@goondocks/myco 0.4.3 → 0.5.0

package/.claude-plugin/marketplace.json

@@ -12,7 +12,7 @@
       "source": {
         "source": "npm",
         "package": "@goondocks/myco",
-        "version": "0.4.2"
+        "version": "0.4.4"
       },
       "description": "Collective agent intelligence — captures session knowledge and serves it back via MCP",
       "license": "MIT",

package/.claude-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "myco",
-  "version": "0.4.3",
+  "version": "0.5.0",
   "description": "Collective agent intelligence — captures session knowledge and serves it back to your team via MCP",
   "author": {
     "name": "goondocks-co",

package/README.md

@@ -50,9 +50,13 @@ myco_context(tier: 3000)                → pre-computed project understanding,
 
 A background daemon reads your agent's conversation transcript after each turn — the full dialogue including prompts, AI responses, tool calls, and screenshots. Observations called **spores** (decisions, gotchas, discoveries, trade-offs, bug fixes) are extracted automatically via a local LLM and written as linked vault notes.
 
+### Curate
+
+As a project evolves, older observations become stale. Myco automatically detects and supersedes outdated spores when new ones are created — using vector similarity to find candidates and an LLM to judge which are truly replaced vs. merely related. Superseded spores are preserved with lineage metadata (never deleted), but filtered from search results and digest synthesis. Run `myco curate` for vault-wide cleanup, or let it happen automatically on every spore write.
+
 ### Digest
 
-A **continuous reasoning engine** runs inside the daemon, periodically synthesizing all accumulated knowledge into tiered context extracts. These pre-computed summaries give agents an instant, rich understanding of the project at session start — no searching required. Four tiers serve different needs: executive briefing (1.5K tokens), team standup (3K), deep onboarding (5K), and institutional knowledge (10K).
+A **continuous reasoning engine** runs inside the daemon, periodically synthesizing all accumulated knowledge into tiered context extracts. These pre-computed summaries give agents an instant, rich understanding of the project at session start — no searching required. Four tiers serve different needs: executive briefing (1.5K tokens), team standup (3K), deep onboarding (5K), and institutional knowledge (10K). Run `myco digest --tier 3000` to reprocess a specific tier from scratch, or `myco digest --full` for a complete rebuild.
 
 ### Index
 

package/dist/chunk-2AMAOSRF.js

@@ -0,0 +1,105 @@
+import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
+import {
+  external_exports
+} from "./chunk-6UJWI4IW.js";
+
+// src/vault/types.ts
+var SessionFrontmatterSchema = external_exports.object({
+  type: external_exports.literal("session"),
+  id: external_exports.string(),
+  agent: external_exports.string(),
+  user: external_exports.string(),
+  started: external_exports.string(),
+  ended: external_exports.string().optional(),
+  parent: external_exports.string().optional(),
+  parent_reason: external_exports.string().optional(),
+  plan: external_exports.string().optional(),
+  // backward compat read path
+  plans: external_exports.array(external_exports.string()).optional(),
+  // new: multiple plans
+  branch: external_exports.string().optional(),
+  tags: external_exports.array(external_exports.string()).default([]),
+  tools_used: external_exports.number().int().optional(),
+  files_changed: external_exports.number().int().optional()
+});
+var PLAN_STATUSES = ["active", "in_progress", "completed", "abandoned"];
+var PlanFrontmatterSchema = external_exports.object({
+  type: external_exports.literal("plan"),
+  id: external_exports.string(),
+  status: external_exports.enum(PLAN_STATUSES).default("active"),
+  created: external_exports.string(),
+  author: external_exports.string().optional(),
+  tags: external_exports.array(external_exports.string()).default([])
+});
+var OBSERVATION_TYPES = ["gotcha", "bug_fix", "decision", "discovery", "trade_off", "cross-cutting"];
+var SPORE_STATUSES = ["active", "superseded", "archived"];
+var SporeFrontmatterSchema = external_exports.object({
+  type: external_exports.literal("spore"),
+  id: external_exports.string(),
+  observation_type: external_exports.string(),
+  status: external_exports.enum(SPORE_STATUSES).default("active"),
+  session: external_exports.string().optional(),
+  plan: external_exports.string().optional(),
+  superseded_by: external_exports.string().optional(),
+  consolidated_from: external_exports.array(external_exports.string()).optional(),
+  created: external_exports.string(),
+  tags: external_exports.array(external_exports.string()).default([])
+});
+var ARTIFACT_TYPES = ["spec", "plan", "rfc", "doc", "other"];
+var ArtifactFrontmatterSchema = external_exports.object({
+  type: external_exports.literal("artifact"),
+  id: external_exports.string(),
+  artifact_type: external_exports.enum(ARTIFACT_TYPES).default("other"),
+  source_path: external_exports.string(),
+  title: external_exports.string(),
+  last_captured_by: external_exports.string(),
+  created: external_exports.string(),
+  updated: external_exports.string(),
+  tags: external_exports.array(external_exports.string()).default([])
+});
+var TeamMemberFrontmatterSchema = external_exports.object({
+  type: external_exports.literal("team-member"),
+  user: external_exports.string(),
+  joined: external_exports.string(),
+  role: external_exports.string().optional(),
+  tags: external_exports.array(external_exports.string()).default([])
+});
+var schemasByType = {
+  session: SessionFrontmatterSchema,
+  plan: PlanFrontmatterSchema,
+  spore: SporeFrontmatterSchema,
+  artifact: ArtifactFrontmatterSchema,
+  "team-member": TeamMemberFrontmatterSchema
+};
+function parseNoteFrontmatter(data) {
+  const type = data.type;
+  const schema = schemasByType[type];
+  if (!schema) {
+    throw new Error(`Unknown note type: ${type}. Known types: ${Object.keys(schemasByType).join(", ")}`);
+  }
+  const coerced = coerceDatesToStrings(data);
+  return schema.parse(coerced);
+}
+function coerceDatesToStrings(obj) {
+  const result = {};
+  for (const [key, value] of Object.entries(obj)) {
+    if (value instanceof Date) {
+      result[key] = value.toISOString();
+    } else if (Array.isArray(value)) {
+      result[key] = value.map((item) => item instanceof Date ? item.toISOString() : item);
+    } else if (value !== null && typeof value === "object" && !Array.isArray(value)) {
+      result[key] = coerceDatesToStrings(value);
+    } else {
+      result[key] = value;
+    }
+  }
+  return result;
+}
+
+export {
+  PLAN_STATUSES,
+  OBSERVATION_TYPES,
+  ARTIFACT_TYPES,
+  parseNoteFrontmatter
+};
+//# sourceMappingURL=chunk-2AMAOSRF.js.map

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

@@ -0,0 +1 @@
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package/dist/{chunk-I7PNZEBO.js → chunk-6LTNFMXO.js}

@@ -201,6 +201,15 @@ ${links.join("\n")}`);
   sections.push(footerTags(allTags));
   return sections.join("\n\n");
 }
+var FOOTER_TAG_PREFIX = "\n#type/";
+function extractSection(body, heading) {
+  const start = body.indexOf(heading);
+  if (start === -1) return "";
+  const section = body.slice(start + heading.length);
+  const footerIdx = section.lastIndexOf(FOOTER_TAG_PREFIX);
+  if (footerIdx !== -1) return section.slice(0, footerIdx).trim();
+  return section.trim();
+}
 function capitalize(s) {
   return s.charAt(0).toUpperCase() + s.slice(1);
 }
@@ -418,8 +427,10 @@ export {
   bareSessionId,
   sessionWikilink,
   sessionRelativePath,
+  callout,
   formatSessionBody,
   formatSporeBody,
+  extractSection,
   VaultWriter
 };
-//# sourceMappingURL=chunk-I7PNZEBO.js.map
+//# sourceMappingURL=chunk-6LTNFMXO.js.map

package/dist/{chunk-I7PNZEBO.js.map → chunk-6LTNFMXO.js.map}

@@ -1 +1 @@
-{"version":3,"sources":["../src/vault/session-id.ts","../src/obsidian/formatter.ts","../src/vault/writer.ts"],"sourcesContent":["/**\n * Session ID convention utilities.\n *\n * The runtime session ID is a bare UUID (e.g., \"abc123\").\n * The vault stores it with a \"session-\" prefix (e.g., \"session-abc123\").\n * These helpers convert between the two forms.\n */\nconst SESSION_PREFIX = 'session-';\n\n/** Convert a bare session ID to a vault note ID: \"abc123\" → \"session-abc123\" */\nexport function sessionNoteId(bareId: string): string {\n  if (bareId.startsWith(SESSION_PREFIX)) return bareId;\n  return `${SESSION_PREFIX}${bareId}`;\n}\n\n/** Convert a vault note ID to a bare session ID: \"session-abc123\" → \"abc123\" */\nexport function bareSessionId(noteId: string): string {\n  if (noteId.startsWith(SESSION_PREFIX)) return noteId.slice(SESSION_PREFIX.length);\n  return noteId;\n}\n\n/** Convert a bare session ID to an Obsidian wikilink: \"abc123\" → \"[[session-abc123]]\" */\nexport function sessionWikilink(bareId: string): string {\n  return `[[${sessionNoteId(bareId)}]]`;\n}\n\n/** Build the relative vault path for a session note */\nexport function sessionRelativePath(bareId: string, date: string): string {\n  return `sessions/${date}/${sessionNoteId(bareId)}.md`;\n}\n\n","/**\n * Pure formatting functions for Obsidian-native vault notes.\n * No I/O, no external dependencies — just string transforms.\n */\nimport type { ArtifactType } from '../vault/types.js';\nimport { sessionNoteId } from '../vault/session-id.js';\n\n// Callout type mapping for observation types\nconst CALLOUT_MAP: Record<string, string> = {\n  gotcha: 'warning',\n  bug_fix: 'bug',\n  decision: 'info',\n  discovery: 'tip',\n  trade_off: 'question',\n};\n\nexport function observationCalloutType(observationType: string): string {\n  return CALLOUT_MAP[observationType] ?? 'note';\n}\n\n/**\n * Escape angle brackets that Obsidian would interpret as HTML tags.\n * Matches `<` followed by a letter, `/`, or `!` (opening/closing tags, comments).\n */\nexport function escapeHtmlTags(text: string): string {\n  return text.replace(/<(?=[a-zA-Z/!])/g, '\\\\<');\n}\n\nexport function callout(type: string, title: string, content: string): string {\n  const safe = escapeHtmlTags(content);\n  const indented = safe.split('\\n').map((line) => `> ${line}`).join('\\n');\n  return `> [!${type}] ${title}\\n${indented}`;\n}\n\nexport function inlineField(key: string, value: string): string {\n  return `${key}:: ${value}`;\n}\n\nexport function wikilink(target: string, display?: string): string {\n  return display ? `[[${target}|${display}]]` : `[[${target}]]`;\n}\n\n/**\n * Normalize an observation_type to a tag-safe form.\n * Frontmatter keeps underscores; tags use hyphens per Obsidian convention.\n */\nfunction tagNormalize(s: string): string {\n  return s.replace(/_/g, '-');\n}\n\n/**\n * Sanitize a user/LLM-provided tag for Obsidian compatibility.\n * Obsidian tags cannot contain spaces — replace with slash (nested tag).\n * Strips leading # if present.\n */\nfunction sanitizeTag(raw: string): string {\n  const stripped = raw.startsWith('#') ? raw.slice(1) : raw;\n  return stripped.replace(/\\s+/g, '/');\n}\n\nexport function buildTags(type: string, subtype: string, extraTags: string[] = []): string[] {\n  const tags: string[] = [`type/${type}`];\n\n  if (subtype) {\n    tags.push(`${type}/${tagNormalize(subtype)}`);\n  }\n\n  for (const tag of extraTags) {\n    const normalized = sanitizeTag(tag);\n    if (normalized && !tags.includes(normalized)) {\n      tags.push(normalized);\n    }\n  }\n\n  return tags;\n}\n\nexport function footerTags(tags: string[]): string {\n  return tags.map((t) => (t.startsWith('#') ? t : `#${t}`)).join(' ');\n}\n\n// --- Session formatting ---\n\nexport interface SessionBodyInput {\n  title: string;\n  narrative: string;\n  sessionId: string;\n  user?: string;\n  started?: string;\n  ended?: string;\n  branch?: string;\n  relatedMemories?: Array<{ id: string; title: string }>;\n  turns: Array<{\n    prompt: string;\n    toolCount: number;\n    aiResponse?: string;\n    /** Filenames of images in the vault attachments folder */\n    images?: string[];\n  }>;\n  tags?: string[];\n}\n\nexport function formatSessionBody(input: SessionBodyInput): string {\n  const sections: string[] = [];\n\n  sections.push(`# ${input.title}`);\n\n  if (input.narrative) {\n    sections.push(callout('abstract', 'Summary', input.narrative));\n  }\n\n  // Inline fields\n  const fields: string[] = [];\n  fields.push(inlineField('Session', wikilink(sessionNoteId(input.sessionId))));\n  if (input.user) fields.push(inlineField('User', input.user));\n  if (input.started && input.ended) {\n    const duration = formatDuration(input.started, input.ended);\n    if (duration) fields.push(inlineField('Duration', duration));\n  }\n  if (input.branch) fields.push(inlineField('Branch', `\\`${input.branch}\\``));\n  sections.push(fields.join('\\n'));\n\n  // Related spores\n  if (input.relatedMemories?.length) {\n    const links = input.relatedMemories.map((m) => `- ${wikilink(m.id, m.title)}`);\n    sections.push(`## Related Spores\\n${links.join('\\n')}`);\n  }\n\n  // Conversation turns — always rebuilt from the full transcript.\n  // The transcript is the source of truth for the complete conversation.\n  if (input.turns.length > 0) {\n    const turnLines: string[] = [];\n    for (let i = 0; i < input.turns.length; i++) {\n      const turn = input.turns[i];\n      const turnNum = i + 1;\n      turnLines.push(`### Turn ${turnNum}`);\n      if (turn.prompt || turn.images?.length) {\n        // Build prompt content: text + images + tool count\n        const parts: string[] = [];\n        if (turn.prompt) parts.push(turn.prompt);\n        if (turn.images?.length) {\n          parts.push(turn.images.map((f) => `![[${f}]]`).join('\\n'));\n        }\n        if (turn.toolCount > 0) parts.push(`*${turn.toolCount} tool calls*`);\n        turnLines.push(callout('user', 'Prompt', parts.join('\\n\\n')));\n      } else if (turn.toolCount > 0) {\n        turnLines.push(callout('user', 'Prompt', `*${turn.toolCount} tool calls*`));\n      }\n      if (turn.aiResponse) {\n        turnLines.push(callout('assistant', 'Response', turn.aiResponse));\n      }\n    }\n    sections.push(`## Conversation\\n\\n${turnLines.join('\\n\\n')}`);\n  }\n\n  // Footer tags\n  const allTags = buildTags('session', 'ended', [\n    ...(input.user ? [`user/${input.user}`] : []),\n    ...(input.tags ?? []),\n  ]);\n  sections.push(footerTags(allTags));\n\n  return sections.join('\\n\\n');\n}\n\n// --- Spore formatting ---\n\nexport interface SporeBodyInput {\n  title: string;\n  observationType: string;\n  content: string;\n  sessionId?: string;\n  root_cause?: string;\n  fix?: string;\n  rationale?: string;\n  alternatives_rejected?: string;\n  gained?: string;\n  sacrificed?: string;\n  tags?: string[];\n}\n\nexport function formatSporeBody(input: SporeBodyInput): string {\n  const sections: string[] = [];\n  const calloutType = observationCalloutType(input.observationType);\n  const calloutTitle = capitalize(tagNormalize(input.observationType));\n\n  sections.push(`# ${input.title}`);\n  sections.push(callout(calloutType, calloutTitle, input.content));\n\n  // Inline fields\n  const fields: string[] = [];\n  if (input.sessionId) {\n    fields.push(inlineField('Session', wikilink(sessionNoteId(input.sessionId))));\n  }\n  fields.push(inlineField('Observation', input.observationType));\n  if (fields.length > 0) sections.push(fields.join('\\n'));\n\n  // Type-specific sub-sections\n  if (input.root_cause) sections.push(`## Root Cause\\n${input.root_cause}`);\n  if (input.fix) sections.push(`## Fix\\n${input.fix}`);\n  if (input.rationale) sections.push(`## Rationale\\n${input.rationale}`);\n  if (input.alternatives_rejected) sections.push(`## Alternatives Rejected\\n${input.alternatives_rejected}`);\n  if (input.gained) sections.push(`## Gained\\n${input.gained}`);\n  if (input.sacrificed) sections.push(`## Sacrificed\\n${input.sacrificed}`);\n\n  // Footer tags\n  const allTags = buildTags('spore', input.observationType, input.tags ?? []);\n  sections.push(footerTags(allTags));\n\n  return sections.join('\\n\\n');\n}\n\n// --- Plan formatting ---\n\nexport interface PlanBodyInput {\n  id: string;\n  status: string;\n  author?: string;\n  created?: string;\n  sessions?: Array<{ id: string; title: string }>;\n  content: string;\n  tags?: string[];\n}\n\nexport function formatPlanBody(input: PlanBodyInput): string {\n  const sections: string[] = [];\n\n  // Inline fields block\n  const fields: string[] = [];\n  fields.push(inlineField('Plan', wikilink(input.id)));\n  fields.push(inlineField('Status', input.status));\n  if (input.author) fields.push(inlineField('Author', input.author));\n  if (input.created) fields.push(inlineField('Created', input.created));\n  sections.push(fields.join('\\n'));\n\n  // User-provided content body (don't restructure)\n  sections.push(input.content);\n\n  // Sessions section\n  if (input.sessions?.length) {\n    const links = input.sessions.map((s) => `- ${wikilink(sessionNoteId(s.id), s.title)}`);\n    sections.push(`## Sessions\\n${links.join('\\n')}`);\n  }\n\n  // Footer tags\n  const statusTag = tagNormalize(input.status);\n  const allTags = buildTags('plan', statusTag, input.tags ?? []);\n  sections.push(footerTags(allTags));\n\n  return sections.join('\\n\\n');\n}\n\n// --- Artifact formatting ---\n\nexport interface ArtifactBodyInput {\n  id: string;\n  title: string;\n  artifact_type: ArtifactType;\n  source_path: string;\n  sessionId: string;\n  content: string;\n  tags?: string[];\n}\n\nexport function formatArtifactBody(input: ArtifactBodyInput): string {\n  const sections: string[] = [];\n\n  // Inline fields\n  const fields: string[] = [];\n  fields.push(inlineField('Artifact', wikilink(input.id)));\n  fields.push(inlineField('Source', `\\`${input.source_path}\\``));\n  fields.push(inlineField('Type', input.artifact_type));\n  fields.push(inlineField('Session', wikilink(sessionNoteId(input.sessionId))));\n  sections.push(fields.join('\\n'));\n\n  // Body: full content from disk\n  sections.push(input.content);\n\n  // Footer tags\n  const allTags = buildTags('artifact', input.artifact_type, input.tags ?? []);\n  sections.push(footerTags(allTags));\n\n  return sections.join('\\n\\n');\n}\n\n// --- Team formatting ---\n\nexport interface TeamBodyInput {\n  user: string;\n  role?: string;\n  recentSessions?: Array<{ id: string; title: string }>;\n}\n\nexport function formatTeamBody(input: TeamBodyInput): string {\n  const sections: string[] = [];\n\n  sections.push(`# ${input.user}`);\n  sections.push(callout('info', 'Team Member', input.role ?? 'Contributor'));\n\n  // Inline fields\n  const fields: string[] = [];\n  fields.push(inlineField('User', input.user));\n  if (input.role) fields.push(inlineField('Role', input.role));\n  sections.push(fields.join('\\n'));\n\n  // Recent sessions\n  if (input.recentSessions?.length) {\n    const links = input.recentSessions.map((s) => `- ${wikilink(sessionNoteId(s.id), s.title)}`);\n    sections.push(`## Recent Sessions\\n${links.join('\\n')}`);\n  }\n\n  // Footer tags\n  const allTags = buildTags('team', '', [`user/${input.user}`]);\n  sections.push(footerTags(allTags));\n\n  return sections.join('\\n\\n');\n}\n\n// --- Helpers ---\n\nfunction capitalize(s: string): string {\n  return s.charAt(0).toUpperCase() + s.slice(1);\n}\n\nfunction formatDuration(started: string, ended: string): string {\n  const ms = new Date(ended).getTime() - new Date(started).getTime();\n  if (isNaN(ms) || ms < 0) return '';\n  const totalMinutes = Math.floor(ms / 60000);\n  if (totalMinutes < 1) return '<1m';\n  const hours = Math.floor(totalMinutes / 60);\n  const minutes = totalMinutes % 60;\n  if (hours === 0) return `${minutes}m`;\n  if (minutes === 0) return `${hours}h`;\n  return `${hours}h ${minutes}m`;\n}\n","import fs from 'node:fs';\nimport path from 'node:path';\nimport YAML from 'yaml';\nimport { buildTags, formatTeamBody, formatPlanBody, formatArtifactBody } from '../obsidian/formatter.js';\nimport type { ArtifactType } from './types.js';\nimport { sessionNoteId, sessionRelativePath } from './session-id.js';\n\ninterface WriteSessionInput {\n  id: string;\n  agent?: string;\n  user?: string;\n  started: string;\n  ended?: string;\n  parent?: string;\n  parent_reason?: string;\n  plans?: string[];\n  branch?: string;\n  tags?: string[];\n  tools_used?: number;\n  files_changed?: number;\n  summary: string;\n}\n\ninterface WritePlanInput {\n  id: string;\n  status?: string;\n  author?: string;\n  tags?: string[];\n  content: string;\n}\n\ninterface WriteSporeInput {\n  id: string;\n  observation_type: string;\n  session?: string;\n  plan?: string;\n  tags?: string[];\n  content: string;\n}\n\ninterface WriteArtifactInput {\n  id: string;\n  artifact_type: ArtifactType;\n  source_path: string;\n  title: string;\n  session: string;\n  tags?: string[];\n  content: string;\n}\n\ninterface WriteTeamMemberInput {\n  user: string;\n  role?: string;\n}\n\nexport class VaultWriter {\n  constructor(private vaultDir: string) {}\n\n  writeSession(input: WriteSessionInput): string {\n    const date = input.started.slice(0, 10);\n    const relativePath = sessionRelativePath(input.id, date);\n\n    const frontmatter: Record<string, unknown> = {\n      type: 'session',\n      id: input.id,\n      agent: input.agent ?? 'claude-code',\n      user: input.user ?? '',\n      started: input.started,\n    };\n    if (input.ended) frontmatter.ended = input.ended;\n    if (input.parent) frontmatter.parent = input.parent;\n    if (input.parent_reason) frontmatter.parent_reason = input.parent_reason;\n    if (input.plans?.length) frontmatter.plans = input.plans;\n    if (input.branch) frontmatter.branch = input.branch;\n    frontmatter.tags = buildTags('session', 'ended', [\n      ...(input.user ? [`user/${input.user}`] : []),\n      ...(input.tags ?? []),\n    ]);\n    if (input.tools_used != null) frontmatter.tools_used = input.tools_used;\n    if (input.files_changed != null) frontmatter.files_changed = input.files_changed;\n\n    this.writeMarkdown(relativePath, frontmatter, input.summary);\n    return relativePath;\n  }\n\n  writePlan(input: WritePlanInput): string {\n    const relativePath = `plans/${input.id}.md`;\n    const fullPath = path.join(this.vaultDir, relativePath);\n\n    const status = input.status ?? 'active';\n    let created = new Date().toISOString();\n\n    // Preserve created from existing file (idempotent)\n    try {\n      const existing = fs.readFileSync(fullPath, 'utf-8');\n      const fmMatch = existing.match(/^---\\n([\\s\\S]*?)\\n---/);\n      if (fmMatch) {\n        const parsed = YAML.parse(fmMatch[1]) as Record<string, unknown>;\n        if (typeof parsed.created === 'string') created = parsed.created;\n      }\n    } catch {\n      // File doesn't exist yet\n    }\n    const frontmatter: Record<string, unknown> = {\n      type: 'plan',\n      id: input.id,\n      status,\n      created,\n    };\n    if (input.author) frontmatter.author = input.author;\n    frontmatter.tags = buildTags('plan', status, input.tags ?? []);\n\n    const body = formatPlanBody({\n      id: input.id,\n      status,\n      author: input.author,\n      created,\n      content: input.content,\n      tags: input.tags,\n    });\n\n    this.writeMarkdown(relativePath, frontmatter, body);\n    return relativePath;\n  }\n\n  writeSpore(input: WriteSporeInput): string {\n    const normalizedType = input.observation_type.replace(/_/g, '-');\n    const relativePath = `spores/${normalizedType}/${input.id}.md`;\n    const fullPath = path.join(this.vaultDir, relativePath);\n    const now = new Date().toISOString();\n\n    // Preserve created from existing file (idempotent)\n    let created = now;\n    try {\n      const existing = fs.readFileSync(fullPath, 'utf-8');\n      const fmMatch = existing.match(/^---\\n([\\s\\S]*?)\\n---/);\n      if (fmMatch) {\n        const parsed = YAML.parse(fmMatch[1]) as Record<string, unknown>;\n        if (typeof parsed.created === 'string') created = parsed.created;\n      }\n    } catch {\n      // File doesn't exist yet — created = now\n    }\n\n    const frontmatter: Record<string, unknown> = {\n      type: 'spore',\n      id: input.id,\n      observation_type: input.observation_type,\n      created,\n    };\n    if (input.session) frontmatter.session = input.session;\n    if (input.plan) frontmatter.plan = input.plan;\n    frontmatter.tags = buildTags('spore', input.observation_type, input.tags ?? []);\n\n    this.writeMarkdown(relativePath, frontmatter, input.content);\n    return relativePath;\n  }\n\n  writeArtifact(input: WriteArtifactInput): string {\n    const relativePath = `artifacts/${input.id}.md`;\n    const fullPath = path.join(this.vaultDir, relativePath);\n    const now = new Date().toISOString();\n\n    let created = now;\n\n    // Preserve created from existing file (latest-wins update)\n    try {\n      const existing = fs.readFileSync(fullPath, 'utf-8');\n      const fmMatch = existing.match(/^---\\n([\\s\\S]*?)\\n---/);\n      if (fmMatch) {\n        const parsed = YAML.parse(fmMatch[1]) as Record<string, unknown>;\n        if (typeof parsed.created === 'string') created = parsed.created;\n      }\n    } catch {\n      // File doesn't exist yet — created = now\n    }\n\n    const frontmatter: Record<string, unknown> = {\n      type: 'artifact',\n      id: input.id,\n      artifact_type: input.artifact_type,\n      source_path: input.source_path,\n      title: input.title,\n      last_captured_by: sessionNoteId(input.session),\n      created,\n      updated: now,\n      tags: buildTags('artifact', input.artifact_type, input.tags ?? []),\n    };\n\n    const body = formatArtifactBody({\n      id: input.id,\n      title: input.title,\n      artifact_type: input.artifact_type,\n      source_path: input.source_path,\n      sessionId: input.session,\n      content: input.content,\n      tags: input.tags,\n    });\n\n    this.writeMarkdown(relativePath, frontmatter, body);\n    return relativePath;\n  }\n\n  writeTeamMember(input: WriteTeamMemberInput): string {\n    const relativePath = `team/${input.user}.md`;\n\n    const frontmatter: Record<string, unknown> = {\n      type: 'team-member',\n      user: input.user,\n      joined: new Date().toISOString(),\n      tags: buildTags('team', '', [`user/${input.user}`]),\n    };\n    if (input.role) frontmatter.role = input.role;\n\n    const body = formatTeamBody({\n      user: input.user,\n      role: input.role,\n    });\n\n    this.writeMarkdown(relativePath, frontmatter, body);\n    return relativePath;\n  }\n\n  /**\n   * Update frontmatter fields on an existing note without touching the body.\n   * By default only adds fields that don't exist. Set overwrite=true to replace existing values.\n   * Returns true if the update was applied, false if the file doesn't exist.\n   */\n  updateNoteFrontmatter(relativePath: string, fields: Record<string, unknown>, overwrite = false): boolean {\n    const fullPath = path.join(this.vaultDir, relativePath);\n    let fileContent: string;\n    try {\n      fileContent = fs.readFileSync(fullPath, 'utf-8');\n    } catch {\n      return false;\n    }\n\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    for (const [key, value] of Object.entries(fields)) {\n      if (overwrite || parsed[key] === undefined) {\n        parsed[key] = value;\n      }\n    }\n\n    const body = fileContent.slice(fmMatch[0].length);\n    const fmYaml = YAML.stringify(parsed, { defaultStringType: 'QUOTE_DOUBLE', defaultKeyType: 'PLAIN' }).trim();\n    this.atomicWrite(fullPath, `---\\n${fmYaml}\\n---${body}`);\n    return true;\n  }\n\n  /** @deprecated Use updateNoteFrontmatter instead */\n  updateSessionFrontmatter(relativePath: string, fields: Record<string, unknown>): boolean {\n    return this.updateNoteFrontmatter(relativePath, fields);\n  }\n\n  private writeMarkdown(relativePath: string, frontmatter: Record<string, unknown>, content: string): void {\n    const fullPath = path.join(this.vaultDir, relativePath);\n    fs.mkdirSync(path.dirname(fullPath), { recursive: true });\n\n    const fmYaml = YAML.stringify(frontmatter, { defaultStringType: 'QUOTE_DOUBLE', defaultKeyType: 'PLAIN' }).trim();\n    const file = `---\\n${fmYaml}\\n---\\n\\n${content}\\n`;\n    this.atomicWrite(fullPath, file);\n  }\n\n  /** Write to a temp file then rename — prevents Obsidian from seeing a truncated file mid-write. */\n  private atomicWrite(fullPath: string, content: string): void {\n    const tmp = `${fullPath}.tmp`;\n    fs.writeFileSync(tmp, content, 'utf-8');\n    fs.renameSync(tmp, fullPath);\n  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package/dist/{chunk-2GJFTIWX.js → chunk-7KQB22DP.js}

@@ -1,7 +1,7 @@
 import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
 import {
   AgentRegistry
-} from "./chunk-BNIYWCST.js";
+} from "./chunk-X6TKHO22.js";
 
 // src/version.ts
 import fs from "fs";
@@ -30,4 +30,4 @@ function readVersionFrom(dir) {
 export {
   getPluginVersion
 };
-//# sourceMappingURL=chunk-2GJFTIWX.js.map
+//# sourceMappingURL=chunk-7KQB22DP.js.map

package/dist/{chunk-JBD5KP5G.js → chunk-B6WVNDA5.js}

@@ -26,6 +26,7 @@ var FILE_WATCH_STABILITY_MS = 1e3;
 var PROVIDER_DETECT_TIMEOUT_MS = 3e3;
 var STALE_BUFFER_MAX_AGE_MS = 24 * 60 * 60 * 1e3;
 var DAEMON_HEALTH_RETRY_DELAYS = [100, 200, 400, 800, 1500];
+var DAEMON_STALE_GRACE_PERIOD_MS = 6e4;
 var MAX_SLUG_LENGTH = 100;
 var CANDIDATE_CONTENT_PREVIEW = 2e3;
 var LINEAGE_RECENT_SESSIONS_LIMIT = 5;
@@ -51,6 +52,11 @@ var DIGEST_SUBSTRATE_TYPE_WEIGHTS = {
   artifact: 1,
   team: 1
 };
+var LLM_REASONING_MODE = "off";
+var SUPERSESSION_CANDIDATE_LIMIT = 5;
+var SUPERSESSION_VECTOR_FETCH_LIMIT = 20;
+var SUPERSESSION_MAX_TOKENS = 256;
+var CURATION_CLUSTER_SIMILARITY = 0.75;
 
 export {
   CHARS_PER_TOKEN,
@@ -76,6 +82,7 @@ export {
   PROVIDER_DETECT_TIMEOUT_MS,
   STALE_BUFFER_MAX_AGE_MS,
   DAEMON_HEALTH_RETRY_DELAYS,
+  DAEMON_STALE_GRACE_PERIOD_MS,
   MAX_SLUG_LENGTH,
   CANDIDATE_CONTENT_PREVIEW,
   LINEAGE_RECENT_SESSIONS_LIMIT,
@@ -89,6 +96,11 @@ export {
   MCP_LOGS_DEFAULT_LIMIT,
   DIGEST_TIERS,
   DIGEST_TIER_MIN_CONTEXT,
-  DIGEST_SUBSTRATE_TYPE_WEIGHTS
+  DIGEST_SUBSTRATE_TYPE_WEIGHTS,
+  LLM_REASONING_MODE,
+  SUPERSESSION_CANDIDATE_LIMIT,
+  SUPERSESSION_VECTOR_FETCH_LIMIT,
+  SUPERSESSION_MAX_TOKENS,
+  CURATION_CLUSTER_SIMILARITY
 };
-//# sourceMappingURL=chunk-JBD5KP5G.js.map
+//# sourceMappingURL=chunk-B6WVNDA5.js.map

package/dist/chunk-B6WVNDA5.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/constants.ts"],"sourcesContent":["/**\n * Shared constants for the Myco codebase.\n * Per CLAUDE.md: \"No Magic Literals — Numeric and string constants\n * MUST NOT appear inline in logic.\"\n */\n\n// --- Token estimation ---\n/** Approximate characters per token for the chars/4 heuristic. */\nexport const CHARS_PER_TOKEN = 4;\n\n/** Estimate token count from character length using the CHARS_PER_TOKEN heuristic. */\nexport function estimateTokens(text: string): number {\n  return Math.ceil(text.length / CHARS_PER_TOKEN);\n}\n\n// --- Embedding ---\n/** Max characters of text sent to the embedding model. */\nexport const EMBEDDING_INPUT_LIMIT = 8000;\n\n// --- Truncation limits (display/preview) ---\n/** Max chars for a user prompt preview in event summaries. */\nexport const PROMPT_PREVIEW_CHARS = 300;\n/** Max chars for an AI response preview in event summaries. */\nexport const AI_RESPONSE_PREVIEW_CHARS = 500;\n/** Max chars for a command string preview. */\nexport const COMMAND_PREVIEW_CHARS = 80;\n/** Max chars for a content snippet in search results. */\nexport const CONTENT_SNIPPET_CHARS = 120;\n/** Max chars for a tool output preview in hooks. */\nexport const TOOL_OUTPUT_PREVIEW_CHARS = 200;\n/** Max chars for a session summary preview in MCP tools. */\nexport const SESSION_SUMMARY_PREVIEW_CHARS = 300;\n/** Max chars for a recall summary preview. */\nexport const RECALL_SUMMARY_PREVIEW_CHARS = 200;\n\n// --- Context injection layer budgets (chars, not tokens — used with .slice()) ---\nexport const CONTEXT_PLAN_PREVIEW_CHARS = 100;\nexport const CONTEXT_SESSION_PREVIEW_CHARS = 80;\nexport const CONTEXT_SPORE_PREVIEW_CHARS = 80;\n\n// --- Processor maxTokens budgets ---\n/** Response token budget for observation extraction. */\nexport const EXTRACTION_MAX_TOKENS = 2048;\n/** Response token budget for session summary. */\nexport const SUMMARY_MAX_TOKENS = 512;\n/** Response token budget for session title generation. */\nexport const TITLE_MAX_TOKENS = 32;\n/** Response token budget for artifact classification. */\nexport const CLASSIFICATION_MAX_TOKENS = 1024;\n\n// --- Timeouts ---\n/** Daemon client HTTP request timeout (ms). */\nexport const DAEMON_CLIENT_TIMEOUT_MS = 2000;\n/** Health check timeout (ms) — fail fast if daemon isn't responding. */\nexport const DAEMON_HEALTH_CHECK_TIMEOUT_MS = 500;\n/** LLM request timeout (ms). All LLM calls are background daemon work — no need to be aggressive. */\nexport const LLM_REQUEST_TIMEOUT_MS = 180_000;\n/** Embedding request timeout (ms). Embeddings run in background batch processing — generous timeout. */\nexport const EMBEDDING_REQUEST_TIMEOUT_MS = 60_000;\n/** Digest LLM request timeout (ms). Digest cycles use large context windows and may need model loading time. */\nexport const DIGEST_LLM_REQUEST_TIMEOUT_MS = 600_000;\n/** Stdin read timeout for hooks (ms). */\nexport const STDIN_TIMEOUT_MS = 100;\n/** Chokidar write stability threshold (ms). */\nexport const FILE_WATCH_STABILITY_MS = 1000;\n/** Provider detection timeout for detect-providers CLI command (ms). */\nexport const PROVIDER_DETECT_TIMEOUT_MS = 3000;\n\n// --- Buffer cleanup ---\n/** Max age for stale buffer files before cleanup (ms). */\nexport const STALE_BUFFER_MAX_AGE_MS = 24 * 60 * 60 * 1000;\n\n// --- Retry backoff ---\n/** Retry delays for daemon health check (ms). */\nexport const DAEMON_HEALTH_RETRY_DELAYS = [100, 200, 400, 800, 1500];\n\n/** Grace period after daemon.json is written before stale checks can trigger a restart (ms).\n *  Prevents rapid restart loops from concurrent hooks or session reloads. */\nexport const DAEMON_STALE_GRACE_PERIOD_MS = 60_000;\n\n// --- Slug limits ---\n/** Max length for slugified artifact IDs. */\nexport const MAX_SLUG_LENGTH = 100;\n\n// --- Content preview for classification prompt ---\n/** Max chars of file content per candidate in classification prompt. */\nexport const CANDIDATE_CONTENT_PREVIEW = 2000;\n\n// --- Transcript mining ---\n/** Minimum content length to consider a transcript entry meaningful. */\nexport const MIN_TRANSCRIPT_CONTENT_LENGTH = 10;\n\n// --- Query limits ---\n/** Max recent sessions to check for lineage heuristics. */\nexport const LINEAGE_RECENT_SESSIONS_LIMIT = 5;\n/** Max related spores to query for session notes. */\nexport const RELATED_SPORES_LIMIT = 50;\n\n// --- Context injection ---\n/** Max active plans to inject at session start. */\nexport const SESSION_CONTEXT_MAX_PLANS = 3;\n/** Max spores to inject per prompt. */\nexport const PROMPT_CONTEXT_MAX_SPORES = 3;\n/** Minimum similarity score for prompt context injection (0-1). */\nexport const PROMPT_CONTEXT_MIN_SIMILARITY = 0.3;\n/** Max token budget for session-start context injection. */\nexport const SESSION_CONTEXT_MAX_TOKENS = 500;\n/** Max token budget for per-prompt context injection. */\nexport const PROMPT_CONTEXT_MAX_TOKENS = 300;\n/** Minimum prompt length to trigger context search. */\nexport const PROMPT_CONTEXT_MIN_LENGTH = 10;\n\n// --- MCP tool defaults ---\n/** Default result limit for myco_search. */\nexport const MCP_SEARCH_DEFAULT_LIMIT = 10;\n/** Default result limit for myco_sessions. */\nexport const MCP_SESSIONS_DEFAULT_LIMIT = 20;\n/** Default result limit for myco_logs. */\nexport const MCP_LOGS_DEFAULT_LIMIT = 50;\n\n// --- Digest — Tiers ---\n/** Available token-budget tiers for digest synthesis. */\nexport const DIGEST_TIERS = [1500, 3000, 5000, 10000] as const;\nexport type DigestTier = (typeof DIGEST_TIERS)[number];\n\n// --- Digest — Context window minimums per tier ---\n/** Minimum context window (tokens) required to run a digest at a given tier. */\nexport const DIGEST_TIER_MIN_CONTEXT: Record<number, number> = {\n  1500: 6500,\n  3000: 11500,\n  5000: 18500,\n  10000: 30500,\n};\n\n// --- Digest — Substrate ---\n/** Scoring weights by note type when selecting substrate for synthesis. */\nexport const DIGEST_SUBSTRATE_TYPE_WEIGHTS: Record<string, number> = {\n  session: 3,\n  spore: 3,\n  plan: 2,\n  artifact: 1,\n  team: 1,\n};\n\n// --- LLM reasoning control ---\n/** Reasoning mode for all Myco LLM calls. Suppresses chain-of-thought tokens from reasoning models. */\nexport const LLM_REASONING_MODE = 'off' as const;\n\n// --- Digest — System prompt overhead estimate ---\n\n// --- Vault curation ---\n/** Max candidate spores after post-filtering for supersession check. */\nexport const SUPERSESSION_CANDIDATE_LIMIT = 5;\n\n/** Over-fetch from vector index before post-filtering by status/type. */\nexport const SUPERSESSION_VECTOR_FETCH_LIMIT = 20;\n\n/** Max output tokens for supersession LLM evaluation. */\nexport const SUPERSESSION_MAX_TOKENS = 256;\n\n/** Similarity threshold for clustering related spores in batch curation. */\nexport const CURATION_CLUSTER_SIMILARITY = 0.75;\n"],"mappings":";;;AAQO,IAAM,kBAAkB;AAGxB,SAAS,eAAe,MAAsB;AACnD,SAAO,KAAK,KAAK,KAAK,SAAS,eAAe;AAChD;AAIO,IAAM,wBAAwB;AAI9B,IAAM,uBAAuB;AAE7B,IAAM,4BAA4B;AAElC,IAAM,wBAAwB;AAE9B,IAAM,wBAAwB;AAE9B,IAAM,4BAA4B;AAElC,IAAM,gCAAgC;AAEtC,IAAM,+BAA+B;AAGrC,IAAM,6BAA6B;AACnC,IAAM,gCAAgC;AACtC,IAAM,8BAA8B;AAcpC,IAAM,2BAA2B;AAEjC,IAAM,iCAAiC;AAEvC,IAAM,yBAAyB;AAE/B,IAAM,+BAA+B;AAErC,IAAM,gCAAgC;AAEtC,IAAM,mBAAmB;AAEzB,IAAM,0BAA0B;AAEhC,IAAM,6BAA6B;AAInC,IAAM,0BAA0B,KAAK,KAAK,KAAK;AAI/C,IAAM,6BAA6B,CAAC,KAAK,KAAK,KAAK,KAAK,IAAI;AAI5D,IAAM,+BAA+B;AAIrC,IAAM,kBAAkB;AAIxB,IAAM,4BAA4B;AAQlC,IAAM,gCAAgC;AAEtC,IAAM,uBAAuB;AAI7B,IAAM,4BAA4B;AAElC,IAAM,4BAA4B;AAElC,IAAM,gCAAgC;AAMtC,IAAM,4BAA4B;AAIlC,IAAM,2BAA2B;AAEjC,IAAM,6BAA6B;AAEnC,IAAM,yBAAyB;AAI/B,IAAM,eAAe,CAAC,MAAM,KAAM,KAAM,GAAK;AAK7C,IAAM,0BAAkD;AAAA,EAC7D,MAAM;AAAA,EACN,KAAM;AAAA,EACN,KAAM;AAAA,EACN,KAAO;AACT;AAIO,IAAM,gCAAwD;AAAA,EACnE,SAAS;AAAA,EACT,OAAO;AAAA,EACP,MAAM;AAAA,EACN,UAAU;AAAA,EACV,MAAM;AACR;AAIO,IAAM,qBAAqB;AAM3B,IAAM,+BAA+B;AAGrC,IAAM,kCAAkC;AAGxC,IAAM,0BAA0B;AAGhC,IAAM,8BAA8B;","names":[]}

package/dist/chunk-FIA5NTRH.js

@@ -0,0 +1,159 @@
+import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
+import {
+  indexNote
+} from "./chunk-JJL6AMDA.js";
+import {
+  generateEmbedding
+} from "./chunk-RGVBGTD6.js";
+import {
+  loadPrompt,
+  stripReasoningTokens
+} from "./chunk-KYL67SKZ.js";
+import {
+  external_exports,
+  require_dist
+} from "./chunk-6UJWI4IW.js";
+import {
+  EMBEDDING_INPUT_LIMIT,
+  LLM_REASONING_MODE,
+  SUPERSESSION_CANDIDATE_LIMIT,
+  SUPERSESSION_MAX_TOKENS,
+  SUPERSESSION_VECTOR_FETCH_LIMIT
+} from "./chunk-B6WVNDA5.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}
+---${body}`, "utf-8");
+  fs.renameSync(tmp, fullPath);
+  indexNote(deps.index, deps.vaultDir, targetPath);
+  deps.vectorIndex?.delete(targetId);
+  return true;
+}
+async function checkSupersession(newSporeId, deps) {
+  const { index, vectorIndex, embeddingProvider, llmProvider, vaultDir, log } = deps;
+  if (!vectorIndex || !llmProvider) {
+    log?.("debug", "checkSupersession: skipped \u2014 vectorIndex or llmProvider unavailable", { newSporeId });
+    return [];
+  }
+  const newSporeResults = index.queryByIds([newSporeId]);
+  if (newSporeResults.length === 0) {
+    log?.("warn", "checkSupersession: new spore not found in index", { newSporeId });
+    return [];
+  }
+  const newSpore = newSporeResults[0];
+  const observationType = newSpore.frontmatter["observation_type"];
+  const embeddingText = newSpore.content.slice(0, EMBEDDING_INPUT_LIMIT);
+  const embeddingResult = await generateEmbedding(embeddingProvider, embeddingText);
+  const vectorResults = vectorIndex.search(embeddingResult.embedding, {
+    type: "spore",
+    limit: SUPERSESSION_VECTOR_FETCH_LIMIT
+  });
+  if (vectorResults.length === 0) {
+    log?.("debug", "checkSupersession: no vector results", { newSporeId });
+    return [];
+  }
+  const candidateIds = vectorResults.map((r) => r.id);
+  const candidateNotes = index.queryByIds(candidateIds);
+  const filtered = candidateNotes.filter((note) => {
+    if (note.id === newSporeId) return false;
+    if (!isActiveSpore(note.frontmatter)) return false;
+    if (observationType && note.frontmatter["observation_type"] !== observationType) return false;
+    return true;
+  }).slice(0, SUPERSESSION_CANDIDATE_LIMIT);
+  if (filtered.length === 0) {
+    log?.("debug", "checkSupersession: no candidates after filtering", { newSporeId, observationType });
+    return [];
+  }
+  const template = loadPrompt("supersession");
+  const newSporeText = `[${newSpore.id}] ${newSpore.title}
+${newSpore.content}`;
+  const candidatesText = filtered.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) {
+    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-FIA5NTRH.js.map

package/dist/chunk-FIA5NTRH.js.map

@@ -0,0 +1 @@
+{"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 } 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 = `[${newSpore.id}] ${newSpore.title}\\n${newSpore.content}`;\n  const candidatesText = filtered\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  // 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', 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package/dist/{chunk-GFBG73P4.js → chunk-FIRMTYFH.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 {
   AgentRegistry
-} from "./chunk-BNIYWCST.js";
+} from "./chunk-X6TKHO22.js";
 
 // src/cli/shared.ts
 import fs from "fs";
@@ -116,4 +116,4 @@ export {
   VAULT_GITIGNORE,
   configureVaultEnv
 };
-//# sourceMappingURL=chunk-GFBG73P4.js.map
+//# sourceMappingURL=chunk-FIRMTYFH.js.map