply.`,
       `</vault-transition-capture>`,
     ];
-    resetCapturePending(projectRoot);
+    resetCapturePending(projectRoot, sessionId);
     emitStop(lines.join("\n"), true);
     return;
   }
@@ -879,11 +931,11 @@ async function handleStop(projectRoot) {
   lines.push(`Before ending: for each still-unsynthesized item above, either call \`mcp__semantic-vault__synthesize_note\` to file it with provenance, or explicitly acknowledge that it was already captured / not worth capturing.`);
   lines.push(`If a cue is a speaker correction (how the user talks — "when I say X I mean Y"), update the speaker profile via \`mcp__semantic-vault__manage_profile\` (action:update_section) instead of synthesize_note.`);
   lines.push(`</vault-capture-prompt>`);
-  resetCapturePending(projectRoot);
+  resetCapturePending(projectRoot, sessionId);
   emitStop(lines.join("\n"), true);
 }
 
-async function handlePrompt(projectRoot, vaultPath, cliBin, input) {
+async function handlePrompt(projectRoot, sources, cliBin, input) {
   const prompt = typeof input.prompt === "string" ? input.prompt : "";
   if (!prompt || prompt.length < 8) {
     emit("UserPromptSubmit", "");
@@ -908,17 +960,17 @@ async function handlePrompt(projectRoot, vaultPath, cliBin, input) {
   // Tier-1 lexicon expansion: search with the alias-expanded query, but keep the
   // original prompt for display in the block.
   const searchQuery = expandQueryViaLexicon(projectRoot, prompt);
-  const hits = runSearchCli(cliBin, ["--notes", vaultPath, "--limit", "8", searchQuery], 30_000);
+  const hits = await searchSources(cliBin, sources, 8, searchQuery);
   state.recent = [fp, ...recent].slice(0, 10);
   saveFingerprints(projectRoot, state);
   const cue = detectCaptureCue(prompt);
   if (cue) {
-    addCapturePending(projectRoot, prompt, cue);
+    addCapturePending(projectRoot, await redactExcerpt(prompt), cue, typeof input.session_id === "string" ? input.session_id : undefined);
   }
   // Two-hop: if the utterance names a tracked entity, lead with its dossier head.
   const dossier = resolveDossierForPrompt(projectRoot, prompt);
   const dossierHead = dossier ? formatDossierHead(dossier) : "";
-  if (!hits || hits.length === 0) {
+  if (hits.length === 0) {
     // Even with no semantic hits, a resolved dossier is worth injecting.
     emit("UserPromptSubmit", dossierHead);
     return;
@@ -932,9 +984,11 @@ async function main() {
   const input = readStdinJson();
   const eventName = input.hook_event_name || process.env.CLAUDE_HOOK_EVENT || "SessionStart";
   const projectRoot = input.cwd || process.env.CLAUDE_PROJECT_DIR || process.cwd();
+  const sessionId = typeof input.session_id === "string" ? input.session_id : undefined;
   debug(`event=${eventName} projectRoot=${projectRoot}`);
 
-  const vaultPath = findVaultPath(projectRoot);
+  const sources = findNotesSources(projectRoot);
+  const vaultPath = pickVaultPath(sources);
   if (!vaultPath) {
     debug(`no vault found under ${projectRoot}`);
     emitNoop(eventName);
@@ -946,15 +1000,15 @@ async function main() {
     emitNoop(eventName);
     return;
   }
-  debug(`vault=${vaultPath} bin=${cliBin}`);
+  debug(`vault=${vaultPath} search=${sources.map((s) => s.path).join(",")} bin=${cliBin}`);
 
   try {
     if (eventName === "UserPromptSubmit") {
-      await handlePrompt(projectRoot, vaultPath, cliBin, input);
+      await handlePrompt(projectRoot, sources, cliBin, input);
     } else if (eventName === "Stop") {
-      await handleStop(projectRoot);
+      await handleStop(projectRoot, sessionId);
     } else {
-      await handleSessionStart(projectRoot, vaultPath, cliBin);
+      await handleSessionStart(projectRoot, vaultPath, cliBin, sources, sessionId);
     }
   } catch (e) {
     debug(`handler failed: ${e.message}`);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@theglitchking/semantic-memory",
-  "version": "1.5.1",
+  "version": "1.5.3",
   "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 @theglitchking/semantic-sidekick at v1.0 — see CHANGELOG for migration.",
   "type": "module",
   "main": "./dist/core/index.js",
@@ -97,17 +97,17 @@
     "vitest": "^4.1.2"
   },
   "comments": {
-    "overrides": "Pin patched versions of transitive deps to keep this package's supply chain clean (v1.5.1). All are same-MAJOR bumps — no breaking changes. NOTE: npm ignores a dependency's overrides in downstream installs, so consuming projects that gate CI on `npm audit` should mirror this block or run `npm audit fix`. Every advisory here is unreachable in practice: this is a local stdio MCP server + hook scripts processing the user's own files — the hono/express-rate-limit/ip-address/qs cluster is the MCP SDK's HTTP transport, which this plugin never instantiates (stdio only). js-yaml (gray-matter) and fast-uri (ajv) are deliberately NOT overridden: their only fixes are MAJOR bumps that would break frontmatter parsing / MCP tool-input validation, and the DoS vectors require attacker-controlled input this plugin never accepts."
+    "overrides": "Pin patched versions of transitive deps to keep this package's supply chain clean (v1.5.1). All are same-MAJOR bumps — no breaking changes. NOTE: npm ignores a dependency's overrides in downstream installs, so consuming projects that gate CI on `npm audit` should mirror this block or run `npm audit fix`. Every advisory here is unreachable in practice: this is a local stdio MCP server + hook scripts processing the user's own files — the hono/express-rate-limit/ip-address/qs cluster is the MCP SDK's HTTP transport, which this plugin never instantiates (stdio only). js-yaml (gray-matter) and fast-uri (ajv) are NOT overridden: they resolve to patched same-major versions (3.15.2 / 3.1.9 as of v1.5.2). v1.5.2 re-pinned the block to current patches. Known open: zod (all 3.x vulnerable, fix is zod 4: breaking for the MCP SDK tool schemas in src/mcp/tools/*) and esbuild (dev-only, via tsup)."
   },
   "overrides": {
-    "protobufjs": "7.6.5",
+    "protobufjs": "7.6.6",
     "@protobufjs/utf8": "1.1.2",
-    "@xmldom/xmldom": "0.9.10",
-    "brace-expansion": "5.0.7",
-    "qs": "6.15.3",
-    "ip-address": "10.2.0",
-    "express-rate-limit": "8.5.2",
-    "hono": "4.12.29",
-    "@hono/node-server": "1.19.14"
+    "@xmldom/xmldom": "0.9.12",
+    "brace-expansion": "5.0.12",
+    "qs": "6.16.1",
+    "ip-address": "10.7.4",
+    "express-rate-limit": "8.7.1",
+    "hono": "4.13.13",
+    "@hono/node-server": "1.19.17"
   }
 }

package/dist/chunk-25EIQWXL.js.map

@@ -1 +0,0 @@
-{"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.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    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}\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 } 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package/dist/chunk-7M3JZOYH.js.map

@@ -1 +0,0 @@
-{"version":3,"sources":["../src/core/profile.ts"],"sourcesContent":["import { readFile, writeFile, mkdir } from \"node:fs/promises\";\nimport { existsSync } from \"node:fs\";\nimport { join, dirname } from \"node:path\";\nimport matter from \"gray-matter\";\nimport { replaceSectionBody, appendToSection } from \"./dossier.js\";\n\n/**\n * Speaker profile (v1.5 Phase 11) — the model of THIS human.\n *\n * The difference between an expert who knows the system and one who knows the\n * system *and knows you*: how this person calibrates severity (\"annoying\" vs\n * \"broken\" vs \"on fire\"), what they chronically leave unsaid, how much detail they\n * want back, and the shorthand they use that isn't an entity. One note, one human\n * (multi-speaker is an explicit non-goal). 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One human, one profile._\n\n## Severity calibration\n\n_What their words map to. e.g. \"annoying\" = low, \"broken\" = ship-blocking, \"on fire\" = drop everything._\n\n## Chronic omissions\n\n_What they habitually leave unsaid — env, repro steps, which service — so you ask up front._\n\n## Verbosity preference\n\n_How much detail they want back: terse answer first, or full reasoning? Code or prose?_\n\n## Shorthand & terms\n\n_Non-entity shorthand: \"the usual\", \"ship it\", \"the thing from yesterday\" — and what each has meant._\n`;\n}\n\n/** True when a line is only a template placeholder (italic prompt) or blank. */\nfunction isPlaceholderLine(line: string): boolean {\n  const t = line.trim();\n  return t === \"\" || /^_.*_$/.test(t);\n}\n\n/**\n * Read the speaker profile, returning a capped injection head that drops the\n * template placeholders (so an unfilled profile injects nothing but its headings,\n * and a filled one injects only the real content). 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