@goondocks/myco 0.4.3 → 0.5.0

package/dist/{cli-PMOFCZQL.js → cli-BLYNNKGJ.js}

@@ -2,14 +2,14 @@
 import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
 import {
   loadEnv
-} from "./chunk-GFBG73P4.js";
+} from "./chunk-FIRMTYFH.js";
 import "./chunk-SAKJMNSR.js";
-import "./chunk-67R6EMYD.js";
+import "./chunk-JI6M2L2W.js";
 import {
   resolveVaultDir
 } from "./chunk-N33KUCFP.js";
-import "./chunk-BNIYWCST.js";
-import "./chunk-JBD5KP5G.js";
+import "./chunk-X6TKHO22.js";
+import "./chunk-B6WVNDA5.js";
 import "./chunk-PZUWP5VK.js";
 
 // src/cli.ts
@@ -21,6 +21,7 @@ var USAGE = `Usage: myco <command> [args]
 Commands:
   init [options]           Initialize a new vault
   config <get|set> [args]  Get or set vault config values
+  curate [options]         Scan vault and supersede stale spores (--dry-run)
   detect-providers         Detect available LLM/embedding providers (JSON)
   verify                   Test LLM and embedding connectivity
   stats                    Vault health, index counts, vector count
@@ -30,9 +31,10 @@ Commands:
   logs [options]           View daemon logs
   setup-llm [options]      Configure LLM and embedding providers
   setup-digest [options]   Configure digest and capture settings
+  digest [options]         Run a digest cycle (--tier N, --full)
   restart                  Restart the daemon
   rebuild                  Reindex the entire vault
-  reprocess [options]      Re-extract observations and re-index sessions
+  reprocess [options]      Re-extract observations, regenerate summaries, re-index
   version                  Show plugin version
 `;
 async function main() {
@@ -41,10 +43,10 @@ async function main() {
     process.stdout.write(USAGE);
     return;
   }
-  if (cmd === "init") return (await import("./init-NUF5UBUJ.js")).run(args);
-  if (cmd === "detect-providers") return (await import("./detect-providers-IRL2TTLK.js")).run(args);
+  if (cmd === "init") return (await import("./init-HPQ77WWF.js")).run(args);
+  if (cmd === "detect-providers") return (await import("./detect-providers-BIHYFK5M.js")).run(args);
   if (cmd === "version" || cmd === "--version" || cmd === "-v") {
-    const { getPluginVersion } = await import("./version-5B2TWXQJ.js");
+    const { getPluginVersion } = await import("./version-HJTVNPOO.js");
     console.log(getPluginVersion());
     return;
   }
@@ -56,26 +58,30 @@ async function main() {
   switch (cmd) {
     case "config":
       return (await import("./config-5FGLQGCW.js")).run(args, vaultDir);
+    case "curate":
+      return (await import("./curate-S4HOYWXA.js")).run(args, vaultDir);
     case "verify":
-      return (await import("./verify-JFHQH55Z.js")).run(args, vaultDir);
+      return (await import("./verify-RACBFT2P.js")).run(args, vaultDir);
     case "stats":
-      return (await import("./stats-6G7SN5YZ.js")).run(args, vaultDir);
+      return (await import("./stats-ZIIJ2GB3.js")).run(args, vaultDir);
     case "search":
-      return (await import("./search-MPD7SFK6.js")).run(args, vaultDir);
+      return (await import("./search-E5JQMTXV.js")).run(args, vaultDir);
     case "vectors":
-      return (await import("./search-MPD7SFK6.js")).runVectors(args, vaultDir);
+      return (await import("./search-E5JQMTXV.js")).runVectors(args, vaultDir);
     case "session":
       return (await import("./session-QF6MILAC.js")).run(args, vaultDir);
     case "setup-llm":
-      return (await import("./setup-llm-XCCH5LYD.js")).run(args, vaultDir);
+      return (await import("./setup-llm-4BZM33YT.js")).run(args, vaultDir);
     case "setup-digest":
-      return (await import("./setup-digest-K732MGOJ.js")).run(args, vaultDir);
+      return (await import("./setup-digest-DZAFIBEF.js")).run(args, vaultDir);
+    case "digest":
+      return (await import("./digest-7NKYXM6G.js")).run(args, vaultDir);
     case "restart":
-      return (await import("./restart-ABW4ZK3P.js")).run(args, vaultDir);
+      return (await import("./restart-FYW662DR.js")).run(args, vaultDir);
     case "rebuild":
-      return (await import("./rebuild-E6YFIRYZ.js")).run(args, vaultDir);
+      return (await import("./rebuild-KQ6G2GZM.js")).run(args, vaultDir);
     case "reprocess":
-      return (await import("./reprocess-7G7KQWCN.js")).run(args, vaultDir);
+      return (await import("./reprocess-ZL4HKTSC.js")).run(args, vaultDir);
     case "logs":
       return (await import("./logs-BSTBZHDR.js")).run(args, vaultDir);
     default:
@@ -88,4 +94,4 @@ main().catch((err) => {
   console.error(`myco: ${err.message}`);
   process.exit(1);
 });
-//# sourceMappingURL=cli-PMOFCZQL.js.map
+//# sourceMappingURL=cli-BLYNNKGJ.js.map

package/dist/cli-BLYNNKGJ.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/cli.ts"],"sourcesContent":["#!/usr/bin/env node\nimport { loadEnv } from './cli/shared.js';\nimport { resolveVaultDir } from './vault/resolve.js';\nimport fs from 'node:fs';\nimport path from 'node:path';\n\nloadEnv();\n\nconst USAGE = `Usage: myco <command> [args]\n\nCommands:\n  init [options]           Initialize a new vault\n  config <get|set> [args]  Get or set vault config values\n  curate [options]         Scan vault and supersede stale spores (--dry-run)\n  detect-providers         Detect available LLM/embedding providers (JSON)\n  verify                   Test LLM and embedding connectivity\n  stats                    Vault health, index counts, vector count\n  search <query>           Combined FTS + vector search with scores\n  vectors <query>          Raw vector search with similarity scores\n  session [id|latest]      Show a session note\n  logs [options]           View daemon logs\n  setup-llm [options]      Configure LLM and embedding providers\n  setup-digest [options]   Configure digest and capture settings\n  digest [options]         Run a digest cycle (--tier N, --full)\n  restart                  Restart the daemon\n  rebuild                  Reindex the entire vault\n  reprocess [options]      Re-extract observations, regenerate summaries, re-index\n  version                  Show plugin version\n`;\n\nasync function main(): Promise<void> {\n  const [cmd, ...args] = process.argv.slice(2);\n  if (!cmd || cmd === '--help' || cmd === '-h') {\n    process.stdout.write(USAGE);\n    return;\n  }\n\n  if (cmd === 'init') return (await import('./cli/init.js')).run(args);\n  if (cmd === 'detect-providers') return (await import('./cli/detect-providers.js')).run(args);\n  if (cmd === 'version' || cmd === '--version' || cmd === '-v') {\n    const { getPluginVersion } = await import('./version.js');\n    console.log(getPluginVersion());\n    return;\n  }\n\n  const vaultDir = resolveVaultDir();\n  if (!fs.existsSync(path.join(vaultDir, 'myco.yaml'))) {\n    console.error(`No myco.yaml found in ${vaultDir}. Run 'myco init' first.`);\n    process.exit(1);\n  }\n\n  switch (cmd) {\n    case 'config': return (await import('./cli/config.js')).run(args, vaultDir);\n    case 'curate': return (await import('./cli/curate.js')).run(args, vaultDir);\n    case 'verify': return (await import('./cli/verify.js')).run(args, vaultDir);\n    case 'stats': return (await import('./cli/stats.js')).run(args, vaultDir);\n    case 'search': return (await import('./cli/search.js')).run(args, vaultDir);\n    case 'vectors': return (await import('./cli/search.js')).runVectors(args, vaultDir);\n    case 'session': return (await import('./cli/session.js')).run(args, vaultDir);\n    case 'setup-llm': return (await import('./cli/setup-llm.js')).run(args, vaultDir);\n    case 'setup-digest': return (await import('./cli/setup-digest.js')).run(args, vaultDir);\n    case 'digest': return (await import('./cli/digest.js')).run(args, vaultDir);\n    case 'restart': return (await import('./cli/restart.js')).run(args, vaultDir);\n    case 'rebuild': return (await import('./cli/rebuild.js')).run(args, vaultDir);\n    case 'reprocess': return (await import('./cli/reprocess.js')).run(args, vaultDir);\n    case 'logs': return (await import('./cli/logs.js')).run(args, vaultDir);\n    default:\n      console.error(`Unknown command: ${cmd}`);\n      process.stdout.write(USAGE);\n      process.exit(1);\n  }\n}\n\nmain().catch((err) => {\n  console.error(`myco: ${(err as Error).message}`);\n  process.exit(1);\n});\n"],"mappings":";;;;;;;;;;;;;;;AAGA,OAAO,QAAQ;AACf,OAAO,UAAU;AAEjB,QAAQ;AAER,IAAM,QAAQ;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAsBd,eAAe,OAAsB;AACnC,QAAM,CAAC,KAAK,GAAG,IAAI,IAAI,QAAQ,KAAK,MAAM,CAAC;AAC3C,MAAI,CAAC,OAAO,QAAQ,YAAY,QAAQ,MAAM;AAC5C,YAAQ,OAAO,MAAM,KAAK;AAC1B;AAAA,EACF;AAEA,MAAI,QAAQ,OAAQ,SAAQ,MAAM,OAAO,oBAAe,GAAG,IAAI,IAAI;AACnE,MAAI,QAAQ,mBAAoB,SAAQ,MAAM,OAAO,gCAA2B,GAAG,IAAI,IAAI;AAC3F,MAAI,QAAQ,aAAa,QAAQ,eAAe,QAAQ,MAAM;AAC5D,UAAM,EAAE,iBAAiB,IAAI,MAAM,OAAO,uBAAc;AACxD,YAAQ,IAAI,iBAAiB,CAAC;AAC9B;AAAA,EACF;AAEA,QAAM,WAAW,gBAAgB;AACjC,MAAI,CAAC,GAAG,WAAW,KAAK,KAAK,UAAU,WAAW,CAAC,GAAG;AACpD,YAAQ,MAAM,yBAAyB,QAAQ,0BAA0B;AACzE,YAAQ,KAAK,CAAC;AAAA,EAChB;AAEA,UAAQ,KAAK;AAAA,IACX,KAAK;AAAU,cAAQ,MAAM,OAAO,sBAAiB,GAAG,IAAI,MAAM,QAAQ;AAAA,IAC1E,KAAK;AAAU,cAAQ,MAAM,OAAO,sBAAiB,GAAG,IAAI,MAAM,QAAQ;AAAA,IAC1E,KAAK;AAAU,cAAQ,MAAM,OAAO,sBAAiB,GAAG,IAAI,MAAM,QAAQ;AAAA,IAC1E,KAAK;AAAS,cAAQ,MAAM,OAAO,qBAAgB,GAAG,IAAI,MAAM,QAAQ;AAAA,IACxE,KAAK;AAAU,cAAQ,MAAM,OAAO,sBAAiB,GAAG,IAAI,MAAM,QAAQ;AAAA,IAC1E,KAAK;AAAW,cAAQ,MAAM,OAAO,sBAAiB,GAAG,WAAW,MAAM,QAAQ;AAAA,IAClF,KAAK;AAAW,cAAQ,MAAM,OAAO,uBAAkB,GAAG,IAAI,MAAM,QAAQ;AAAA,IAC5E,KAAK;AAAa,cAAQ,MAAM,OAAO,yBAAoB,GAAG,IAAI,MAAM,QAAQ;AAAA,IAChF,KAAK;AAAgB,cAAQ,MAAM,OAAO,4BAAuB,GAAG,IAAI,MAAM,QAAQ;AAAA,IACtF,KAAK;AAAU,cAAQ,MAAM,OAAO,sBAAiB,GAAG,IAAI,MAAM,QAAQ;AAAA,IAC1E,KAAK;AAAW,cAAQ,MAAM,OAAO,uBAAkB,GAAG,IAAI,MAAM,QAAQ;AAAA,IAC5E,KAAK;AAAW,cAAQ,MAAM,OAAO,uBAAkB,GAAG,IAAI,MAAM,QAAQ;AAAA,IAC5E,KAAK;AAAa,cAAQ,MAAM,OAAO,yBAAoB,GAAG,IAAI,MAAM,QAAQ;AAAA,IAChF,KAAK;AAAQ,cAAQ,MAAM,OAAO,oBAAe,GAAG,IAAI,MAAM,QAAQ;AAAA,IACtE;AACE,cAAQ,MAAM,oBAAoB,GAAG,EAAE;AACvC,cAAQ,OAAO,MAAM,KAAK;AAC1B,cAAQ,KAAK,CAAC;AAAA,EAClB;AACF;AAEA,KAAK,EAAE,MAAM,CAAC,QAAQ;AACpB,UAAQ,MAAM,SAAU,IAAc,OAAO,EAAE;AAC/C,UAAQ,KAAK,CAAC;AAChB,CAAC;","names":[]}

package/dist/{client-5SUO2UYH.js → client-5GB4WVXE.js}

@@ -1,12 +1,12 @@
 import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
 import {
   DaemonClient
-} from "./chunk-OUFSLZTX.js";
-import "./chunk-2GJFTIWX.js";
-import "./chunk-BNIYWCST.js";
-import "./chunk-JBD5KP5G.js";
+} from "./chunk-ZWUFTOG3.js";
+import "./chunk-7KQB22DP.js";
+import "./chunk-X6TKHO22.js";
+import "./chunk-B6WVNDA5.js";
 import "./chunk-PZUWP5VK.js";
 export {
   DaemonClient
 };
-//# sourceMappingURL=client-5SUO2UYH.js.map
+//# sourceMappingURL=client-5GB4WVXE.js.map

package/dist/curate-S4HOYWXA.js

@@ -0,0 +1,231 @@
+import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
+import {
+  isActiveSpore,
+  supersedeSpore,
+  supersededIdsSchema
+} from "./chunk-FIA5NTRH.js";
+import "./chunk-JJL6AMDA.js";
+import {
+  generateEmbedding
+} from "./chunk-RGVBGTD6.js";
+import {
+  VectorIndex
+} from "./chunk-XQXXF6MU.js";
+import {
+  loadPrompt,
+  stripReasoningTokens
+} from "./chunk-KYL67SKZ.js";
+import "./chunk-2AMAOSRF.js";
+import {
+  createEmbeddingProvider,
+  createLlmProvider
+} from "./chunk-RCV2I4AI.js";
+import {
+  MycoIndex
+} from "./chunk-AK6GNLPV.js";
+import "./chunk-JI6M2L2W.js";
+import {
+  loadConfig
+} from "./chunk-TBRZAJ7W.js";
+import "./chunk-6UJWI4IW.js";
+import {
+  CURATION_CLUSTER_SIMILARITY,
+  EMBEDDING_INPUT_LIMIT,
+  LLM_REASONING_MODE,
+  SUPERSESSION_MAX_TOKENS
+} from "./chunk-B6WVNDA5.js";
+import "./chunk-PZUWP5VK.js";
+
+// src/cli/curate.ts
+import path from "path";
+var 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 run(args, vaultDir) {
+  const isDryRun = args.includes("--dry-run");
+  const config = loadConfig(vaultDir);
+  const index = new MycoIndex(path.join(vaultDir, "index.db"));
+  const llmProvider = createLlmProvider(config.intelligence.llm);
+  const embeddingProvider = createEmbeddingProvider(config.intelligence.embedding);
+  let vectorIndex = null;
+  try {
+    const testEmbed = await embeddingProvider.embed("test");
+    vectorIndex = new VectorIndex(path.join(vaultDir, "vectors.db"), testEmbed.dimensions);
+  } catch (e) {
+    console.error(`Vector index unavailable: ${e.message}`);
+    console.error("Curate requires a working embedding provider.");
+    index.close();
+    process.exit(1);
+  }
+  try {
+    if (isDryRun) {
+      console.log("Dry run \u2014 no changes will be written.\n");
+    }
+    const allSpores = index.query({ type: "spore" });
+    const activeSpores = allSpores.filter((n) => isActiveSpore(n.frontmatter));
+    console.log(`Scanning ${activeSpores.length} active spores...`);
+    if (activeSpores.length === 0) {
+      console.log("No active spores found.");
+      return;
+    }
+    const sporesWithEmbeddings = [];
+    let embedFailures = 0;
+    for (let i = 0; i < activeSpores.length; i += EMBEDDING_BATCH_SIZE) {
+      const batch = activeSpores.slice(i, i + 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) {
+      console.log(`Warning: ${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;
+      console.log(`
+Type: ${obsType} \u2014 ${typeSpores.length} spores, ${multiSpore.length} cluster(s) to evaluate`);
+      totalClusters += multiSpore.length;
+      for (const cluster of multiSpore) {
+        const sorted = [...cluster.spores].sort((a, b) => a.created.localeCompare(b.created));
+        const newest = sorted[sorted.length - 1];
+        const candidates = sorted.slice(0, sorted.length - 1);
+        const newSporeText = `[${newest.id}] ${newest.title}
+${newest.content}`;
+        const candidatesText = candidates.map((c) => `[${c.id}] ${c.title}
+${c.content}`).join("\n\n");
+        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) {
+          console.log(`  Warning: LLM call failed for cluster in ${obsType}: ${String(err)}`);
+          continue;
+        }
+        let rawIds;
+        try {
+          rawIds = JSON.parse(responseText);
+        } catch {
+          console.log(`  Warning: Could not parse LLM response for cluster in ${obsType}`);
+          continue;
+        }
+        const parsed = supersededIdsSchema.safeParse(rawIds);
+        if (!parsed.success) {
+          console.log(`  Warning: 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 (isDryRun) {
+            console.log(`  [dry-run] Would supersede: ${candidate.title} (${id})`);
+            console.log(`            Superseded by: ${newest.title} (${newest.id})`);
+            totalSuperseded++;
+            continue;
+          }
+          const wrote = supersedeSpore(id, newest.id, candidate.path, { index, vectorIndex, vaultDir });
+          if (!wrote) {
+            console.log(`  Warning: file not found for ${id}, skipping write`);
+            continue;
+          }
+          console.log(`  Superseded: ${candidate.title} (${id})`);
+          console.log(`  By: ${newest.title} (${newest.id})`);
+          totalSuperseded++;
+        }
+      }
+    }
+    console.log(`
+Curation complete:`);
+    console.log(`  Scanned: ${activeSpores.length} active spores`);
+    console.log(`  Clusters evaluated: ${totalClusters}`);
+    if (isDryRun) {
+      console.log(`  Would supersede: ${totalSuperseded}`);
+    } else {
+      console.log(`  Superseded: ${totalSuperseded}`);
+    }
+  } finally {
+    index.close();
+    vectorIndex?.close();
+  }
+}
+export {
+  run
+};
+//# sourceMappingURL=curate-S4HOYWXA.js.map

package/dist/curate-S4HOYWXA.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/cli/curate.ts"],"sourcesContent":["/**\n * myco curate — scan the vault for stale spores and supersede them.\n *\n * Usage:\n *   myco curate              Scan and supersede stale spores\n *   myco curate --dry-run    Show what would be superseded without writing\n *\n * Algorithm:\n *   1. Load all active spores from the index\n *   2. Group by observation_type\n *   3. Within each group, embed spores and cluster by cosine similarity\n *   4. For each cluster with 2+ members, ask the LLM which are outdated\n *   5. Mark superseded: update frontmatter, append notice, re-index, remove vector\n */\nimport path from 'node:path';\nimport { loadConfig } from '../config/loader.js';\nimport { MycoIndex } from '../index/sqlite.js';\nimport { VectorIndex } from '../index/vectors.js';\nimport { createLlmProvider, createEmbeddingProvider } from '../intelligence/llm.js';\nimport { generateEmbedding } from '../intelligence/embeddings.js';\nimport { stripReasoningTokens } from '../intelligence/response.js';\nimport { loadPrompt } from '../prompts/index.js';\nimport { supersedeSpore, supersededIdsSchema, isActiveSpore } from '../vault/curation.js';\nimport {\n  CURATION_CLUSTER_SIMILARITY,\n  EMBEDDING_INPUT_LIMIT,\n  SUPERSESSION_MAX_TOKENS,\n  LLM_REASONING_MODE,\n} from '../constants.js';\n\n/** Max concurrent embedding requests to avoid overwhelming the provider. */\nconst EMBEDDING_BATCH_SIZE = 10;\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\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 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\n  for (const spore of spores) {\n    let bestCluster: Cluster | null = null;\n    let bestSimilarity = -1;\n\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\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\n  return clusters;\n}\n\nexport async function run(args: string[], vaultDir: string): Promise<void> {\n  const isDryRun = args.includes('--dry-run');\n\n  const config = loadConfig(vaultDir);\n  const index = new MycoIndex(path.join(vaultDir, 'index.db'));\n\n  const llmProvider = createLlmProvider(config.intelligence.llm);\n  const embeddingProvider = createEmbeddingProvider(config.intelligence.embedding);\n\n  let vectorIndex: VectorIndex | null = null;\n  try {\n    const testEmbed = await embeddingProvider.embed('test');\n    vectorIndex = new VectorIndex(path.join(vaultDir, 'vectors.db'), testEmbed.dimensions);\n  } catch (e) {\n    console.error(`Vector index unavailable: ${(e as Error).message}`);\n    console.error('Curate requires a working embedding provider.');\n    index.close();\n    process.exit(1);\n  }\n\n  try {\n    if (isDryRun) {\n      console.log('Dry run — no changes will be written.\\n');\n    }\n\n    // 1. Query all spores and filter for active ones\n    const allSpores = index.query({ type: 'spore' });\n    const activeSpores = allSpores.filter((n) => isActiveSpore(n.frontmatter));\n\n    console.log(`Scanning ${activeSpores.length} active spores...`);\n\n    if (activeSpores.length === 0) {\n      console.log('No active spores found.');\n      return;\n    }\n\n    // 2. 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 += EMBEDDING_BATCH_SIZE) {\n      const batch = activeSpores.slice(i, i + 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      console.log(`Warning: ${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\n      if (multiSpore.length === 0) continue;\n\n      console.log(`\\nType: ${obsType} — ${typeSpores.length} spores, ${multiSpore.length} cluster(s) to evaluate`);\n      totalClusters += multiSpore.length;\n\n      for (const cluster of multiSpore) {\n        // Sort by created date ascending; newest is last\n        const sorted = [...cluster.spores].sort((a, b) => a.created.localeCompare(b.created));\n        const newest = sorted[sorted.length - 1];\n        const candidates = sorted.slice(0, sorted.length - 1);\n\n        // 5. Build supersession prompt\n        const newSporeText = `[${newest.id}] ${newest.title}\\n${newest.content}`;\n        const candidatesText = candidates\n          .map((c) => `[${c.id}] ${c.title}\\n${c.content}`)\n          .join('\\n\\n');\n\n        const prompt = template\n          .replace('{{new_spore}}', newSporeText)\n          .replace('{{candidates}}', candidatesText);\n\n        // 6. Ask LLM which candidates are outdated\n        let responseText: string;\n        try {\n          const response = await llmProvider.summarize(prompt, {\n            maxTokens: SUPERSESSION_MAX_TOKENS,\n            reasoning: LLM_REASONING_MODE,\n          });\n          responseText = stripReasoningTokens(response.text);\n        } catch (err) {\n          console.log(`  Warning: LLM call failed for cluster in ${obsType}: ${String(err)}`);\n          continue;\n        }\n\n        // Parse response\n        let rawIds: unknown;\n        try {\n          rawIds = JSON.parse(responseText);\n        } catch {\n          console.log(`  Warning: Could not parse LLM response for cluster in ${obsType}`);\n          continue;\n        }\n\n        const parsed = supersededIdsSchema.safeParse(rawIds);\n        if (!parsed.success) {\n          console.log(`  Warning: LLM response schema invalid for cluster in ${obsType}`);\n          continue;\n        }\n\n        // Validate IDs against actual candidates\n        const candidateMap = new Map(candidates.map((c) => [c.id, c]));\n        const validIds = parsed.data.filter((id) => candidateMap.has(id));\n\n        if (validIds.length === 0) continue;\n\n        for (const id of validIds) {\n          const candidate = candidateMap.get(id)!;\n\n          if (isDryRun) {\n            console.log(`  [dry-run] Would supersede: ${candidate.title} (${id})`);\n            console.log(`            Superseded by: ${newest.title} (${newest.id})`);\n            totalSuperseded++;\n            continue;\n          }\n\n          const wrote = supersedeSpore(id, newest.id, candidate.path, { index, vectorIndex, vaultDir });\n\n          if (!wrote) {\n            console.log(`  Warning: file not found for ${id}, skipping write`);\n            continue;\n          }\n\n          console.log(`  Superseded: ${candidate.title} (${id})`);\n          console.log(`  By: ${newest.title} (${newest.id})`);\n          totalSuperseded++;\n        }\n      }\n    }\n\n    // 8. Summary\n    console.log(`\\nCuration complete:`);\n    console.log(`  Scanned: ${activeSpores.length} active spores`);\n    console.log(`  Clusters evaluated: ${totalClusters}`);\n    if (isDryRun) {\n      console.log(`  Would supersede: ${totalSuperseded}`);\n    } else {\n      console.log(`  Superseded: ${totalSuperseded}`);\n    }\n  } finally {\n    index.close();\n    vectorIndex?.close();\n  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package/dist/{detect-providers-IRL2TTLK.js → detect-providers-BIHYFK5M.js}

@@ -2,10 +2,10 @@ import { createRequire as __cr } from 'node:module'; const require = __cr(import
 import {
   LmStudioBackend,
   OllamaBackend
-} from "./chunk-67R6EMYD.js";
+} from "./chunk-JI6M2L2W.js";
 import {
   PROVIDER_DETECT_TIMEOUT_MS
-} from "./chunk-JBD5KP5G.js";
+} from "./chunk-B6WVNDA5.js";
 import "./chunk-PZUWP5VK.js";
 
 // src/cli/detect-providers.ts
@@ -32,4 +32,4 @@ async function run(_args) {
 export {
   run
 };
-//# sourceMappingURL=detect-providers-IRL2TTLK.js.map
+//# sourceMappingURL=detect-providers-BIHYFK5M.js.map

package/dist/digest-7NKYXM6G.js

@@ -0,0 +1,96 @@
+import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
+import {
+  DigestEngine
+} from "./chunk-HL2S5QZG.js";
+import "./chunk-KYL67SKZ.js";
+import "./chunk-2AMAOSRF.js";
+import {
+  createLlmProvider
+} from "./chunk-RCV2I4AI.js";
+import "./chunk-MIU3DKLN.js";
+import {
+  MycoIndex
+} from "./chunk-AK6GNLPV.js";
+import "./chunk-FIRMTYFH.js";
+import {
+  parseIntFlag
+} from "./chunk-SAKJMNSR.js";
+import "./chunk-JI6M2L2W.js";
+import {
+  loadConfig
+} from "./chunk-TBRZAJ7W.js";
+import "./chunk-6UJWI4IW.js";
+import "./chunk-X6TKHO22.js";
+import "./chunk-B6WVNDA5.js";
+import "./chunk-PZUWP5VK.js";
+
+// src/cli/digest.ts
+import path from "path";
+async function run(args, vaultDir) {
+  const config = loadConfig(vaultDir);
+  if (!config.digest.enabled) {
+    console.error("Digest is not enabled. Set digest.enabled: true in myco.yaml.");
+    process.exit(1);
+  }
+  const tierArg = parseIntFlag(args, "--tier");
+  const isFull = args.includes("--full");
+  const isReprocess = isFull || tierArg !== void 0;
+  const digestLlmConfig = {
+    provider: config.digest.intelligence.provider ?? config.intelligence.llm.provider,
+    model: config.digest.intelligence.model ?? config.intelligence.llm.model,
+    base_url: config.digest.intelligence.base_url ?? config.intelligence.llm.base_url,
+    context_window: config.digest.intelligence.context_window
+  };
+  const llmProvider = createLlmProvider(digestLlmConfig);
+  const index = new MycoIndex(path.join(vaultDir, "index.db"));
+  const engine = new DigestEngine({
+    vaultDir,
+    index,
+    llmProvider,
+    config,
+    log: (level, message, data) => {
+      const prefix = level === "warn" ? "\u26A0" : level === "info" ? "\u2192" : "  ";
+      const suffix = data ? ` ${JSON.stringify(data)}` : "";
+      console.log(`${prefix} ${message}${suffix}`);
+    }
+  });
+  const opts = {};
+  if (isReprocess) {
+    opts.fullReprocess = true;
+    opts.cleanSlate = true;
+  }
+  if (tierArg !== void 0) {
+    const eligible = engine.getEligibleTiers();
+    if (!eligible.includes(tierArg)) {
+      console.error(`Tier ${tierArg} is not eligible. Eligible tiers: [${eligible.join(", ")}]`);
+      index.close();
+      process.exit(1);
+    }
+    opts.tiers = [tierArg];
+  }
+  if (isReprocess) {
+    const tierLabel = tierArg ? `tier ${tierArg}` : "all tiers";
+    console.log(`Full reprocess of ${tierLabel} \u2014 clean slate, all substrate`);
+  } else {
+    console.log("Running incremental digest cycle");
+  }
+  try {
+    const result = await engine.runCycle(opts);
+    if (!result) {
+      console.log("No substrate found \u2014 nothing to digest.");
+      return;
+    }
+    console.log(`
+Digest cycle complete:`);
+    console.log(`  Tiers generated: [${result.tiersGenerated.join(", ")}]`);
+    console.log(`  Substrate: ${Object.values(result.substrate).flat().length} notes`);
+    console.log(`  Duration: ${(result.durationMs / 1e3).toFixed(1)}s`);
+    console.log(`  Model: ${result.model}`);
+  } finally {
+    index.close();
+  }
+}
+export {
+  run
+};
+//# sourceMappingURL=digest-7NKYXM6G.js.map

package/dist/digest-7NKYXM6G.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/cli/digest.ts"],"sourcesContent":["/**\n * myco digest — run a digest cycle from the CLI.\n *\n * Usage:\n *   myco digest              Incremental cycle (only new substrate)\n *   myco digest --full       Full reprocess of all tiers from clean slate\n *   myco digest --tier 3000  Reprocess a specific tier from clean slate\n *\n * When --tier or --full is used, the cycle processes ALL vault notes (not just\n * new ones) and ignores previous extracts, producing a clean synthesis.\n */\nimport { loadConfig } from '../config/loader.js';\nimport { MycoIndex } from '../index/sqlite.js';\nimport { createLlmProvider } from '../intelligence/llm.js';\nimport { DigestEngine } from '../daemon/digest.js';\nimport type { DigestCycleOptions } from '../daemon/digest.js';\nimport { parseIntFlag } from './shared.js';\nimport path from 'node:path';\n\nexport async function run(args: string[], vaultDir: string): Promise<void> {\n  const config = loadConfig(vaultDir);\n\n  if (!config.digest.enabled) {\n    console.error('Digest is not enabled. Set digest.enabled: true in myco.yaml.');\n    process.exit(1);\n  }\n\n  const tierArg = parseIntFlag(args, '--tier');\n  const isFull = args.includes('--full');\n  const isReprocess = isFull || tierArg !== undefined;\n\n  // Resolve the digest LLM provider\n  const digestLlmConfig = {\n    provider: config.digest.intelligence.provider ?? config.intelligence.llm.provider,\n    model: config.digest.intelligence.model ?? config.intelligence.llm.model,\n    base_url: config.digest.intelligence.base_url ?? config.intelligence.llm.base_url,\n    context_window: config.digest.intelligence.context_window,\n  };\n  const llmProvider = createLlmProvider(digestLlmConfig);\n\n  const index = new MycoIndex(path.join(vaultDir, 'index.db'));\n\n  const engine = new DigestEngine({\n    vaultDir,\n    index,\n    llmProvider,\n    config,\n    log: (level, message, data) => {\n      const prefix = level === 'warn' ? '⚠' : level === 'info' ? '→' : '  ';\n      const suffix = data ? ` ${JSON.stringify(data)}` : '';\n      console.log(`${prefix} ${message}${suffix}`);\n    },\n  });\n\n  const opts: DigestCycleOptions = {};\n  if (isReprocess) {\n    opts.fullReprocess = true;\n    opts.cleanSlate = true;\n  }\n  if (tierArg !== undefined) {\n    const eligible = engine.getEligibleTiers();\n    if (!eligible.includes(tierArg)) {\n      console.error(`Tier ${tierArg} is not eligible. Eligible tiers: [${eligible.join(', ')}]`);\n      index.close();\n      process.exit(1);\n    }\n    opts.tiers = [tierArg];\n  }\n\n  if (isReprocess) {\n    const tierLabel = tierArg ? `tier ${tierArg}` : 'all tiers';\n    console.log(`Full reprocess of ${tierLabel} — clean slate, all substrate`);\n  } else {\n    console.log('Running incremental digest cycle');\n  }\n\n  try {\n    const result = await engine.runCycle(opts);\n\n    if (!result) {\n      console.log('No substrate found — nothing to digest.');\n      return;\n    }\n\n    console.log(`\\nDigest cycle complete:`);\n    console.log(`  Tiers generated: [${result.tiersGenerated.join(', ')}]`);\n    console.log(`  Substrate: ${Object.values(result.substrate).flat().length} notes`);\n    console.log(`  Duration: ${(result.durationMs / 1000).toFixed(1)}s`);\n    console.log(`  Model: ${result.model}`);\n  } finally {\n    index.close();\n  }\n}\n"],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;AAiBA,OAAO,UAAU;AAEjB,eAAsB,IAAI,MAAgB,UAAiC;AACzE,QAAM,SAAS,WAAW,QAAQ;AAElC,MAAI,CAAC,OAAO,OAAO,SAAS;AAC1B,YAAQ,MAAM,+DAA+D;AAC7E,YAAQ,KAAK,CAAC;AAAA,EAChB;AAEA,QAAM,UAAU,aAAa,MAAM,QAAQ;AAC3C,QAAM,SAAS,KAAK,SAAS,QAAQ;AACrC,QAAM,cAAc,UAAU,YAAY;AAG1C,QAAM,kBAAkB;AAAA,IACtB,UAAU,OAAO,OAAO,aAAa,YAAY,OAAO,aAAa,IAAI;AAAA,IACzE,OAAO,OAAO,OAAO,aAAa,SAAS,OAAO,aAAa,IAAI;AAAA,IACnE,UAAU,OAAO,OAAO,aAAa,YAAY,OAAO,aAAa,IAAI;AAAA,IACzE,gBAAgB,OAAO,OAAO,aAAa;AAAA,EAC7C;AACA,QAAM,cAAc,kBAAkB,eAAe;AAErD,QAAM,QAAQ,IAAI,UAAU,KAAK,KAAK,UAAU,UAAU,CAAC;AAE3D,QAAM,SAAS,IAAI,aAAa;AAAA,IAC9B;AAAA,IACA;AAAA,IACA;AAAA,IACA;AAAA,IACA,KAAK,CAAC,OAAO,SAAS,SAAS;AAC7B,YAAM,SAAS,UAAU,SAAS,WAAM,UAAU,SAAS,WAAM;AACjE,YAAM,SAAS,OAAO,IAAI,KAAK,UAAU,IAAI,CAAC,KAAK;AACnD,cAAQ,IAAI,GAAG,MAAM,IAAI,OAAO,GAAG,MAAM,EAAE;AAAA,IAC7C;AAAA,EACF,CAAC;AAED,QAAM,OAA2B,CAAC;AAClC,MAAI,aAAa;AACf,SAAK,gBAAgB;AACrB,SAAK,aAAa;AAAA,EACpB;AACA,MAAI,YAAY,QAAW;AACzB,UAAM,WAAW,OAAO,iBAAiB;AACzC,QAAI,CAAC,SAAS,SAAS,OAAO,GAAG;AAC/B,cAAQ,MAAM,QAAQ,OAAO,sCAAsC,SAAS,KAAK,IAAI,CAAC,GAAG;AACzF,YAAM,MAAM;AACZ,cAAQ,KAAK,CAAC;AAAA,IAChB;AACA,SAAK,QAAQ,CAAC,OAAO;AAAA,EACvB;AAEA,MAAI,aAAa;AACf,UAAM,YAAY,UAAU,QAAQ,OAAO,KAAK;AAChD,YAAQ,IAAI,qBAAqB,SAAS,oCAA+B;AAAA,EAC3E,OAAO;AACL,YAAQ,IAAI,kCAAkC;AAAA,EAChD;AAEA,MAAI;AACF,UAAM,SAAS,MAAM,OAAO,SAAS,IAAI;AAEzC,QAAI,CAAC,QAAQ;AACX,cAAQ,IAAI,8CAAyC;AACrD;AAAA,IACF;AAEA,YAAQ,IAAI;AAAA,uBAA0B;AACtC,YAAQ,IAAI,uBAAuB,OAAO,eAAe,KAAK,IAAI,CAAC,GAAG;AACtE,YAAQ,IAAI,gBAAgB,OAAO,OAAO,OAAO,SAAS,EAAE,KAAK,EAAE,MAAM,QAAQ;AACjF,YAAQ,IAAI,gBAAgB,OAAO,aAAa,KAAM,QAAQ,CAAC,CAAC,GAAG;AACnE,YAAQ,IAAI,YAAY,OAAO,KAAK,EAAE;AAAA,EACxC,UAAE;AACA,UAAM,MAAM;AAAA,EACd;AACF;","names":[]}

package/dist/{init-NUF5UBUJ.js → init-HPQ77WWF.js}

@@ -15,11 +15,11 @@ import {
   DASHBOARD_CONTENT,
   VAULT_GITIGNORE,
   configureVaultEnv
-} from "./chunk-GFBG73P4.js";
+} from "./chunk-FIRMTYFH.js";
 import {
   parseStringFlag
 } from "./chunk-SAKJMNSR.js";
-import "./chunk-67R6EMYD.js";
+import "./chunk-JI6M2L2W.js";
 import {
   MycoConfigSchema,
   require_dist
@@ -27,8 +27,8 @@ import {
 import {
   resolveVaultDir
 } from "./chunk-N33KUCFP.js";
-import "./chunk-BNIYWCST.js";
-import "./chunk-JBD5KP5G.js";
+import "./chunk-X6TKHO22.js";
+import "./chunk-B6WVNDA5.js";
 import {
   __toESM
 } from "./chunk-PZUWP5VK.js";
@@ -108,4 +108,4 @@ async function run3(args) {
 export {
   run3 as run
 };
-//# sourceMappingURL=init-NUF5UBUJ.js.map
+//# sourceMappingURL=init-HPQ77WWF.js.map