@goondocks/myco 0.5.0 → 0.6.0

package/dist/{chunk-ZWUFTOG3.js → chunk-2GSX3BK2.js}

@@ -1,16 +1,16 @@
 import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
 import {
   getPluginVersion
-} from "./chunk-7KQB22DP.js";
+} from "./chunk-E7OBRBCQ.js";
 import {
   AgentRegistry
-} from "./chunk-X6TKHO22.js";
+} from "./chunk-5QWZT4AB.js";
 import {
   DAEMON_CLIENT_TIMEOUT_MS,
   DAEMON_HEALTH_CHECK_TIMEOUT_MS,
   DAEMON_HEALTH_RETRY_DELAYS,
   DAEMON_STALE_GRACE_PERIOD_MS
-} from "./chunk-B6WVNDA5.js";
+} from "./chunk-6BSDCZ5Q.js";
 
 // src/hooks/client.ts
 import fs from "fs";
@@ -178,4 +178,4 @@ var DaemonClient = class {
 export {
   DaemonClient
 };
-//# sourceMappingURL=chunk-ZWUFTOG3.js.map
+//# sourceMappingURL=chunk-2GSX3BK2.js.map

package/dist/{chunk-FIRMTYFH.js → chunk-2YBUL3IL.js}

@@ -2,10 +2,10 @@ import { createRequire as __cr } from 'node:module'; const require = __cr(import
 import {
   LmStudioBackend,
   OllamaBackend
-} from "./chunk-JI6M2L2W.js";
+} from "./chunk-QGJ2ZIUZ.js";
 import {
   AgentRegistry
-} from "./chunk-X6TKHO22.js";
+} from "./chunk-5QWZT4AB.js";
 
 // src/cli/shared.ts
 import fs from "fs";
@@ -33,39 +33,6 @@ var PROVIDER_DEFAULTS = {
   ollama: { base_url: OllamaBackend.DEFAULT_BASE_URL },
   "lm-studio": { base_url: LmStudioBackend.DEFAULT_BASE_URL }
 };
-var DASHBOARD_CONTENT = `# Myco Vault
-
-## Active Plans
-\`\`\`dataview
-TABLE status, tags FROM #type/plan
-WHERE status = "active" OR status = "in_progress"
-SORT created DESC
-\`\`\`
-
-## Recent Sessions
-\`\`\`dataview
-TABLE user, started, tools_used FROM #type/session
-SORT started DESC LIMIT 10
-\`\`\`
-
-## Recent Spores
-\`\`\`dataview
-TABLE observation_type AS "Type", created FROM #type/spore
-SORT created DESC LIMIT 15
-\`\`\`
-
-## Spores by Type
-\`\`\`dataview
-TABLE WITHOUT ID observation_type AS "Type", length(rows) AS "Count"
-FROM #type/spore GROUP BY observation_type
-SORT length(rows) DESC
-\`\`\`
-
-## Gotchas
-\`\`\`dataview
-LIST FROM #spore/gotcha SORT created DESC LIMIT 10
-\`\`\`
-`;
 var VAULT_GITIGNORE = `# Runtime \u2014 rebuilt on daemon startup
 index.db
 index.db-wal
@@ -74,6 +41,7 @@ vectors.db
 
 # Daemon state \u2014 per-machine, ephemeral
 daemon.json
+_portal.md
 buffer/
 logs/
 
@@ -112,8 +80,7 @@ For other agents, add to your shell profile:`);
 export {
   loadEnv,
   isProcessAlive,
-  DASHBOARD_CONTENT,
   VAULT_GITIGNORE,
   configureVaultEnv
 };
-//# sourceMappingURL=chunk-FIRMTYFH.js.map
+//# sourceMappingURL=chunk-2YBUL3IL.js.map

package/dist/chunk-2YBUL3IL.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/cli/shared.ts"],"sourcesContent":["import fs from 'node:fs';\nimport path from 'node:path';\nimport os from 'node:os';\nimport { AgentRegistry } from '../agents/registry.js';\nimport { OllamaBackend } from '../intelligence/ollama.js';\nimport { LmStudioBackend } from '../intelligence/lm-studio.js';\n\nexport { parseStringFlag, parseIntFlag } from '../logs/format.js';\n\n/** Load .env from cwd (not script location — that's the plugin install dir). */\nexport function loadEnv(): void {\n  const envPath = path.resolve(process.cwd(), '.env');\n  if (!fs.existsSync(envPath)) return;\n  for (const line of fs.readFileSync(envPath, 'utf-8').split('\\n')) {\n    const match = line.match(/^\\s*([^#=]+?)\\s*=\\s*(.*?)\\s*$/);\n    if (match && !process.env[match[1]]) {\n      process.env[match[1]] = match[2];\n    }\n  }\n}\n\nexport function isProcessAlive(pid: number): boolean {\n  try { process.kill(pid, 0); return true; } catch { return false; }\n}\n\n// --- Provider defaults (sourced from backend classes) ---\nexport const PROVIDER_DEFAULTS: Record<string, { base_url: string }> = {\n  ollama: { base_url: OllamaBackend.DEFAULT_BASE_URL },\n  'lm-studio': { base_url: LmStudioBackend.DEFAULT_BASE_URL },\n};\n\n\nexport const VAULT_GITIGNORE = `# Runtime — rebuilt on daemon startup\nindex.db\nindex.db-wal\nindex.db-shm\nvectors.db\n\n# Daemon state — per-machine, ephemeral\ndaemon.json\n_portal.md\nbuffer/\nlogs/\n\n# Obsidian — per-user workspace config\n.obsidian/\n`;\n\n/** Collapse an absolute home-dir path to its `~/` form for portable config storage. */\nexport function collapseHomePath(absPath: string): string {\n  const home = os.homedir();\n  if (absPath.startsWith(home + path.sep) || absPath === home) {\n    return '~' + absPath.slice(home.length);\n  }\n  return absPath;\n}\n\n/** Set MYCO_VAULT_DIR in the active agent's config, falling back to all known agents. */\nexport function configureVaultEnv(projectRoot: string, vaultDir: string): void {\n  const registry = new AgentRegistry();\n  const active = registry.detectActiveAgent();\n  // Store the portable ~/... form so config files don't leak the username\n  const portableDir = collapseHomePath(vaultDir);\n\n  if (active) {\n    if (active.configureVaultEnv(projectRoot, portableDir)) {\n      console.log(`Set MYCO_VAULT_DIR for ${active.displayName}`);\n    }\n  } else {\n    // No active agent detected — try all adapters\n    for (const name of registry.adapterNames) {\n      const adapter = registry.getAdapter(name);\n      if (adapter?.configureVaultEnv(projectRoot, portableDir)) {\n        console.log(`Set MYCO_VAULT_DIR for ${adapter.displayName}`);\n      }\n    }\n  }\n\n  console.log(`\\nFor other agents, add to your shell profile:`);\n  console.log(`  export MYCO_VAULT_DIR=\"${portableDir}\"\\n`);\n}\n"],"mappings":";;;;;;;;;;AAAA,OAAO,QAAQ;AACf,OAAO,UAAU;AACjB,OAAO,QAAQ;AAQR,SAAS,UAAgB;AAC9B,QAAM,UAAU,KAAK,QAAQ,QAAQ,IAAI,GAAG,MAAM;AAClD,MAAI,CAAC,GAAG,WAAW,OAAO,EAAG;AAC7B,aAAW,QAAQ,GAAG,aAAa,SAAS,OAAO,EAAE,MAAM,IAAI,GAAG;AAChE,UAAM,QAAQ,KAAK,MAAM,+BAA+B;AACxD,QAAI,SAAS,CAAC,QAAQ,IAAI,MAAM,CAAC,CAAC,GAAG;AACnC,cAAQ,IAAI,MAAM,CAAC,CAAC,IAAI,MAAM,CAAC;AAAA,IACjC;AAAA,EACF;AACF;AAEO,SAAS,eAAe,KAAsB;AACnD,MAAI;AAAE,YAAQ,KAAK,KAAK,CAAC;AAAG,WAAO;AAAA,EAAM,QAAQ;AAAE,WAAO;AAAA,EAAO;AACnE;AAGO,IAAM,oBAA0D;AAAA,EACrE,QAAQ,EAAE,UAAU,cAAc,iBAAiB;AAAA,EACnD,aAAa,EAAE,UAAU,gBAAgB,iBAAiB;AAC5D;AAGO,IAAM,kBAAkB;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAiBxB,SAAS,iBAAiB,SAAyB;AACxD,QAAM,OAAO,GAAG,QAAQ;AACxB,MAAI,QAAQ,WAAW,OAAO,KAAK,GAAG,KAAK,YAAY,MAAM;AAC3D,WAAO,MAAM,QAAQ,MAAM,KAAK,MAAM;AAAA,EACxC;AACA,SAAO;AACT;AAGO,SAAS,kBAAkB,aAAqB,UAAwB;AAC7E,QAAM,WAAW,IAAI,cAAc;AACnC,QAAM,SAAS,SAAS,kBAAkB;AAE1C,QAAM,cAAc,iBAAiB,QAAQ;AAE7C,MAAI,QAAQ;AACV,QAAI,OAAO,kBAAkB,aAAa,WAAW,GAAG;AACtD,cAAQ,IAAI,0BAA0B,OAAO,WAAW,EAAE;AAAA,IAC5D;AAAA,EACF,OAAO;AAEL,eAAW,QAAQ,SAAS,cAAc;AACxC,YAAM,UAAU,SAAS,WAAW,IAAI;AACxC,UAAI,SAAS,kBAAkB,aAAa,WAAW,GAAG;AACxD,gBAAQ,IAAI,0BAA0B,QAAQ,WAAW,EAAE;AAAA,MAC7D;AAAA,IACF;AAAA,EACF;AAEA,UAAQ,IAAI;AAAA,6CAAgD;AAC5D,UAAQ,IAAI,4BAA4B,WAAW;AAAA,CAAK;AAC1D;","names":[]}

package/dist/{chunk-HL2S5QZG.js → chunk-2ZBB3MQT.js}

@@ -1,31 +1,79 @@
 import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
 import {
+  EMBEDDING_BATCH_CONCURRENCY,
+  batchExecute
+} from "./chunk-3JCXYLHD.js";
+import {
+  isActiveSpore,
+  supersedeSpore,
+  supersededIdsSchema
+} from "./chunk-UVGAVYWZ.js";
+import {
+  formatNoteForPrompt,
+  formatNotesForPrompt,
   loadPrompt,
+  rebuildIndex,
   stripReasoningTokens
-} from "./chunk-KYL67SKZ.js";
+} from "./chunk-24DOZEUJ.js";
+import {
+  generateEmbedding
+} from "./chunk-RGVBGTD6.js";
 import {
   stripFrontmatter
-} from "./chunk-MIU3DKLN.js";
+} from "./chunk-GNR3QAER.js";
+import {
+  initFts
+} from "./chunk-6FQISQNA.js";
 import {
   require_dist
-} from "./chunk-6UJWI4IW.js";
+} from "./chunk-MQSYSQ6T.js";
 import {
   CHARS_PER_TOKEN,
+  CURATION_CLUSTER_SIMILARITY,
   DIGEST_LLM_REQUEST_TIMEOUT_MS,
   DIGEST_SUBSTRATE_TYPE_WEIGHTS,
   DIGEST_TIER_MIN_CONTEXT,
+  EMBEDDING_INPUT_LIMIT,
   LLM_REASONING_MODE,
+  SUPERSESSION_MAX_TOKENS,
   estimateTokens
-} from "./chunk-B6WVNDA5.js";
+} from "./chunk-6BSDCZ5Q.js";
 import {
   __toESM
 } from "./chunk-PZUWP5VK.js";
 
 // src/daemon/digest.ts
 var import_yaml = __toESM(require_dist(), 1);
+import fs2 from "fs";
+import path2 from "path";
+import crypto from "crypto";
+
+// src/daemon/trace.ts
 import fs from "fs";
 import path from "path";
-import crypto from "crypto";
+function readLastTimestamp(filePath) {
+  let content;
+  try {
+    content = fs.readFileSync(filePath, "utf-8").trim();
+  } catch {
+    return null;
+  }
+  if (!content) return null;
+  const lines = content.split("\n");
+  const lastLine = lines[lines.length - 1];
+  try {
+    const record = JSON.parse(lastLine);
+    return record.timestamp ?? null;
+  } catch {
+    return null;
+  }
+}
+function appendTraceRecord(filePath, record) {
+  fs.mkdirSync(path.dirname(filePath), { recursive: true });
+  fs.appendFileSync(filePath, JSON.stringify(record) + "\n", "utf-8");
+}
+
+// src/daemon/digest.ts
 var PREVIOUS_EXTRACT_OVERHEAD_TOKENS = 50;
 var CONTEXT_SAFETY_MARGIN = 0.7;
 var EXTRACT_TYPE = "extract";
@@ -37,6 +85,10 @@ var DigestEngine = class {
   log;
   lastCycleTimestampCache = void 0;
   cycleInProgress = false;
+  /** Hooks that run before each digest cycle (e.g., consolidation). */
+  prePassHooks = [];
+  /** Hooks that run after each successful digest cycle. */
+  postPassHooks = [];
   constructor(engineConfig) {
     this.vaultDir = engineConfig.vaultDir;
     this.index = engineConfig.index;
@@ -45,6 +97,14 @@ var DigestEngine = class {
     this.log = engineConfig.log ?? (() => {
     });
   }
+  /** Register a hook that runs before each digest cycle. Best-effort — errors are logged, not thrown. */
+  registerPrePass(name, fn) {
+    this.prePassHooks.push({ name, fn });
+  }
+  /** Register a hook that runs after each successful digest cycle. Best-effort — errors are logged, not thrown. */
+  registerPostPass(name, fn) {
+    this.postPassHooks.push({ name, fn });
+  }
   /**
    * Query index for recent vault notes to feed into the digest.
    * Filters out extract notes (our own output) and caps at max_notes_per_cycle.
@@ -98,10 +158,10 @@ ${note.content}`;
    * Returns the body (stripped of YAML frontmatter), or null if not found.
    */
   readPreviousExtract(tier) {
-    const extractPath = path.join(this.vaultDir, "digest", `extract-${tier}.md`);
+    const extractPath = path2.join(this.vaultDir, "digest", `extract-${tier}.md`);
     let content;
     try {
-      content = fs.readFileSync(extractPath, "utf-8");
+      content = fs2.readFileSync(extractPath, "utf-8");
     } catch {
       return null;
     }
@@ -112,8 +172,8 @@ ${note.content}`;
    * Uses atomic write pattern (temp file + rename).
    */
   writeExtract(tier, body, cycleId, model, substrateCount) {
-    const digestDir = path.join(this.vaultDir, "digest");
-    fs.mkdirSync(digestDir, { recursive: true });
+    const digestDir = path2.join(this.vaultDir, "digest");
+    fs2.mkdirSync(digestDir, { recursive: true });
     const frontmatter = {
       type: EXTRACT_TYPE,
       tier,
@@ -132,19 +192,17 @@ ${fmYaml}
 
 ${body}
 `;
-    const fullPath = path.join(digestDir, `extract-${tier}.md`);
+    const fullPath = path2.join(digestDir, `extract-${tier}.md`);
     const tmpPath = `${fullPath}.tmp`;
-    fs.writeFileSync(tmpPath, file, "utf-8");
-    fs.renameSync(tmpPath, fullPath);
+    fs2.writeFileSync(tmpPath, file, "utf-8");
+    fs2.renameSync(tmpPath, fullPath);
   }
   /**
    * Append a digest cycle result as a JSON line to trace.jsonl.
    */
   appendTrace(record) {
-    const digestDir = path.join(this.vaultDir, "digest");
-    fs.mkdirSync(digestDir, { recursive: true });
-    const tracePath = path.join(digestDir, "trace.jsonl");
-    fs.appendFileSync(tracePath, JSON.stringify(record) + "\n", "utf-8");
+    const tracePath = path2.join(this.vaultDir, "digest", "trace.jsonl");
+    appendTraceRecord(tracePath, record);
     this.lastCycleTimestampCache = record.timestamp;
   }
   /**
@@ -153,28 +211,9 @@ ${body}
    */
   getLastCycleTimestamp() {
     if (this.lastCycleTimestampCache !== void 0) return this.lastCycleTimestampCache;
-    const tracePath = path.join(this.vaultDir, "digest", "trace.jsonl");
-    let content;
-    try {
-      content = fs.readFileSync(tracePath, "utf-8").trim();
-    } catch {
-      this.lastCycleTimestampCache = null;
-      return null;
-    }
-    if (!content) {
-      this.lastCycleTimestampCache = null;
-      return null;
-    }
-    const lines = content.split("\n");
-    const lastLine = lines[lines.length - 1];
-    try {
-      const record = JSON.parse(lastLine);
-      this.lastCycleTimestampCache = record.timestamp;
-      return record.timestamp;
-    } catch {
-      this.lastCycleTimestampCache = null;
-      return null;
-    }
+    const tracePath = path2.join(this.vaultDir, "digest", "trace.jsonl");
+    this.lastCycleTimestampCache = readLastTimestamp(tracePath);
+    return this.lastCycleTimestampCache;
   }
   /**
    * Run a full digest cycle: discover substrate, generate extracts for each tier.
@@ -187,6 +226,13 @@ ${body}
     }
     this.cycleInProgress = true;
     try {
+      for (const hook of this.prePassHooks) {
+        try {
+          await hook.fn();
+        } catch (err) {
+          this.log("warn", `Pre-pass hook "${hook.name}" failed`, { error: err.message });
+        }
+      }
       return await this.runCycleInternal(opts);
     } finally {
       this.cycleInProgress = false;
@@ -295,6 +341,13 @@ ${body}
       tokensUsed: totalTokensUsed
     };
     this.appendTrace(result);
+    for (const hook of this.postPassHooks) {
+      try {
+        await hook.fn(result);
+      } catch (err) {
+        this.log("warn", `Post-pass hook "${hook.name}" failed`, { error: err.message });
+      }
+    }
     return result;
   }
 };
@@ -378,8 +431,234 @@ var Metabolism = class {
   }
 };
 
+// src/services/vault-ops.ts
+async function runRebuild(ctx, embeddingProvider, onProgress) {
+  const { index, vaultDir } = ctx;
+  initFts(index);
+  const ftsCount = rebuildIndex(index, vaultDir);
+  if (!ctx.vectorIndex) {
+    return { ftsCount, embeddedCount: 0, failedCount: 0, skippedCount: 0 };
+  }
+  const allNotes = index.query({});
+  const activeNotes = allNotes.filter((n) => {
+    const status = n.frontmatter?.status;
+    return status !== "superseded" && status !== "archived";
+  });
+  const skippedCount = allNotes.length - activeNotes.length;
+  const vec = ctx.vectorIndex;
+  const result = await batchExecute(
+    activeNotes,
+    async (note) => {
+      const text = `${note.title}
+${note.content}`.slice(0, EMBEDDING_INPUT_LIMIT);
+      const emb = await generateEmbedding(embeddingProvider, text);
+      vec.upsert(note.id, emb.embedding, {
+        type: note.type,
+        session_id: note.frontmatter?.session ?? ""
+      });
+    },
+    {
+      concurrency: EMBEDDING_BATCH_CONCURRENCY,
+      onProgress
+    }
+  );
+  return {
+    ftsCount,
+    embeddedCount: result.succeeded,
+    failedCount: result.failed,
+    skippedCount
+  };
+}
+async function runDigest(ctx, llmProvider, options) {
+  const { config, vaultDir, index } = ctx;
+  const log = ctx.log ? (level, message, data) => ctx.log(level, message, data) : () => {
+  };
+  const engine = new DigestEngine({
+    vaultDir,
+    index,
+    llmProvider,
+    config,
+    log
+  });
+  const opts = {};
+  const isReprocess = options?.full || options?.tier !== void 0;
+  if (isReprocess) {
+    opts.fullReprocess = true;
+    opts.cleanSlate = true;
+  }
+  if (options?.tier !== void 0) {
+    const eligible = engine.getEligibleTiers();
+    if (!eligible.includes(options.tier)) {
+      throw new Error(`Tier ${options.tier} is not eligible. Eligible tiers: [${eligible.join(", ")}]`);
+    }
+    opts.tiers = [options.tier];
+  }
+  return engine.runCycle(opts);
+}
+var CURATION_EMBEDDING_BATCH_SIZE = 10;
+function cosineSimilarity(a, b) {
+  let dot = 0, normA = 0, normB = 0;
+  for (let i = 0; i < a.length; i++) {
+    dot += a[i] * b[i];
+    normA += a[i] * a[i];
+    normB += b[i] * b[i];
+  }
+  return dot / (Math.sqrt(normA) * Math.sqrt(normB));
+}
+function updateCentroid(spores) {
+  if (spores.length === 0) return [];
+  const dim = spores[0].embedding.length;
+  const centroid = new Array(dim).fill(0);
+  for (const s of spores) {
+    for (let i = 0; i < dim; i++) {
+      centroid[i] += s.embedding[i];
+    }
+  }
+  for (let i = 0; i < dim; i++) {
+    centroid[i] /= spores.length;
+  }
+  return centroid;
+}
+function clusterSpores(spores) {
+  const clusters = [];
+  for (const spore of spores) {
+    let bestCluster = null;
+    let bestSimilarity = -1;
+    for (const cluster of clusters) {
+      const sim = cosineSimilarity(spore.embedding, cluster.centroid);
+      if (sim > bestSimilarity) {
+        bestSimilarity = sim;
+        bestCluster = cluster;
+      }
+    }
+    if (bestCluster !== null && bestSimilarity >= CURATION_CLUSTER_SIMILARITY) {
+      bestCluster.spores.push(spore);
+      bestCluster.centroid = updateCentroid(bestCluster.spores);
+    } else {
+      clusters.push({ spores: [spore], centroid: [...spore.embedding] });
+    }
+  }
+  return clusters;
+}
+async function runCuration(deps, dryRun) {
+  const { index, vectorIndex, llmProvider, embeddingProvider, vaultDir } = deps;
+  const log = deps.log ?? (() => {
+  });
+  const allSpores = index.query({ type: "spore" });
+  const activeSpores = allSpores.filter((n) => isActiveSpore(n.frontmatter));
+  if (activeSpores.length === 0) {
+    return { scanned: 0, clustersEvaluated: 0, superseded: 0 };
+  }
+  const sporesWithEmbeddings = [];
+  let embedFailures = 0;
+  for (let i = 0; i < activeSpores.length; i += CURATION_EMBEDDING_BATCH_SIZE) {
+    const batch = activeSpores.slice(i, i + CURATION_EMBEDDING_BATCH_SIZE);
+    const results = await Promise.allSettled(
+      batch.map(async (spore) => {
+        const text = spore.content.slice(0, EMBEDDING_INPUT_LIMIT);
+        const result = await generateEmbedding(embeddingProvider, text);
+        return { spore, embedding: result.embedding };
+      })
+    );
+    for (const result of results) {
+      if (result.status === "fulfilled") {
+        const { spore, embedding } = result.value;
+        sporesWithEmbeddings.push({
+          id: spore.id,
+          path: spore.path,
+          title: spore.title,
+          content: spore.content,
+          created: spore.created,
+          frontmatter: spore.frontmatter,
+          embedding
+        });
+      } else {
+        embedFailures++;
+      }
+    }
+  }
+  if (embedFailures > 0) {
+    log("warn", `${embedFailures} spore(s) could not be embedded and were skipped`);
+  }
+  const byType = /* @__PURE__ */ new Map();
+  for (const spore of sporesWithEmbeddings) {
+    const obsType = spore.frontmatter["observation_type"] ?? "unknown";
+    if (!byType.has(obsType)) byType.set(obsType, []);
+    byType.get(obsType).push(spore);
+  }
+  const template = loadPrompt("supersession");
+  let totalClusters = 0;
+  let totalSuperseded = 0;
+  for (const [obsType, typeSpores] of byType) {
+    const clusters = clusterSpores(typeSpores);
+    const multiSpore = clusters.filter((c) => c.spores.length >= 2);
+    if (multiSpore.length === 0) continue;
+    log("info", `Type: ${obsType} \u2014 ${typeSpores.length} spores, ${multiSpore.length} cluster(s) to evaluate`);
+    totalClusters += multiSpore.length;
+    for (const cluster of multiSpore) {
+      const sorted = [...cluster.spores].sort((a, b) => a.created.localeCompare(b.created));
+      const newest = sorted[sorted.length - 1];
+      const candidates = sorted.slice(0, sorted.length - 1);
+      const newSporeText = formatNoteForPrompt(newest);
+      const candidatesText = formatNotesForPrompt(candidates);
+      const prompt = template.replace("{{new_spore}}", newSporeText).replace("{{candidates}}", candidatesText);
+      let responseText;
+      try {
+        const response = await llmProvider.summarize(prompt, {
+          maxTokens: SUPERSESSION_MAX_TOKENS,
+          reasoning: LLM_REASONING_MODE
+        });
+        responseText = stripReasoningTokens(response.text);
+      } catch (err) {
+        log("warn", `LLM call failed for cluster in ${obsType}: ${String(err)}`);
+        continue;
+      }
+      let rawIds;
+      try {
+        rawIds = JSON.parse(responseText);
+      } catch {
+        log("warn", `Could not parse LLM response for cluster in ${obsType}`);
+        continue;
+      }
+      const parsed = supersededIdsSchema.safeParse(rawIds);
+      if (!parsed.success) {
+        log("warn", `LLM response schema invalid for cluster in ${obsType}`);
+        continue;
+      }
+      const candidateMap = new Map(candidates.map((c) => [c.id, c]));
+      const validIds = parsed.data.filter((id) => candidateMap.has(id));
+      if (validIds.length === 0) continue;
+      for (const id of validIds) {
+        const candidate = candidateMap.get(id);
+        if (dryRun) {
+          log("info", `[dry-run] Would supersede: ${candidate.title} (${id}) by ${newest.title} (${newest.id})`);
+          totalSuperseded++;
+          continue;
+        }
+        const wrote = supersedeSpore(id, newest.id, candidate.path, { index, vectorIndex, vaultDir });
+        if (!wrote) {
+          log("warn", `File not found for ${id}, skipping write`);
+          continue;
+        }
+        log("info", `Superseded: ${candidate.title} (${id}) by ${newest.title} (${newest.id})`);
+        totalSuperseded++;
+      }
+    }
+  }
+  return {
+    scanned: activeSpores.length,
+    clustersEvaluated: totalClusters,
+    superseded: totalSuperseded
+  };
+}
+
 export {
+  readLastTimestamp,
+  appendTraceRecord,
   DigestEngine,
-  Metabolism
+  Metabolism,
+  runRebuild,
+  runDigest,
+  runCuration
 };
-//# sourceMappingURL=chunk-HL2S5QZG.js.map
+//# sourceMappingURL=chunk-2ZBB3MQT.js.map

package/dist/chunk-2ZBB3MQT.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/daemon/digest.ts","../src/daemon/trace.ts","../src/services/vault-ops.ts"],"sourcesContent":["/**\n * DigestEngine — synthesizes vault knowledge into tiered context extracts.\n * Metabolism — adaptive timer that throttles digest cycles based on activity.\n */\n\nimport fs from 'node:fs';\nimport path from 'node:path';\nimport crypto from 'node:crypto';\nimport YAML from 'yaml';\n\nimport type { MycoIndex, IndexedNote } from '@myco/index/sqlite.js';\nimport type { LlmProvider, LlmRequestOptions } from '@myco/intelligence/llm.js';\nimport type { MycoConfig } from '@myco/config/schema.js';\nimport { loadPrompt } from '@myco/prompts/index.js';\nimport { stripReasoningTokens } from '@myco/intelligence/response.js';\nimport { stripFrontmatter } from '@myco/vault/frontmatter.js';\nimport { readLastTimestamp, appendTraceRecord } from './trace.js';\nimport {\n  estimateTokens,\n  CHARS_PER_TOKEN,\n  DIGEST_TIER_MIN_CONTEXT,\n  DIGEST_SUBSTRATE_TYPE_WEIGHTS,\n  DIGEST_LLM_REQUEST_TIMEOUT_MS,\n  LLM_REASONING_MODE,\n} from '@myco/constants.js';\n\n// --- Interfaces ---\n\nexport interface DigestCycleResult {\n  cycleId: string;\n  timestamp: string;\n  substrate: {\n    sessions: string[];\n    spores: string[];\n    plans: string[];\n    artifacts: string[];\n    team: string[];\n  };\n  tiersGenerated: number[];\n  model: string;\n  durationMs: number;\n  tokensUsed: number;\n}\n\n/** Simple log function signature for digest progress reporting. */\nexport type DigestLogFn = (level: 'debug' | 'info' | 'warn', message: string, data?: Record<string, unknown>) => void;\n\nexport interface DigestCycleOptions {\n  /** Process all substrate regardless of last cycle timestamp. */\n  fullReprocess?: boolean;\n  /** Only generate these tiers (default: all eligible). */\n  tiers?: number[];\n  /** Skip previous extract — start from clean slate. */\n  cleanSlate?: boolean;\n}\n\nexport interface DigestEngineConfig {\n  vaultDir: string;\n  index: MycoIndex;\n  llmProvider: LlmProvider;\n  config: MycoConfig;\n  log?: DigestLogFn;\n}\n\n// --- Constants ---\n\n/** Token overhead estimate for previous extract section wrapper. */\nconst PREVIOUS_EXTRACT_OVERHEAD_TOKENS = 50;\n\n/** Safety margin for context window — our CHARS_PER_TOKEN=4 heuristic significantly\n *  underestimates real token counts (observed ~3.2 chars/token for mixed content).\n *  0.70 provides a safe buffer: 32K * 0.70 = 22.4K usable tokens. */\nconst CONTEXT_SAFETY_MARGIN = 0.70;\n\n/** Types that are digest output — excluded from substrate to avoid self-digestion. */\nconst EXTRACT_TYPE = 'extract';\n\n// --- DigestEngine ---\n\nexport class DigestEngine {\n  private vaultDir: string;\n  private index: MycoIndex;\n  private llm: LlmProvider;\n  private config: MycoConfig;\n  private log: DigestLogFn;\n  private lastCycleTimestampCache: string | null | undefined = undefined;\n  private cycleInProgress = false;\n\n  /** Hooks that run before each digest cycle (e.g., consolidation). */\n  private prePassHooks: Array<{ name: string; fn: () => Promise<void> }> = [];\n\n  /** Hooks that run after each successful digest cycle. */\n  private postPassHooks: Array<{ name: string; fn: (result: DigestCycleResult) => Promise<void> }> = [];\n\n  constructor(engineConfig: DigestEngineConfig) {\n    this.vaultDir = engineConfig.vaultDir;\n    this.index = engineConfig.index;\n    this.llm = engineConfig.llmProvider;\n    this.config = engineConfig.config;\n    this.log = engineConfig.log ?? (() => {});\n  }\n\n  /** Register a hook that runs before each digest cycle. Best-effort — errors are logged, not thrown. */\n  registerPrePass(name: string, fn: () => Promise<void>): void {\n    this.prePassHooks.push({ name, fn });\n  }\n\n  /** Register a hook that runs after each successful digest cycle. Best-effort — errors are logged, not thrown. */\n  registerPostPass(name: string, fn: (result: DigestCycleResult) => Promise<void>): void {\n    this.postPassHooks.push({ name, fn });\n  }\n\n  /**\n   * Query index for recent vault notes to feed into the digest.\n   * Filters out extract notes (our own output) and caps at max_notes_per_cycle.\n   */\n  discoverSubstrate(lastCycleTimestamp: string | null): IndexedNote[] {\n    const maxNotes = this.config.digest.substrate.max_notes_per_cycle;\n\n    const notes = lastCycleTimestamp\n      ? this.index.query({ updatedSince: lastCycleTimestamp, limit: maxNotes })\n      : this.index.query({ limit: maxNotes });\n\n    // Guard against self-digestion: extract files are not currently indexed,\n    // but this filter prevents feedback loops if they ever are (e.g., via rebuild)\n    const filtered = notes\n      .filter((n) => n.type !== EXTRACT_TYPE)\n      .filter((n) => {\n        if (n.type !== 'spore') return true;\n        const status = n.frontmatter.status as string | undefined;\n        return !status || status === 'active';\n      });\n\n    // Sort by type weight (descending) then by recency (descending)\n    filtered.sort((a, b) => {\n      const weightA = DIGEST_SUBSTRATE_TYPE_WEIGHTS[a.type] ?? 0;\n      const weightB = DIGEST_SUBSTRATE_TYPE_WEIGHTS[b.type] ?? 0;\n      if (weightB !== weightA) return weightB - weightA;\n      // More recent first — created is ISO string, lexicographic sort works\n      return b.created.localeCompare(a.created);\n    });\n\n    return filtered.slice(0, maxNotes);\n  }\n\n  /**\n   * Filter configured tiers by the context window available.\n   * Only tiers whose minimum context requirement is met are eligible.\n   */\n  getEligibleTiers(): number[] {\n    const contextWindow = this.config.digest.intelligence.context_window;\n    return this.config.digest.tiers.filter((tier) => {\n      const minContext = DIGEST_TIER_MIN_CONTEXT[tier];\n      return minContext !== undefined && minContext <= contextWindow;\n    });\n  }\n\n  /**\n   * Format notes compactly for inclusion in the digest prompt.\n   * Stops adding notes once the token budget is exceeded.\n   */\n  formatSubstrate(notes: IndexedNote[], tokenBudget: number): string {\n    const charBudget = tokenBudget * CHARS_PER_TOKEN;\n    const parts: string[] = [];\n    let usedChars = 0;\n\n    for (const note of notes) {\n      const entry = `### [${note.type}] ${note.id} — \"${note.title}\"\\n${note.content}`;\n      if (usedChars + entry.length > charBudget && parts.length > 0) break;\n      parts.push(entry);\n      usedChars += entry.length;\n    }\n\n    return parts.join('\\n\\n');\n  }\n\n  /**\n   * Read a previously generated extract for a given tier.\n   * Returns the body (stripped of YAML frontmatter), or null if not found.\n   */\n  readPreviousExtract(tier: number): string | null {\n    const extractPath = path.join(this.vaultDir, 'digest', `extract-${tier}.md`);\n    let content: string;\n    try {\n      content = fs.readFileSync(extractPath, 'utf-8');\n    } catch {\n      return null;\n    }\n\n    return stripFrontmatter(content).body;\n  }\n\n  /**\n   * Write a digest extract to the vault with YAML frontmatter.\n   * Uses atomic write pattern (temp file + rename).\n   */\n  writeExtract(\n    tier: number,\n    body: string,\n    cycleId: string,\n    model: string,\n    substrateCount: number,\n  ): void {\n    const digestDir = path.join(this.vaultDir, 'digest');\n    fs.mkdirSync(digestDir, { recursive: true });\n\n    const frontmatter: Record<string, unknown> = {\n      type: EXTRACT_TYPE,\n      tier,\n      generated: new Date().toISOString(),\n      cycle_id: cycleId,\n      substrate_count: substrateCount,\n      model,\n    };\n\n    const fmYaml = YAML.stringify(frontmatter, {\n      defaultStringType: 'QUOTE_DOUBLE',\n      defaultKeyType: 'PLAIN',\n    }).trim();\n    const file = `---\\n${fmYaml}\\n---\\n\\n${body}\\n`;\n\n    const fullPath = path.join(digestDir, `extract-${tier}.md`);\n    const tmpPath = `${fullPath}.tmp`;\n    fs.writeFileSync(tmpPath, file, 'utf-8');\n    fs.renameSync(tmpPath, fullPath);\n  }\n\n  /**\n   * Append a digest cycle result as a JSON line to trace.jsonl.\n   */\n  appendTrace(record: DigestCycleResult): void {\n    const tracePath = path.join(this.vaultDir, 'digest', 'trace.jsonl');\n    appendTraceRecord(tracePath, record as unknown as Record<string, unknown>);\n    this.lastCycleTimestampCache = record.timestamp;\n  }\n\n  /**\n   * Read the last cycle timestamp from trace.jsonl.\n   * Cached in memory after first read — subsequent calls are O(1).\n   */\n  getLastCycleTimestamp(): string | null {\n    if (this.lastCycleTimestampCache !== undefined) return this.lastCycleTimestampCache;\n\n    const tracePath = path.join(this.vaultDir, 'digest', 'trace.jsonl');\n    this.lastCycleTimestampCache = readLastTimestamp(tracePath);\n    return this.lastCycleTimestampCache;\n  }\n\n  /**\n   * Run a full digest cycle: discover substrate, generate extracts for each tier.\n   * Returns the cycle result, or null if no substrate was found.\n   */\n  async runCycle(opts?: DigestCycleOptions): Promise<DigestCycleResult | null> {\n    if (this.cycleInProgress) {\n      this.log('debug', 'Cycle already in progress — skipping');\n      return null;\n    }\n    this.cycleInProgress = true;\n\n    try {\n      // Run pre-pass hooks (e.g., consolidation) before discovering substrate\n      for (const hook of this.prePassHooks) {\n        try {\n          await hook.fn();\n        } catch (err) {\n          this.log('warn', `Pre-pass hook \"${hook.name}\" failed`, { error: (err as Error).message });\n        }\n      }\n\n      return await this.runCycleInternal(opts);\n    } finally {\n      this.cycleInProgress = false;\n    }\n  }\n\n  private async runCycleInternal(opts?: DigestCycleOptions): Promise<DigestCycleResult | null> {\n    // Ensure model is loaded with correct settings every cycle.\n    // LM Studio's idle TTL can evict our instance between cycles — without\n    // re-running ensureLoaded, the auto-reloaded instance would use LM Studio's\n    // UI defaults (wrong KV cache setting). This is fast (~26ms) when the\n    // instance is still alive (just a getLoadedInstances check).\n    if (this.llm.ensureLoaded) {\n      const { context_window: contextWindow, gpu_kv_cache: gpuKvCache } = this.config.digest.intelligence;\n      this.log('debug', 'Verifying digest model', { contextWindow, gpuKvCache });\n      await this.llm.ensureLoaded(contextWindow, gpuKvCache);\n    }\n\n    const startTime = Date.now();\n    const fullReprocess = opts?.fullReprocess ?? false;\n    const lastTimestamp = fullReprocess ? null : this.getLastCycleTimestamp();\n    const substrate = this.discoverSubstrate(lastTimestamp);\n\n    this.log('debug', 'Discovering substrate', { lastTimestamp: lastTimestamp ?? 'full reprocess', substrateCount: substrate.length });\n    if (substrate.length === 0) {\n      this.log('debug', 'No substrate found — skipping cycle');\n      return null;\n    }\n\n    this.log('info', `Starting digest cycle`, { substrateCount: substrate.length, fullReprocess });\n    const cycleId = crypto.randomUUID();\n    const allEligible = this.getEligibleTiers();\n    const eligibleTiers = opts?.tiers\n      ? allEligible.filter((t) => opts.tiers!.includes(t))\n      : allEligible;\n    this.log('debug', `Eligible tiers: [${eligibleTiers.join(', ')}]`);\n    const tiersGenerated: number[] = [];\n    let totalTokensUsed = 0;\n    let model = '';\n\n    // Categorize substrate by type for the result\n    const typeToKey: Record<string, keyof DigestCycleResult['substrate']> = {\n      session: 'sessions',\n      spore: 'spores',\n      plan: 'plans',\n      artifact: 'artifacts',\n      'team-member': 'team',\n    };\n    const substrateIndex: DigestCycleResult['substrate'] = {\n      sessions: [],\n      spores: [],\n      plans: [],\n      artifacts: [],\n      team: [],\n    };\n    for (const note of substrate) {\n      const key = typeToKey[note.type];\n      if (key) {\n        substrateIndex[key].push(note.id);\n      }\n    }\n\n    // Record the cycle timestamp NOW, before tier processing. This ensures the\n    // timestamp advances even if LLM calls fail, preventing the same substrate\n    // from being rediscovered on every subsequent timer fire.\n    const cycleTimestamp = new Date().toISOString();\n\n    const systemPrompt = loadPrompt('digest-system');\n\n    for (const tier of eligibleTiers) {\n      const tierPrompt = loadPrompt(`digest-${tier}`);\n      const previousExtract = opts?.cleanSlate ? null : this.readPreviousExtract(tier);\n\n      // Calculate token budget for substrate:\n      // (context_window * safety_margin) - output - system_prompt - tier_prompt - previous_extract\n      const contextWindow = this.config.digest.intelligence.context_window;\n      const systemPromptTokens = estimateTokens(systemPrompt);\n      const tierPromptTokens = estimateTokens(tierPrompt);\n      const previousExtractTokens = previousExtract\n        ? estimateTokens(previousExtract) + PREVIOUS_EXTRACT_OVERHEAD_TOKENS\n        : 0;\n      const availableTokens = Math.floor(contextWindow * CONTEXT_SAFETY_MARGIN);\n      const substrateBudget = availableTokens - tier - systemPromptTokens - tierPromptTokens - previousExtractTokens;\n\n      if (substrateBudget <= 0) continue;\n\n      const formattedSubstrate = this.formatSubstrate(substrate, substrateBudget);\n\n      // Build user prompt (system prompt sent separately via LlmRequestOptions)\n      const promptParts = [tierPrompt];\n\n      if (previousExtract) {\n        promptParts.push('', '## Previous Synthesis', '', previousExtract);\n      }\n\n      promptParts.push('', '## New Substrate', '', formattedSubstrate);\n      promptParts.push(\n        '',\n        '---',\n        'Produce your updated synthesis now. Stay within the token budget specified above.',\n      );\n\n      const userPrompt = promptParts.join('\\n');\n      const promptTokens = estimateTokens(systemPrompt + userPrompt);\n      this.log('debug', `Tier ${tier}: sending LLM request`, { promptTokens, maxTokens: tier, substrateBudget });\n\n      try {\n        const tierStart = Date.now();\n        const digestConfig = this.config.digest.intelligence;\n        const opts: LlmRequestOptions = {\n          maxTokens: tier,\n          timeoutMs: DIGEST_LLM_REQUEST_TIMEOUT_MS,\n          contextLength: contextWindow,\n          reasoning: LLM_REASONING_MODE,\n          systemPrompt,\n          keepAlive: digestConfig.keep_alive ?? undefined,\n        };\n        const response = await this.llm.summarize(userPrompt, opts);\n        const tierDuration = Date.now() - tierStart;\n\n        // Strip reasoning tokens if present (some models output chain-of-thought)\n        const extractText = stripReasoningTokens(response.text);\n        model = response.model;\n        const responseTokens = estimateTokens(extractText);\n        totalTokensUsed += promptTokens + responseTokens;\n\n        this.log('info', `Tier ${tier}: completed`, { durationMs: tierDuration, responseTokens, model: response.model });\n        this.writeExtract(tier, extractText, cycleId, response.model, substrate.length);\n        tiersGenerated.push(tier);\n      } catch (err) {\n        this.log('warn', `Tier ${tier}: failed`, { error: (err as Error).message });\n      }\n    }\n\n    const result: DigestCycleResult = {\n      cycleId,\n      timestamp: cycleTimestamp,\n      substrate: substrateIndex,\n      tiersGenerated,\n      model,\n      durationMs: Date.now() - startTime,\n      tokensUsed: totalTokensUsed,\n    };\n\n    this.appendTrace(result);\n\n    // Run post-pass hooks after successful digest\n    for (const hook of this.postPassHooks) {\n      try {\n        await hook.fn(result);\n      } catch (err) {\n        this.log('warn', `Post-pass hook \"${hook.name}\" failed`, { error: (err as Error).message });\n      }\n    }\n\n    return result;\n  }\n}\n\n// --- Metabolism (Adaptive Timer) ---\n\nexport type MetabolismState = 'active' | 'cooling' | 'dormant';\n\n/** Milliseconds per second for config conversion. */\nconst MS_PER_SECOND = 1000;\n\nexport class Metabolism {\n  state: MetabolismState = 'active';\n  currentIntervalMs: number;\n\n  private cooldownStep = 0;\n  private lastSubstrateTime: number;\n  private timer: ReturnType<typeof setTimeout> | null = null;\n  private activeIntervalMs: number;\n  private cooldownIntervalsMs: number[];\n  private dormancyThresholdMs: number;\n\n  constructor(config: MycoConfig['digest']['metabolism']) {\n    this.activeIntervalMs = config.active_interval * MS_PER_SECOND;\n    this.cooldownIntervalsMs = config.cooldown_intervals.map((s) => s * MS_PER_SECOND);\n    this.dormancyThresholdMs = config.dormancy_threshold * MS_PER_SECOND;\n    this.currentIntervalMs = this.activeIntervalMs;\n    this.lastSubstrateTime = Date.now();\n  }\n\n  /** Reset to active state when new substrate is found. */\n  onSubstrateFound(): void {\n    this.state = 'active';\n    this.cooldownStep = 0;\n    this.currentIntervalMs = this.activeIntervalMs;\n    this.lastSubstrateTime = Date.now();\n  }\n\n  /** Advance cooldown when a cycle finds no new substrate. */\n  onEmptyCycle(): void {\n    if (this.state === 'dormant') return;\n\n    this.state = 'cooling';\n    if (this.cooldownStep < this.cooldownIntervalsMs.length) {\n      this.currentIntervalMs = this.cooldownIntervalsMs[this.cooldownStep];\n      this.cooldownStep++;\n    }\n\n    this.checkDormancy();\n  }\n\n  /** Enter dormant state if enough time has elapsed since last substrate. */\n  checkDormancy(): void {\n    const elapsed = Date.now() - this.lastSubstrateTime;\n    if (elapsed >= this.dormancyThresholdMs) {\n      this.state = 'dormant';\n      // Keep the last cooldown interval as the dormant polling rate\n    }\n  }\n\n  /** Return to active from any state, resetting timers and rescheduling immediately. */\n  activate(): void {\n    this.onSubstrateFound();\n    // Reschedule with the new active interval — without this, the old\n    // (possibly dormant) timer continues ticking at the wrong rate\n    if (this.callback) {\n      this.reschedule();\n    }\n  }\n\n  /** Set lastSubstrateTime explicitly (for testing). */\n  markLastSubstrate(time: number): void {\n    this.lastSubstrateTime = time;\n  }\n\n  /** Begin scheduling digest cycles with adaptive intervals. */\n  start(callback: () => Promise<void>): void {\n    this.callback = callback;\n    this.reschedule();\n  }\n\n  /** Stop the timer. */\n  stop(): void {\n    if (this.timer) {\n      clearTimeout(this.timer);\n      this.timer = null;\n    }\n  }\n\n  private callback: (() => Promise<void>) | null = null;\n\n  private reschedule(): void {\n    this.stop();\n    if (!this.callback) return;\n    const cb = this.callback;\n    const schedule = (): void => {\n      this.timer = setTimeout(async () => {\n        await cb();\n        schedule();\n      }, this.currentIntervalMs);\n      this.timer.unref();\n    };\n    schedule();\n  }\n}\n","/**\n * Shared JSONL trace file utilities.\n *\n * Used by DigestEngine and ConsolidationEngine to read/write append-only\n * trace records with timestamp caching.\n */\n\nimport fs from 'node:fs';\nimport path from 'node:path';\n\n/** Read the last JSON record's `timestamp` field from a JSONL file. Returns null if file is missing or empty. */\nexport function readLastTimestamp(filePath: string): string | null {\n  let content: string;\n  try {\n    content = fs.readFileSync(filePath, 'utf-8').trim();\n  } catch {\n    return null;\n  }\n\n  if (!content) return null;\n\n  const lines = content.split('\\n');\n  const lastLine = lines[lines.length - 1];\n  try {\n    const record = JSON.parse(lastLine) as { timestamp: string };\n    return record.timestamp ?? null;\n  } catch {\n    return null;\n  }\n}\n\n/** Append a JSON record to a JSONL file, creating parent directories if needed. */\nexport function appendTraceRecord(filePath: string, record: Record<string, unknown>): void {\n  fs.mkdirSync(path.dirname(filePath), { recursive: true });\n  fs.appendFileSync(filePath, JSON.stringify(record) + '\\n', 'utf-8');\n}\n","import type { MycoIndex } from '../index/sqlite.js';\nimport type { VectorIndex } from '../index/vectors.js';\nimport type { MycoConfig } from '../config/schema.js';\nimport type { LlmProvider, EmbeddingProvider } from '../intelligence/llm.js';\nimport type { DigestCycleResult, DigestLogFn } from '../daemon/digest.js';\nimport { rebuildIndex } from '../index/rebuild.js';\nimport { initFts } from '../index/fts.js';\nimport { generateEmbedding } from '../intelligence/embeddings.js';\nimport { batchExecute, EMBEDDING_BATCH_CONCURRENCY } from '../intelligence/batch.js';\nimport { DigestEngine } from '../daemon/digest.js';\nimport type { DigestCycleOptions } from '../daemon/digest.js';\nimport {\n  EMBEDDING_INPUT_LIMIT,\n  CURATION_CLUSTER_SIMILARITY,\n  SUPERSESSION_MAX_TOKENS,\n  LLM_REASONING_MODE,\n} from '../constants.js';\nimport { stripReasoningTokens } from '../intelligence/response.js';\nimport { loadPrompt, formatNoteForPrompt, formatNotesForPrompt } from '../prompts/index.js';\nimport { supersedeSpore, supersededIdsSchema, isActiveSpore } from '../vault/curation.js';\n\nexport interface OperationContext {\n  vaultDir: string;\n  config: MycoConfig;\n  index: MycoIndex;\n  vectorIndex?: VectorIndex;\n  log?: (level: string, message: string, data?: Record<string, unknown>) => void;\n}\n\n// --- Rebuild ---\n\nexport interface RebuildResult {\n  ftsCount: number;\n  embeddedCount: number;\n  failedCount: number;\n  skippedCount: number;\n}\n\n/**\n * Rebuild FTS index and re-embed all active notes.\n * Core logic shared between CLI (`myco rebuild`) and daemon API (`POST /api/rebuild`).\n */\nexport async function runRebuild(\n  ctx: OperationContext,\n  embeddingProvider: EmbeddingProvider,\n  onProgress?: (done: number, total: number) => void,\n): Promise<RebuildResult> {\n  const { index, vaultDir } = ctx;\n\n  // Phase 1: FTS rebuild\n  initFts(index);\n  const ftsCount = rebuildIndex(index, vaultDir);\n\n  // Phase 2: Vector embeddings\n  if (!ctx.vectorIndex) {\n    return { ftsCount, embeddedCount: 0, failedCount: 0, skippedCount: 0 };\n  }\n\n  const allNotes = index.query({});\n  // Skip superseded/archived spores\n  const activeNotes = allNotes.filter((n) => {\n    const status = (n.frontmatter as Record<string, unknown>)?.status as string | undefined;\n    return status !== 'superseded' && status !== 'archived';\n  });\n  const skippedCount = allNotes.length - activeNotes.length;\n\n  const vec = ctx.vectorIndex;\n  const result = await batchExecute(\n    activeNotes,\n    async (note) => {\n      const text = `${note.title}\\n${note.content}`.slice(0, EMBEDDING_INPUT_LIMIT);\n      const emb = await generateEmbedding(embeddingProvider, text);\n      vec.upsert(note.id, emb.embedding, {\n        type: note.type,\n        session_id: (note.frontmatter as Record<string, unknown>)?.session as string ?? '',\n      });\n    },\n    {\n      concurrency: EMBEDDING_BATCH_CONCURRENCY,\n      onProgress,\n    },\n  );\n\n  return {\n    ftsCount,\n    embeddedCount: result.succeeded,\n    failedCount: result.failed,\n    skippedCount,\n  };\n}\n\n// --- Digest ---\n\nexport interface DigestOptions {\n  tier?: number;\n  full?: boolean;\n}\n\n/**\n * Run a single digest cycle.\n * Core logic shared between CLI (`myco digest`) and daemon API (`POST /api/digest`).\n */\nexport async function runDigest(\n  ctx: OperationContext,\n  llmProvider: LlmProvider,\n  options?: DigestOptions,\n): Promise<DigestCycleResult | null> {\n  const { config, vaultDir, index } = ctx;\n\n  const log: DigestLogFn = ctx.log\n    ? (level, message, data) => ctx.log!(level, message, data)\n    : () => {};\n\n  const engine = new DigestEngine({\n    vaultDir,\n    index,\n    llmProvider,\n    config,\n    log,\n  });\n\n  const opts: DigestCycleOptions = {};\n  const isReprocess = options?.full || options?.tier !== undefined;\n\n  if (isReprocess) {\n    opts.fullReprocess = true;\n    opts.cleanSlate = true;\n  }\n  if (options?.tier !== undefined) {\n    const eligible = engine.getEligibleTiers();\n    if (!eligible.includes(options.tier)) {\n      throw new Error(`Tier ${options.tier} is not eligible. Eligible tiers: [${eligible.join(', ')}]`);\n    }\n    opts.tiers = [options.tier];\n  }\n\n  return engine.runCycle(opts);\n}\n\n// --- Curation ---\n\nexport interface CurationDeps {\n  vaultDir: string;\n  config: MycoConfig;\n  index: MycoIndex;\n  vectorIndex: VectorIndex;\n  llmProvider: LlmProvider;\n  embeddingProvider: EmbeddingProvider;\n  log?: (level: string, message: string, data?: Record<string, unknown>) => void;\n}\n\nexport interface CurationResult {\n  scanned: number;\n  clustersEvaluated: number;\n  superseded: number;\n}\n\n// --- Curation internals ---\n\n/** Max concurrent embedding requests to avoid overwhelming the provider. */\nconst CURATION_EMBEDDING_BATCH_SIZE = 10;\n\ninterface SporeWithEmbedding {\n  id: string;\n  path: string;\n  title: string;\n  content: string;\n  created: string;\n  frontmatter: Record<string, unknown>;\n  embedding: number[];\n}\n\ninterface Cluster {\n  spores: SporeWithEmbedding[];\n  centroid: number[];\n}\n\nfunction cosineSimilarity(a: number[], b: number[]): number {\n  let dot = 0, normA = 0, normB = 0;\n  for (let i = 0; i < a.length; i++) {\n    dot += a[i] * b[i];\n    normA += a[i] * a[i];\n    normB += b[i] * b[i];\n  }\n  return dot / (Math.sqrt(normA) * Math.sqrt(normB));\n}\n\nfunction updateCentroid(spores: SporeWithEmbedding[]): number[] {\n  if (spores.length === 0) return [];\n  const dim = spores[0].embedding.length;\n  const centroid = new Array<number>(dim).fill(0);\n  for (const s of spores) {\n    for (let i = 0; i < dim; i++) {\n      centroid[i] += s.embedding[i];\n    }\n  }\n  for (let i = 0; i < dim; i++) {\n    centroid[i] /= spores.length;\n  }\n  return centroid;\n}\n\nfunction clusterSpores(spores: SporeWithEmbedding[]): Cluster[] {\n  const clusters: Cluster[] = [];\n  for (const spore of spores) {\n    let bestCluster: Cluster | null = null;\n    let bestSimilarity = -1;\n    for (const cluster of clusters) {\n      const sim = cosineSimilarity(spore.embedding, cluster.centroid);\n      if (sim > bestSimilarity) {\n        bestSimilarity = sim;\n        bestCluster = cluster;\n      }\n    }\n    if (bestCluster !== null && bestSimilarity >= CURATION_CLUSTER_SIMILARITY) {\n      bestCluster.spores.push(spore);\n      bestCluster.centroid = updateCentroid(bestCluster.spores);\n    } else {\n      clusters.push({ spores: [spore], centroid: [...spore.embedding] });\n    }\n  }\n  return clusters;\n}\n\n/**\n * Run vault curation: embed spores, cluster, ask LLM which are outdated, supersede.\n * Core logic shared between CLI (`myco curate`) and daemon API (`POST /api/curate`).\n */\nexport async function runCuration(\n  deps: CurationDeps,\n  dryRun: boolean,\n): Promise<CurationResult> {\n  const { index, vectorIndex, llmProvider, embeddingProvider, vaultDir } = deps;\n  const log = deps.log ?? 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Embed all active spores (batched for concurrency)\n  const sporesWithEmbeddings: SporeWithEmbedding[] = [];\n  let embedFailures = 0;\n\n  for (let i = 0; i < activeSpores.length; i += CURATION_EMBEDDING_BATCH_SIZE) {\n    const batch = activeSpores.slice(i, i + CURATION_EMBEDDING_BATCH_SIZE);\n    const results = await Promise.allSettled(\n      batch.map(async (spore) => {\n        const text = spore.content.slice(0, EMBEDDING_INPUT_LIMIT);\n        const result = await generateEmbedding(embeddingProvider, text);\n        return { spore, embedding: result.embedding };\n      }),\n    );\n\n    for (const result of results) {\n      if (result.status === 'fulfilled') {\n        const { spore, embedding } = result.value;\n        sporesWithEmbeddings.push({\n          id: spore.id,\n          path: spore.path,\n          title: spore.title,\n          content: spore.content,\n          created: spore.created,\n          frontmatter: spore.frontmatter,\n          embedding,\n        });\n      } else {\n        embedFailures++;\n      }\n    }\n  }\n\n  if (embedFailures > 0) {\n    log('warn', `${embedFailures} spore(s) could not be embedded and were skipped`);\n  }\n\n  // 3. Group by observation_type\n  const byType = new Map<string, SporeWithEmbedding[]>();\n  for (const spore of sporesWithEmbeddings) {\n    const obsType = (spore.frontmatter['observation_type'] as string | undefined) ?? 'unknown';\n    if (!byType.has(obsType)) byType.set(obsType, []);\n    byType.get(obsType)!.push(spore);\n  }\n\n  // 4. Cluster within each type group\n  const template = loadPrompt('supersession');\n  let totalClusters = 0;\n  let totalSuperseded = 0;\n\n  for (const [obsType, typeSpores] of byType) {\n    const clusters = clusterSpores(typeSpores);\n    const multiSpore = clusters.filter((c) => c.spores.length >= 2);\n    if (multiSpore.length === 0) continue;\n\n    log('info', `Type: ${obsType} — ${typeSpores.length} spores, ${multiSpore.length} cluster(s) to evaluate`);\n    totalClusters += multiSpore.length;\n\n    for (const cluster of multiSpore) {\n      const sorted = [...cluster.spores].sort((a, b) => a.created.localeCompare(b.created));\n      const newest = sorted[sorted.length - 1];\n      const candidates = sorted.slice(0, sorted.length - 1);\n\n      // Build supersession prompt\n      const newSporeText = formatNoteForPrompt(newest);\n      const candidatesText = formatNotesForPrompt(candidates);\n\n      const prompt = template\n        .replace('{{new_spore}}', newSporeText)\n        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const candidateMap = new Map(candidates.map((c) => [c.id, c]));\n      const validIds = parsed.data.filter((id) => candidateMap.has(id));\n      if (validIds.length === 0) continue;\n\n      for (const id of validIds) {\n        const candidate = candidateMap.get(id)!;\n\n        if (dryRun) {\n          log('info', `[dry-run] Would supersede: ${candidate.title} (${id}) by ${newest.title} (${newest.id})`);\n          totalSuperseded++;\n          continue;\n        }\n\n        const wrote = supersedeSpore(id, newest.id, candidate.path, { index, vectorIndex, vaultDir });\n        if (!wrote) {\n          log('warn', `File not found for ${id}, skipping write`);\n          continue;\n        }\n\n        log('info', `Superseded: ${candidate.title} (${id}) by ${newest.title} (${newest.id})`);\n        totalSuperseded++;\n      }\n    }\n  }\n\n  return {\n    scanned: activeSpores.length,\n    clustersEvaluated: totalClusters,\n    superseded: totalSuperseded,\n  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