@goondocks/myco 0.5.1 → 0.6.0

package/dist/chunk-KYL67SKZ.js

@@ -1,150 +0,0 @@
-import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
-import {
-  ARTIFACT_TYPES
-} from "./chunk-2AMAOSRF.js";
-import {
-  CANDIDATE_CONTENT_PREVIEW
-} from "./chunk-B6WVNDA5.js";
-
-// src/intelligence/response.ts
-var REASONING_PATTERNS = [
-  // <think>...</think>answer  (DeepSeek, Qwen, GLM, many others)
-  /<think>[\s\S]*?<\/think>\s*/gi,
-  // Implicit opening: reasoning...</think>answer  (GLM-4.7 observed)
-  /^[\s\S]*?<\/think>\s*/i,
-  // <reasoning>...</reasoning>answer
-  /<reasoning>[\s\S]*?<\/reasoning>\s*/gi,
-  // <|thinking|>...<|/thinking|>answer
-  /<\|thinking\|>[\s\S]*?<\|\/thinking\|>\s*/gi,
-  // Plain-text "Thinking Process:" block followed by actual content
-  // (Qwen 3.5 via LM Studio without native thinking mode)
-  // Matches from "Thinking Process:" up to the last numbered step, then the synthesis follows
-  /^Thinking Process:[\s\S]*?(?=\n(?:## |# |\*\*[A-Z]))/i
-];
-function stripReasoningTokens(text) {
-  if (!text) return text;
-  for (const pattern of REASONING_PATTERNS) {
-    const stripped = text.replace(pattern, "").trim();
-    if (stripped && stripped !== text.trim()) {
-      return stripped;
-    }
-  }
-  return text;
-}
-function extractJson(text) {
-  const cleaned = stripReasoningTokens(text);
-  const fenceMatch = cleaned.match(/```(?:json)?\s*\n?([\s\S]*?)\n?```/);
-  if (fenceMatch) {
-    return JSON.parse(fenceMatch[1].trim());
-  }
-  const objectMatch = cleaned.match(/\{[\s\S]*\}/);
-  if (objectMatch) {
-    return JSON.parse(objectMatch[0]);
-  }
-  return JSON.parse(cleaned);
-}
-function extractNumber(text) {
-  const cleaned = stripReasoningTokens(text).trim();
-  const match = cleaned.match(/(\d+\.?\d*)/);
-  if (match) return parseFloat(match[1]);
-  return parseFloat(cleaned);
-}
-
-// src/prompts/index.ts
-import fs from "fs";
-import path from "path";
-import { fileURLToPath } from "url";
-function resolvePromptsDir() {
-  let dir = path.dirname(fileURLToPath(import.meta.url));
-  for (let i = 0; i < 5; i++) {
-    if (fs.existsSync(path.join(dir, "package.json"))) {
-      return path.join(dir, "dist", "src", "prompts");
-    }
-    if (fs.existsSync(path.join(dir, "extraction.md"))) {
-      return dir;
-    }
-    dir = path.dirname(dir);
-  }
-  return path.dirname(fileURLToPath(import.meta.url));
-}
-var PROMPTS_DIR = resolvePromptsDir();
-var promptCache = /* @__PURE__ */ new Map();
-function loadPrompt(name) {
-  let cached = promptCache.get(name);
-  if (!cached) {
-    cached = fs.readFileSync(path.join(PROMPTS_DIR, `${name}.md`), "utf-8").trim();
-    promptCache.set(name, cached);
-  }
-  return cached;
-}
-function interpolate(template, vars) {
-  let result = template;
-  for (const [key, value] of Object.entries(vars)) {
-    result = result.replaceAll(`{{${key}}}`, value);
-  }
-  return result;
-}
-function buildExtractionPrompt(sessionId, eventCount, toolSummary, maxTokens) {
-  return interpolate(loadPrompt("extraction"), {
-    sessionId,
-    eventCount: String(eventCount),
-    toolSummary,
-    maxTokens: String(maxTokens ?? 2048)
-  });
-}
-function buildSummaryPrompt(sessionId, user, content, maxTokens) {
-  return interpolate(loadPrompt("summary"), {
-    sessionId,
-    user,
-    content,
-    maxTokens: String(maxTokens ?? 1024)
-  });
-}
-function buildTitlePrompt(summary, sessionId) {
-  return interpolate(loadPrompt("title"), {
-    summary,
-    sessionId
-  });
-}
-var ARTIFACT_TYPE_DESCRIPTIONS = [
-  '"spec" \u2014 Design specifications, architecture documents',
-  '"plan" \u2014 Implementation plans, roadmaps',
-  '"rfc" \u2014 Requests for comment, proposals',
-  '"doc" \u2014 Documentation, guides, READMEs',
-  '"other" \u2014 Other substantive documents'
-];
-function buildSimilarityPrompt(currentSummary, candidateSummary) {
-  return interpolate(loadPrompt("session-similarity"), {
-    currentSummary,
-    candidateSummary
-  });
-}
-function buildClassificationPrompt(sessionId, candidates, maxTokens) {
-  const fileList = candidates.map((c) => {
-    const truncated = c.content.slice(0, CANDIDATE_CONTENT_PREVIEW);
-    return `### ${c.path}
-\`\`\`
-${truncated}
-\`\`\``;
-  }).join("\n\n");
-  return interpolate(loadPrompt("classification"), {
-    sessionId,
-    fileList,
-    artifactTypes: ARTIFACT_TYPE_DESCRIPTIONS.map((d) => `- ${d}`).join("\n"),
-    validTypes: ARTIFACT_TYPES.join("|"),
-    maxTokens: String(maxTokens ?? 1024)
-  });
-}
-
-export {
-  stripReasoningTokens,
-  extractJson,
-  extractNumber,
-  loadPrompt,
-  buildExtractionPrompt,
-  buildSummaryPrompt,
-  buildTitlePrompt,
-  buildSimilarityPrompt,
-  buildClassificationPrompt
-};
-//# sourceMappingURL=chunk-KYL67SKZ.js.map

package/dist/chunk-KYL67SKZ.js.map

@@ -1 +0,0 @@
-{"version":3,"sources":["../src/intelligence/response.ts","../src/prompts/index.ts"],"sourcesContent":["/**\n * Clean LLM response text before parsing.\n *\n * Reasoning models (DeepSeek, Qwen, GLM, etc.) embed chain-of-thought\n * in the response using special tags. These must be stripped before\n * JSON parsing or value extraction.\n */\n\n// Patterns for reasoning model chain-of-thought tokens.\n// Order matters: most specific patterns first.\nconst REASONING_PATTERNS = [\n  // <think>...</think>answer  (DeepSeek, Qwen, GLM, many others)\n  /<think>[\\s\\S]*?<\\/think>\\s*/gi,\n  // Implicit opening: reasoning...</think>answer  (GLM-4.7 observed)\n  /^[\\s\\S]*?<\\/think>\\s*/i,\n  // <reasoning>...</reasoning>answer\n  /<reasoning>[\\s\\S]*?<\\/reasoning>\\s*/gi,\n  // <|thinking|>...<|/thinking|>answer\n  /<\\|thinking\\|>[\\s\\S]*?<\\|\\/thinking\\|>\\s*/gi,\n  // Plain-text \"Thinking Process:\" block followed by actual content\n  // (Qwen 3.5 via LM Studio without native thinking mode)\n  // Matches from \"Thinking Process:\" up to the last numbered step, then the synthesis follows\n  /^Thinking Process:[\\s\\S]*?(?=\\n(?:## |# |\\*\\*[A-Z]))/i,\n];\n\n/**\n * Strip reasoning/chain-of-thought tokens from LLM response text.\n * Returns the final answer without the thinking process.\n */\nexport function stripReasoningTokens(text: string): string {\n  if (!text) return text;\n\n  for (const pattern of REASONING_PATTERNS) {\n    const stripped = text.replace(pattern, '').trim();\n    if (stripped && stripped !== text.trim()) {\n      return stripped;\n    }\n  }\n\n  return text;\n}\n\n/**\n * Extract JSON from an LLM response that may contain markdown fences,\n * reasoning tokens, or other wrapper text.\n *\n * Tries in order:\n * 1. Strip reasoning tokens\n * 2. Extract from ```json ... ``` code fences\n * 3. Find bare {...} JSON object\n * 4. Parse the cleaned text directly\n */\nexport function extractJson(text: string): unknown {\n  const cleaned = stripReasoningTokens(text);\n\n  // Try code fence extraction\n  const fenceMatch = cleaned.match(/```(?:json)?\\s*\\n?([\\s\\S]*?)\\n?```/);\n  if (fenceMatch) {\n    return JSON.parse(fenceMatch[1].trim());\n  }\n\n  // Try bare JSON object\n  const objectMatch = cleaned.match(/\\{[\\s\\S]*\\}/);\n  if (objectMatch) {\n    return JSON.parse(objectMatch[0]);\n  }\n\n  // Try direct parse\n  return JSON.parse(cleaned);\n}\n\n/**\n * Extract a numeric value from an LLM response that may contain\n * reasoning tokens or extra text around the number.\n */\nexport function extractNumber(text: string): number {\n  const cleaned = stripReasoningTokens(text).trim();\n  const match = cleaned.match(/(\\d+\\.?\\d*)/);\n  if (match) return parseFloat(match[1]);\n  return parseFloat(cleaned);\n}\n","/**\n * Prompt loader — reads .md templates from disk and interpolates variables.\n * Prompts are markdown files in this directory, not TypeScript strings.\n */\n\nimport fs from 'node:fs';\nimport path from 'node:path';\nimport { fileURLToPath } from 'node:url';\nimport { ARTIFACT_TYPES } from '../vault/types.js';\nimport { CANDIDATE_CONTENT_PREVIEW } from '../constants.js';\n\n/**\n * Resolve the prompts directory. With tsup code-splitting, import.meta.url\n * points to a chunk file (dist/chunk-XXXX.js), not dist/src/prompts/.\n * Walk up from the current file to find package.json, then use dist/src/prompts/.\n */\nfunction resolvePromptsDir(): string {\n  let dir = path.dirname(fileURLToPath(import.meta.url));\n  for (let i = 0; i < 5; i++) {\n    if (fs.existsSync(path.join(dir, 'package.json'))) {\n      return path.join(dir, 'dist', 'src', 'prompts');\n    }\n    // Also check if we're already in the right place (tsc output or dev mode)\n    if (fs.existsSync(path.join(dir, 'extraction.md'))) {\n      return dir;\n    }\n    dir = path.dirname(dir);\n  }\n  // Final fallback: adjacent to current file (works with tsc)\n  return path.dirname(fileURLToPath(import.meta.url));\n}\n\nconst PROMPTS_DIR = resolvePromptsDir();\n\nconst promptCache = new Map<string, string>();\n\nexport function loadPrompt(name: string): string {\n  let cached = promptCache.get(name);\n  if (!cached) {\n    cached = fs.readFileSync(path.join(PROMPTS_DIR, `${name}.md`), 'utf-8').trim();\n    promptCache.set(name, cached);\n  }\n  return cached;\n}\n\nfunction interpolate(template: string, vars: Record<string, string>): string {\n  let result = template;\n  for (const [key, value] of Object.entries(vars)) {\n    result = result.replaceAll(`{{${key}}}`, value);\n  }\n  return result;\n}\n\n// --- Prompt builders ---\n\nexport function buildExtractionPrompt(\n  sessionId: string,\n  eventCount: number,\n  toolSummary: string,\n  maxTokens?: number,\n): string {\n  return interpolate(loadPrompt('extraction'), {\n    sessionId,\n    eventCount: String(eventCount),\n    toolSummary,\n    maxTokens: String(maxTokens ?? 2048),\n  });\n}\n\nexport function buildSummaryPrompt(\n  sessionId: string,\n  user: string,\n  content: string,\n  maxTokens?: number,\n): string {\n  return interpolate(loadPrompt('summary'), {\n    sessionId,\n    user,\n    content,\n    maxTokens: String(maxTokens ?? 1024),\n  });\n}\n\nexport function buildTitlePrompt(\n  summary: string,\n  sessionId: string,\n): string {\n  return interpolate(loadPrompt('title'), {\n    summary,\n    sessionId,\n  });\n}\n\nconst ARTIFACT_TYPE_DESCRIPTIONS = [\n  '\"spec\" — Design specifications, architecture documents',\n  '\"plan\" — Implementation plans, roadmaps',\n  '\"rfc\" — Requests for comment, proposals',\n  '\"doc\" — Documentation, guides, READMEs',\n  '\"other\" — Other substantive documents',\n];\n\nexport function buildSimilarityPrompt(\n  currentSummary: string,\n  candidateSummary: string,\n): string {\n  return interpolate(loadPrompt('session-similarity'), {\n    currentSummary,\n    candidateSummary,\n  });\n}\n\nexport function buildClassificationPrompt(\n  sessionId: string,\n  candidates: Array<{ path: string; content: string }>,\n  maxTokens?: number,\n): string {\n  const fileList = candidates\n    .map((c) => {\n      const truncated = c.content.slice(0, CANDIDATE_CONTENT_PREVIEW);\n      return `### ${c.path}\\n\\`\\`\\`\\n${truncated}\\n\\`\\`\\``;\n    })\n    .join('\\n\\n');\n\n  return interpolate(loadPrompt('classification'), {\n    sessionId,\n    fileList,\n    artifactTypes: ARTIFACT_TYPE_DESCRIPTIONS.map((d) => `- ${d}`).join('\\n'),\n    validTypes: ARTIFACT_TYPES.join('|'),\n    maxTokens: String(maxTokens ?? 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package/dist/chunk-TBRZAJ7W.js.map

@@ -1 +0,0 @@
-{"version":3,"sources":["../src/config/loader.ts","../src/config/migrations.ts"],"sourcesContent":["import fs from 'node:fs';\nimport path from 'node:path';\nimport YAML from 'yaml';\nimport { MycoConfigSchema, type MycoConfig } from './schema.js';\nimport { runMigrations, CURRENT_MIGRATION_VERSION } from './migrations.js';\n\nconst CONFIG_FILENAME = 'myco.yaml';\n\nexport function loadConfig(vaultDir: string): MycoConfig {\n  const configPath = path.join(vaultDir, CONFIG_FILENAME);\n\n  if (!fs.existsSync(configPath)) {\n    throw new Error(`myco.yaml not found in ${vaultDir}`);\n  }\n\n  const raw = fs.readFileSync(configPath, 'utf-8');\n  const parsed = YAML.parse(raw) as Record<string, unknown>;\n\n  // Detect v1 config and guide migration\n  if (parsed.version === 1 || (parsed.intelligence as Record<string, unknown>)?.backend) {\n    throw new Error(\n      'Myco config uses v1 format. Run /myco:setup-llm to reconfigure for v2.',\n    );\n  }\n\n  // Auto-map legacy 'haiku' provider name to 'anthropic'\n  const intel = parsed.intelligence as Record<string, unknown> | undefined;\n  const llm = intel?.llm as Record<string, unknown> | undefined;\n  if (llm?.provider === 'haiku') {\n    llm.provider = 'anthropic';\n  }\n\n  // Run numbered migrations\n  const migrationsRan = runMigrations(parsed, vaultDir, (msg) => {\n    // Log to stderr since this runs during config loading (before logger is available)\n    process.stderr.write(`[myco migration] ${msg}\\n`);\n  });\n\n  // Parse with Zod to fill in defaults for new config sections\n  const config = MycoConfigSchema.parse(parsed);\n\n  // Write back if migrations ran or new defaults were added\n  const needsWrite = migrationsRan\n    || (parsed.config_version as number ?? 0) < CURRENT_MIGRATION_VERSION\n    || !('digest' in parsed);\n\n  if (needsWrite) {\n    const fullConfig = JSON.parse(JSON.stringify(config)) as Record<string, unknown>;\n    fs.writeFileSync(configPath, YAML.stringify(fullConfig), 'utf-8');\n  }\n\n  return config;\n}\n\nexport function saveConfig(vaultDir: string, config: MycoConfig): void {\n  // Validate before writing — OAK lesson: validate on write, not just read\n  const validated = MycoConfigSchema.parse(config);\n\n  const configPath = path.join(vaultDir, CONFIG_FILENAME);\n  fs.mkdirSync(vaultDir, { recursive: true });\n  fs.writeFileSync(configPath, YAML.stringify(validated), 'utf-8');\n}\n","/**\n * Config and vault migrations — run once per version, tracked by config_version.\n *\n * Each migration has a version number, a name, and a function that receives\n * the raw parsed YAML doc and the vault directory. Migrations run in order\n * and are skipped if config_version is already past them.\n *\n * To add a new migration:\n * 1. Add an entry to MIGRATIONS with the next version number\n * 2. Write the migrate function — it receives the mutable doc and vaultDir\n * 3. The framework handles version tracking and writing the config back\n */\n\nimport fs from 'node:fs';\nimport path from 'node:path';\n\nexport interface Migration {\n  version: number;\n  name: string;\n  migrate: (doc: Record<string, unknown>, vaultDir: string) => void;\n}\n\n/** Regex matching both quoted and unquoted YAML: type: memory, type: \"memory\", type: 'memory' */\nconst MEMORY_TYPE_PATTERN = /type:\\s*[\"']?memory[\"']?/g;\n\nexport const MIGRATIONS: Migration[] = [\n  {\n    version: 1,\n    name: 'rename-memories-to-spores',\n    migrate: (doc, vaultDir) => {\n      // Config: rename context.layers.memories → context.layers.spores\n      const context = doc.context as Record<string, unknown> | undefined;\n      const layers = context?.layers as Record<string, unknown> | undefined;\n      if (layers && 'memories' in layers && !('spores' in layers)) {\n        layers.spores = layers.memories;\n        delete layers.memories;\n      }\n\n      // Vault: rename memories/ directory → spores/\n      const memoriesDir = path.join(vaultDir, 'memories');\n      const sporesDir = path.join(vaultDir, 'spores');\n\n      if (!fs.existsSync(memoriesDir)) return;\n\n      if (fs.existsSync(sporesDir)) {\n        // Both exist (interrupted migration) — merge remaining files\n        const moveRemaining = (srcDir: string, destDir: string): void => {\n          for (const entry of fs.readdirSync(srcDir, { withFileTypes: true })) {\n            const srcPath = path.join(srcDir, entry.name);\n            const destPath = path.join(destDir, entry.name);\n            if (entry.isDirectory()) {\n              if (!fs.existsSync(destPath)) fs.mkdirSync(destPath, { recursive: true });\n              moveRemaining(srcPath, destPath);\n            } else if (!fs.existsSync(destPath)) {\n              fs.renameSync(srcPath, destPath);\n            }\n          }\n        };\n        moveRemaining(memoriesDir, sporesDir);\n        fs.rmSync(memoriesDir, { recursive: true, force: true });\n      } else {\n        fs.renameSync(memoriesDir, sporesDir);\n      }\n\n      // Update frontmatter type: memory → type: spore (handles quoted and unquoted)\n      const walkUpdate = (dir: string): void => {\n        for (const entry of fs.readdirSync(dir, { withFileTypes: true })) {\n          const fullPath = path.join(dir, entry.name);\n          if (entry.isDirectory()) { walkUpdate(fullPath); continue; }\n          if (!entry.name.endsWith('.md')) continue;\n          const content = fs.readFileSync(fullPath, 'utf-8');\n          MEMORY_TYPE_PATTERN.lastIndex = 0;\n          if (MEMORY_TYPE_PATTERN.test(content)) {\n            MEMORY_TYPE_PATTERN.lastIndex = 0;\n            fs.writeFileSync(fullPath, content.replace(MEMORY_TYPE_PATTERN, 'type: spore'));\n          }\n        }\n      };\n      walkUpdate(sporesDir);\n\n      // Update wikilinks in ALL vault files: [[memories/...]] → [[spores/...]]\n      const walkLinks = (dir: string): void => {\n        for (const entry of fs.readdirSync(dir, { withFileTypes: true })) {\n          const fullPath = path.join(dir, entry.name);\n          if (entry.isDirectory()) { walkLinks(fullPath); continue; }\n          if (!entry.name.endsWith('.md')) continue;\n          const content = fs.readFileSync(fullPath, 'utf-8');\n          if (content.includes('memories/')) {\n            fs.writeFileSync(fullPath, content.replace(/memories\\//g, 'spores/'));\n          }\n        }\n      };\n      walkLinks(vaultDir);\n    },\n  },\n];\n\n/** Current migration version — the highest version in MIGRATIONS. */\nexport const CURRENT_MIGRATION_VERSION = MIGRATIONS[MIGRATIONS.length - 1]?.version ?? 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package/dist/curate-S4HOYWXA.js

@@ -1,231 +0,0 @@
-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

@@ -1 +0,0 @@
-{"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. 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package/dist/digest-7NKYXM6G.js.map

@@ -1 +0,0 @@
-{"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' ? 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package/dist/init-HPQ77WWF.js.map

@@ -1 +0,0 @@
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