@goondocks/myco 0.6.0 → 0.6.2

package/dist/chunk-UVGAVYWZ.js

@@ -1,157 +0,0 @@
-import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
-import {
-  formatNoteForPrompt,
-  formatNotesForPrompt,
-  indexNote,
-  loadPrompt,
-  stripReasoningTokens
-} from "./chunk-24DOZEUJ.js";
-import {
-  generateEmbedding
-} from "./chunk-RGVBGTD6.js";
-import {
-  external_exports,
-  require_dist
-} from "./chunk-MQSYSQ6T.js";
-import {
-  EMBEDDING_INPUT_LIMIT,
-  LLM_REASONING_MODE,
-  SUPERSESSION_CANDIDATE_LIMIT,
-  SUPERSESSION_MAX_TOKENS,
-  SUPERSESSION_VECTOR_FETCH_LIMIT
-} from "./chunk-6BSDCZ5Q.js";
-import {
-  __toESM
-} from "./chunk-PZUWP5VK.js";
-
-// src/vault/curation.ts
-var import_yaml = __toESM(require_dist(), 1);
-import fs from "fs";
-import path from "path";
-var supersededIdsSchema = external_exports.array(external_exports.string());
-var SUPERSESSION_NOTICE_MARKER = "Superseded by::";
-function isActiveSpore(frontmatter) {
-  const status = frontmatter.status;
-  return !status || status === "active";
-}
-function supersedeSpore(targetId, newSporeId, targetPath, deps) {
-  const fullPath = path.join(deps.vaultDir, targetPath);
-  let fileContent;
-  try {
-    fileContent = fs.readFileSync(fullPath, "utf-8");
-  } catch {
-    return false;
-  }
-  const fmMatch = fileContent.match(/^---\n([\s\S]*?)\n---/);
-  if (!fmMatch) return false;
-  const parsed = import_yaml.default.parse(fmMatch[1]);
-  parsed.status = "superseded";
-  parsed.superseded_by = newSporeId;
-  const fmYaml = import_yaml.default.stringify(parsed, { defaultStringType: "QUOTE_DOUBLE", defaultKeyType: "PLAIN" }).trim();
-  let body = fileContent.slice(fmMatch[0].length);
-  if (!body.includes(SUPERSESSION_NOTICE_MARKER)) {
-    const notice = `
-
-> [!warning] Superseded
-> This observation has been superseded.
-
-${SUPERSESSION_NOTICE_MARKER} [[${newSporeId}]]`;
-    body = body.trimEnd() + notice + "\n";
-  }
-  const tmp = `${fullPath}.tmp`;
-  fs.writeFileSync(tmp, `---
-${fmYaml}
----${body}`, "utf-8");
-  fs.renameSync(tmp, fullPath);
-  indexNote(deps.index, deps.vaultDir, targetPath);
-  deps.vectorIndex?.delete(targetId);
-  return true;
-}
-async function checkSupersession(newSporeId, deps) {
-  const { index, vectorIndex, embeddingProvider, llmProvider, vaultDir, log } = deps;
-  if (!vectorIndex || !llmProvider) {
-    log?.("debug", "checkSupersession: skipped \u2014 vectorIndex or llmProvider unavailable", { newSporeId });
-    return [];
-  }
-  const newSporeResults = index.queryByIds([newSporeId]);
-  if (newSporeResults.length === 0) {
-    log?.("warn", "checkSupersession: new spore not found in index", { newSporeId });
-    return [];
-  }
-  const newSpore = newSporeResults[0];
-  const observationType = newSpore.frontmatter["observation_type"];
-  const embeddingText = newSpore.content.slice(0, EMBEDDING_INPUT_LIMIT);
-  const embeddingResult = await generateEmbedding(embeddingProvider, embeddingText);
-  const vectorResults = vectorIndex.search(embeddingResult.embedding, {
-    type: "spore",
-    limit: SUPERSESSION_VECTOR_FETCH_LIMIT
-  });
-  if (vectorResults.length === 0) {
-    log?.("debug", "checkSupersession: no vector results", { newSporeId });
-    return [];
-  }
-  const candidateIds = vectorResults.map((r) => r.id);
-  const candidateNotes = index.queryByIds(candidateIds);
-  const filtered = candidateNotes.filter((note) => {
-    if (note.id === newSporeId) return false;
-    if (!isActiveSpore(note.frontmatter)) return false;
-    if (observationType && note.frontmatter["observation_type"] !== observationType) return false;
-    return true;
-  }).slice(0, SUPERSESSION_CANDIDATE_LIMIT);
-  if (filtered.length === 0) {
-    log?.("debug", "checkSupersession: no candidates after filtering", { newSporeId, observationType });
-    return [];
-  }
-  const template = loadPrompt("supersession");
-  const newSporeText = formatNoteForPrompt(newSpore);
-  const candidatesText = formatNotesForPrompt(filtered);
-  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", "checkSupersession: LLM call failed", { newSporeId, error: String(err) });
-    return [];
-  }
-  let rawIds;
-  try {
-    rawIds = JSON.parse(responseText);
-  } catch {
-    log?.("warn", "checkSupersession: failed to parse LLM response", { newSporeId, responseText });
-    return [];
-  }
-  const parsed = supersededIdsSchema.safeParse(rawIds);
-  if (!parsed.success) {
-    log?.("warn", "checkSupersession: LLM response failed schema validation", { newSporeId });
-    return [];
-  }
-  const candidateMap = new Map(filtered.map((c) => [c.id, c]));
-  const validIds = parsed.data.filter((id) => candidateMap.has(id));
-  if (validIds.length === 0) {
-    return [];
-  }
-  const supersededIds = [];
-  for (const id of validIds) {
-    const candidate = candidateMap.get(id);
-    const wrote = supersedeSpore(id, newSporeId, candidate.path, { index, vectorIndex, vaultDir });
-    if (!wrote) {
-      log?.("warn", "checkSupersession: file not found for candidate, skipping", { id, path: candidate.path });
-      continue;
-    }
-    supersededIds.push(id);
-    log?.("info", "checkSupersession: marked superseded", { supersededId: id, newSporeId });
-  }
-  return supersededIds;
-}
-
-export {
-  supersededIdsSchema,
-  isActiveSpore,
-  supersedeSpore,
-  checkSupersession
-};
-//# sourceMappingURL=chunk-UVGAVYWZ.js.map

package/dist/chunk-UVGAVYWZ.js.map

@@ -1 +0,0 @@
-{"version":3,"sources":["../src/vault/curation.ts"],"sourcesContent":["/**\n * Vault curation — supersession detection pipeline.\n *\n * Given a newly written spore ID, finds older spores of the same observation_type\n * that have been rendered outdated, and marks them as superseded.\n */\n\nimport { z } from 'zod';\nimport fs from 'node:fs';\nimport path from 'node:path';\nimport YAML from 'yaml';\nimport type { MycoIndex, IndexedNote } from '../index/sqlite.js';\nimport type { VectorIndex } from '../index/vectors.js';\nimport type { LlmProvider, EmbeddingProvider } from '../intelligence/llm.js';\nimport { generateEmbedding } from '../intelligence/embeddings.js';\nimport { stripReasoningTokens } from '../intelligence/response.js';\nimport { indexNote } from '../index/rebuild.js';\nimport { loadPrompt, formatNoteForPrompt, formatNotesForPrompt } from '../prompts/index.js';\nimport {\n  SUPERSESSION_CANDIDATE_LIMIT,\n  SUPERSESSION_VECTOR_FETCH_LIMIT,\n  SUPERSESSION_MAX_TOKENS,\n  EMBEDDING_INPUT_LIMIT,\n  LLM_REASONING_MODE,\n} from '../constants.js';\n\ntype LogLevel = 'debug' | 'info' | 'warn';\ntype LogFn = (level: LogLevel, message: string, data?: Record<string, unknown>) => void;\n\n/** Zod schema for validating LLM supersession responses. */\nexport const supersededIdsSchema = z.array(z.string());\n\n/** Marker string used to detect whether a supersession notice has already been appended. */\nexport const SUPERSESSION_NOTICE_MARKER = 'Superseded by::';\n\n/** Returns true if a spore should be considered active (including legacy spores without status). */\nexport function isActiveSpore(frontmatter: Record<string, unknown>): boolean {\n  const status = frontmatter.status as string | undefined;\n  return !status || status === 'active';\n}\n\n/**\n * Mark a single spore as superseded: update frontmatter + append notice in a\n * single read-modify-write, then re-index and remove from vector index.\n * Returns true if the write succeeded, false if the file was not found.\n */\nexport function supersedeSpore(\n  targetId: string,\n  newSporeId: string,\n  targetPath: string,\n  deps: { index: MycoIndex; vectorIndex: VectorIndex | null; vaultDir: string },\n): boolean {\n  const fullPath = path.join(deps.vaultDir, targetPath);\n  let fileContent: string;\n  try {\n    fileContent = fs.readFileSync(fullPath, 'utf-8');\n  } catch {\n    return false;\n  }\n\n  // Parse and update frontmatter\n  const fmMatch = fileContent.match(/^---\\n([\\s\\S]*?)\\n---/);\n  if (!fmMatch) return false;\n\n  const parsed = YAML.parse(fmMatch[1]) as Record<string, unknown>;\n  parsed.status = 'superseded';\n  parsed.superseded_by = newSporeId;\n\n  const fmYaml = YAML.stringify(parsed, { defaultStringType: 'QUOTE_DOUBLE', defaultKeyType: 'PLAIN' }).trim();\n  let body = fileContent.slice(fmMatch[0].length);\n\n  // Append supersession notice (idempotent: skip if already present)\n  if (!body.includes(SUPERSESSION_NOTICE_MARKER)) {\n    const notice = `\\n\\n> [!warning] Superseded\\n> This observation has been superseded.\\n\\n${SUPERSESSION_NOTICE_MARKER} [[${newSporeId}]]`;\n    body = body.trimEnd() + notice + '\\n';\n  }\n\n  // Atomic write (temp file + rename)\n  const tmp = `${fullPath}.tmp`;\n  fs.writeFileSync(tmp, `---\\n${fmYaml}\\n---${body}`, 'utf-8');\n  fs.renameSync(tmp, fullPath);\n\n  // Re-index the updated file and remove stale vector\n  indexNote(deps.index, deps.vaultDir, targetPath);\n  deps.vectorIndex?.delete(targetId);\n\n  return true;\n}\n\n/**\n * Check whether the newly written spore with `newSporeId` supersedes any\n * existing active spores of the same observation_type.\n *\n * Returns the list of spore IDs that were marked superseded.\n */\nexport async function checkSupersession(\n  newSporeId: string,\n  deps: {\n    index: MycoIndex;\n    vectorIndex: VectorIndex | null;\n    embeddingProvider: EmbeddingProvider;\n    llmProvider: LlmProvider | null;\n    vaultDir: string;\n    log?: LogFn;\n  },\n): Promise<string[]> {\n  const { index, vectorIndex, embeddingProvider, llmProvider, vaultDir, log } = deps;\n\n  // Early-exit if no vector index or LLM available\n  if (!vectorIndex || !llmProvider) {\n    log?.('debug', 'checkSupersession: skipped — vectorIndex or llmProvider unavailable', { newSporeId });\n    return [];\n  }\n\n  // Look up the new spore to get its content and observation_type\n  const newSporeResults = index.queryByIds([newSporeId]);\n  if (newSporeResults.length === 0) {\n    log?.('warn', 'checkSupersession: new spore not found in index', { newSporeId });\n    return [];\n  }\n  const newSpore = newSporeResults[0];\n  const observationType = newSpore.frontmatter['observation_type'] as string | undefined;\n\n  // Embed the spore content for similarity search\n  const embeddingText = newSpore.content.slice(0, EMBEDDING_INPUT_LIMIT);\n  const embeddingResult = await generateEmbedding(embeddingProvider, embeddingText);\n\n  // Fetch candidate spore IDs from vector index\n  const vectorResults = vectorIndex.search(embeddingResult.embedding, {\n    type: 'spore',\n    limit: SUPERSESSION_VECTOR_FETCH_LIMIT,\n  });\n\n  if (vectorResults.length === 0) {\n    log?.('debug', 'checkSupersession: no vector results', { newSporeId });\n    return [];\n  }\n\n  const candidateIds = vectorResults.map((r) => r.id);\n\n  // Look up candidate notes and post-filter:\n  // - same observation_type as the new spore\n  // - active status (including legacy spores without status field)\n  // - not the new spore itself\n  const candidateNotes = index.queryByIds(candidateIds);\n  const filtered = candidateNotes\n    .filter((note) => {\n      if (note.id === newSporeId) return false;\n      if (!isActiveSpore(note.frontmatter)) return false;\n      if (observationType && note.frontmatter['observation_type'] !== observationType) return false;\n      return true;\n    })\n    .slice(0, SUPERSESSION_CANDIDATE_LIMIT);\n\n  if (filtered.length === 0) {\n    log?.('debug', 'checkSupersession: no candidates after filtering', { newSporeId, observationType });\n    return [];\n  }\n\n  // Build the supersession prompt\n  const template = loadPrompt('supersession');\n  const newSporeText = formatNoteForPrompt(newSpore);\n  const candidatesText = formatNotesForPrompt(filtered);\n\n  const prompt = template\n    .replace('{{new_spore}}', newSporeText)\n    .replace('{{candidates}}', candidatesText);\n\n  // Ask the LLM which candidates are superseded\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    log?.('warn', 'checkSupersession: LLM call failed', { newSporeId, error: String(err) });\n    return [];\n  }\n\n  // Parse the LLM response as a JSON array of IDs\n  let rawIds: unknown;\n  try {\n    rawIds = JSON.parse(responseText);\n  } catch {\n    log?.('warn', 'checkSupersession: failed to parse LLM response', { newSporeId, responseText });\n    return [];\n  }\n\n  const parsed = supersededIdsSchema.safeParse(rawIds);\n  if (!parsed.success) {\n    log?.('warn', 'checkSupersession: LLM response failed schema validation', { newSporeId });\n    return [];\n  }\n\n  // Filter to IDs that actually exist in the candidate list and are still active\n  const candidateMap = new Map<string, IndexedNote>(filtered.map((c) => [c.id, c]));\n  const validIds = parsed.data.filter((id) => candidateMap.has(id));\n\n  if (validIds.length === 0) {\n    return [];\n  }\n\n  // Mark each validated candidate as superseded\n  const supersededIds: string[] = [];\n\n  for (const id of validIds) {\n    const candidate = candidateMap.get(id)!;\n    const wrote = supersedeSpore(id, newSporeId, candidate.path, { index, vectorIndex, vaultDir });\n\n    if (!wrote) {\n      log?.('warn', 'checkSupersession: file not found for candidate, skipping', { id, path: candidate.path });\n      continue;\n    }\n\n    supersededIds.push(id);\n    log?.('info', 'checkSupersession: marked superseded', { supersededId: id, newSporeId });\n  }\n\n  return 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package/dist/chunk-ZMYNRTTD.js.map

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-{"version":3,"sources":["../src/services/stats.ts"],"sourcesContent":["import { MycoIndex } from '../index/sqlite.js';\nimport { VectorIndex } from '../index/vectors.js';\nimport { isProcessAlive } from '../cli/shared.js';\nimport fs from 'node:fs';\nimport path from 'node:path';\n\n/** Fallback dimension for opening VectorIndex when the actual dimension is unknown. */\nconst VECTOR_FALLBACK_DIMENSION = 1024;\n\nexport interface VaultStats {\n  vault: {\n    path: string;\n    name: string;\n    spore_counts: Record<string, number>;\n    session_count: number;\n    plan_count: number;\n  };\n  index: {\n    fts_entries: number;\n    vector_count: number;\n  };\n  daemon: {\n    pid: number;\n    port: number;\n    started: string;\n    active_sessions: string[];\n    alive: boolean;\n  } | null;\n}\n\nexport function gatherStats(vaultDir: string, index: MycoIndex, vectorIndex?: VectorIndex): VaultStats {\n  const typeCounts = index.countByType();\n  const spore_counts = index.sporeCountsByObservationType();\n\n  let vector_count = 0;\n  if (vectorIndex) {\n    vector_count = vectorIndex.count();\n  } else {\n    const vecDb = path.join(vaultDir, 'vectors.db');\n    if (fs.existsSync(vecDb)) {\n      try {\n        const vec = new VectorIndex(vecDb, VECTOR_FALLBACK_DIMENSION);\n        vector_count = vec.count();\n        vec.close();\n      } catch { /* ignore */ }\n    }\n  }\n\n  let daemon: VaultStats['daemon'] = null;\n  const daemonPath = path.join(vaultDir, 'daemon.json');\n  if (fs.existsSync(daemonPath)) {\n    try {\n      const info = JSON.parse(fs.readFileSync(daemonPath, 'utf-8'));\n      daemon = {\n        pid: info.pid,\n        port: info.port,\n        started: info.started,\n        active_sessions: info.sessions || [],\n        alive: isProcessAlive(info.pid),\n      };\n    } catch { /* ignore */ }\n  }\n\n  return {\n    vault: {\n      path: vaultDir,\n      name: path.basename(vaultDir),\n      spore_counts,\n      session_count: typeCounts['session'] ?? 0,\n      plan_count: typeCounts['plan'] ?? 0,\n    },\n    index: {\n      fts_entries: Object.values(typeCounts).reduce((sum, n) => sum + n, 0),\n      vector_count,\n    },\n    daemon,\n  };\n}\n"],"mappings":";;;;;;;;;AAGA,OAAO,QAAQ;AACf,OAAO,UAAU;AAGjB,IAAM,4BAA4B;AAuB3B,SAAS,YAAY,UAAkB,OAAkB,aAAuC;AACrG,QAAM,aAAa,MAAM,YAAY;AACrC,QAAM,eAAe,MAAM,6BAA6B;AAExD,MAAI,eAAe;AACnB,MAAI,aAAa;AACf,mBAAe,YAAY,MAAM;AAAA,EACnC,OAAO;AACL,UAAM,QAAQ,KAAK,KAAK,UAAU,YAAY;AAC9C,QAAI,GAAG,WAAW,KAAK,GAAG;AACxB,UAAI;AACF,cAAM,MAAM,IAAI,YAAY,OAAO,yBAAyB;AAC5D,uBAAe,IAAI,MAAM;AACzB,YAAI,MAAM;AAAA,MACZ,QAAQ;AAAA,MAAe;AAAA,IACzB;AAAA,EACF;AAEA,MAAI,SAA+B;AACnC,QAAM,aAAa,KAAK,KAAK,UAAU,aAAa;AACpD,MAAI,GAAG,WAAW,UAAU,GAAG;AAC7B,QAAI;AACF,YAAM,OAAO,KAAK,MAAM,GAAG,aAAa,YAAY,OAAO,CAAC;AAC5D,eAAS;AAAA,QACP,KAAK,KAAK;AAAA,QACV,MAAM,KAAK;AAAA,QACX,SAAS,KAAK;AAAA,QACd,iBAAiB,KAAK,YAAY,CAAC;AAAA,QACnC,OAAO,eAAe,KAAK,GAAG;AAAA,MAChC;AAAA,IACF,QAAQ;AAAA,IAAe;AAAA,EACzB;AAEA,SAAO;AAAA,IACL,OAAO;AAAA,MACL,MAAM;AAAA,MACN,MAAM,KAAK,SAAS,QAAQ;AAAA,MAC5B;AAAA,MACA,eAAe,WAAW,SAAS,KAAK;AAAA,MACxC,YAAY,WAAW,MAAM,KAAK;AAAA,IACpC;AAAA,IACA,OAAO;AAAA,MACL,aAAa,OAAO,OAAO,UAAU,EAAE,OAAO,CAAC,KAAK,MAAM,MAAM,GAAG,CAAC;AAAA,MACpE;AAAA,IACF;AAAA,IACA;AAAA,EACF;AACF;","names":[]}