npm - @goondocks/myco - Versions diffs - 0.6.4 → 0.6.5 - Mend

@goondocks/myco 0.6.4 → 0.6.5

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package/dist/chunk-TK7A4RX7.js.map ADDED Viewed

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+ {"version":3,"sources":["../src/daemon/digest.ts","../src/daemon/trace.ts","../src/daemon/processor.ts","../src/vault/observations.ts","../src/services/vault-ops.ts","../src/intelligence/batch.ts"],"sourcesContent":["/**\n * DigestEngine — synthesizes vault knowledge into tiered context extracts.\n * Metabolism — adaptive timer that throttles digest cycles based on activity.\n */\n\nimport fs from 'node:fs';\nimport path from 'node:path';\nimport crypto from 'node:crypto';\nimport YAML from 'yaml';\n\nimport type { MycoIndex, IndexedNote } from '@myco/index/sqlite.js';\nimport type { LlmProvider, LlmRequestOptions } from '@myco/intelligence/llm.js';\nimport type { MycoConfig } from '@myco/config/schema.js';\nimport { loadPrompt } from '@myco/prompts/index.js';\nimport { stripReasoningTokens } from '@myco/intelligence/response.js';\nimport { stripFrontmatter } from '@myco/vault/frontmatter.js';\nimport { readLastTimestamp, appendTraceRecord } from './trace.js';\nimport {\n estimateTokens,\n CHARS_PER_TOKEN,\n DIGEST_TIERS,\n DIGEST_TIER_MIN_CONTEXT,\n DIGEST_SUBSTRATE_TYPE_WEIGHTS,\n DIGEST_LLM_REQUEST_TIMEOUT_MS,\n LLM_REASONING_MODE,\n} from '@myco/constants.js';\n\n// --- Interfaces ---\n\nexport interface DigestCycleResult {\n cycleId: string;\n timestamp: string;\n substrate: {\n sessions: string[];\n spores: string[];\n plans: string[];\n artifacts: string[];\n team: string[];\n };\n tiersGenerated: number[];\n model: string;\n durationMs: number;\n tokensUsed: number;\n}\n\n/** Simple log function signature for digest progress reporting. */\nexport type DigestLogFn = (level: 'debug' | 'info' | 'warn', message: string, data?: Record<string, unknown>) => void;\n\nexport interface DigestCycleOptions {\n /** Process all substrate regardless of last cycle timestamp. */\n fullReprocess?: boolean;\n /** Only generate these tiers (default: all eligible). */\n tiers?: number[];\n /** Skip previous extract — start from clean slate. */\n cleanSlate?: boolean;\n}\n\nexport interface DigestEngineConfig {\n vaultDir: string;\n index: MycoIndex;\n llmProvider: LlmProvider;\n config: MycoConfig;\n log?: DigestLogFn;\n}\n\n// --- Constants ---\n\n/** Token overhead estimate for previous extract section wrapper. */\nconst PREVIOUS_EXTRACT_OVERHEAD_TOKENS = 50;\n\n/** Safety margin for context window — our CHARS_PER_TOKEN=4 heuristic significantly\n * underestimates real token counts (observed ~3.2 chars/token for mixed content).\n * 0.70 provides a safe buffer: 32K * 0.70 = 22.4K usable tokens. */\nconst CONTEXT_SAFETY_MARGIN = 0.70;\n\n/** Types that are digest output — excluded from substrate to avoid self-digestion. */\nconst EXTRACT_TYPE = 'extract';\n\n// --- DigestEngine ---\n\nexport class DigestEngine {\n private vaultDir: string;\n private index: MycoIndex;\n private llm: LlmProvider;\n private config: MycoConfig;\n private log: DigestLogFn;\n private lastCycleTimestampCache: string | null | undefined = undefined;\n private cycleInProgress = false;\n\n /** Whether a digest cycle is currently running. */\n get isCycleInProgress(): boolean {\n return this.cycleInProgress;\n }\n\n /** Hooks that run before each digest cycle (e.g., consolidation). */\n private prePassHooks: Array<{ name: string; fn: () => Promise<void> }> = [];\n\n /** Hooks that run after each successful digest cycle. */\n private postPassHooks: Array<{ name: string; fn: (result: DigestCycleResult) => Promise<void> }> = [];\n\n constructor(engineConfig: DigestEngineConfig) {\n this.vaultDir = engineConfig.vaultDir;\n this.index = engineConfig.index;\n this.llm = engineConfig.llmProvider;\n this.config = engineConfig.config;\n this.log = engineConfig.log ?? (() => {});\n }\n\n /** Register a hook that runs before each digest cycle. Best-effort — errors are logged, not thrown. */\n registerPrePass(name: string, fn: () => Promise<void>): void {\n this.prePassHooks.push({ name, fn });\n }\n\n /** Register a hook that runs after each successful digest cycle. Best-effort — errors are logged, not thrown. */\n registerPostPass(name: string, fn: (result: DigestCycleResult) => Promise<void>): void {\n this.postPassHooks.push({ name, fn });\n }\n\n /**\n * Query index for recent vault notes to feed into the digest.\n * Filters out extract notes (our own output) and caps at max_notes_per_cycle.\n */\n discoverSubstrate(lastCycleTimestamp: string | null): IndexedNote[] {\n const maxNotes = this.config.digest.substrate.max_notes_per_cycle;\n\n const notes = lastCycleTimestamp\n ? this.index.query({ updatedSince: lastCycleTimestamp, limit: maxNotes })\n : this.index.query({ limit: maxNotes });\n\n // Guard against self-digestion: extract files are not currently indexed,\n // but this filter prevents feedback loops if they ever are (e.g., via rebuild)\n const filtered = notes\n .filter((n) => n.type !== EXTRACT_TYPE)\n .filter((n) => {\n if (n.type !== 'spore') return true;\n const status = n.frontmatter.status as string | undefined;\n return !status || status === 'active';\n });\n\n // Sort by type weight (descending) then by recency (descending)\n filtered.sort((a, b) => {\n const weightA = DIGEST_SUBSTRATE_TYPE_WEIGHTS[a.type] ?? 0;\n const weightB = DIGEST_SUBSTRATE_TYPE_WEIGHTS[b.type] ?? 0;\n if (weightB !== weightA) return weightB - weightA;\n // More recent first — created is ISO string, lexicographic sort works\n return b.created.localeCompare(a.created);\n });\n\n return filtered.slice(0, maxNotes);\n }\n\n /**\n * Filter configured tiers by the context window available.\n * Only tiers whose minimum context requirement is met are eligible.\n */\n getEligibleTiers(): number[] {\n const contextWindow = this.config.digest.intelligence.context_window;\n return DIGEST_TIERS.filter((tier) => {\n const minContext = DIGEST_TIER_MIN_CONTEXT[tier];\n return minContext !== undefined && minContext <= contextWindow;\n });\n }\n\n /**\n * Format notes compactly for inclusion in the digest prompt.\n * Stops adding notes once the token budget is exceeded.\n */\n formatSubstrate(notes: IndexedNote[], tokenBudget: number): string {\n const charBudget = tokenBudget * CHARS_PER_TOKEN;\n const parts: string[] = [];\n let usedChars = 0;\n\n for (const note of notes) {\n const entry = `### [${note.type}] ${note.id} — \"${note.title}\"\\n${note.content}`;\n if (usedChars + entry.length > charBudget && parts.length > 0) break;\n parts.push(entry);\n usedChars += entry.length;\n }\n\n return parts.join('\\n\\n');\n }\n\n /**\n * Read a previously generated extract for a given tier.\n * Returns the body (stripped of YAML frontmatter), or null if not found.\n */\n readPreviousExtract(tier: number): string | null {\n const extractPath = path.join(this.vaultDir, 'digest', `extract-${tier}.md`);\n let content: string;\n try {\n content = fs.readFileSync(extractPath, 'utf-8');\n } catch {\n return null;\n }\n\n return stripFrontmatter(content).body;\n }\n\n /**\n * Write a digest extract to the vault with YAML frontmatter.\n * Uses atomic write pattern (temp file + rename).\n */\n writeExtract(\n tier: number,\n body: string,\n cycleId: string,\n model: string,\n substrateCount: number,\n substrateNotes?: string[],\n tokensUsed?: number,\n ): void {\n const digestDir = path.join(this.vaultDir, 'digest');\n fs.mkdirSync(digestDir, { recursive: true });\n\n const frontmatter: Record<string, unknown> = {\n type: EXTRACT_TYPE,\n tier,\n generated: new Date().toISOString(),\n cycle_id: cycleId,\n substrate_count: substrateCount,\n model,\n };\n if (substrateNotes && substrateNotes.length > 0) frontmatter.substrate_notes = substrateNotes;\n if (tokensUsed !== undefined) frontmatter.tokens_used = tokensUsed;\n\n const fmYaml = YAML.stringify(frontmatter, {\n defaultStringType: 'QUOTE_DOUBLE',\n defaultKeyType: 'PLAIN',\n }).trim();\n const file = `---\\n${fmYaml}\\n---\\n\\n${body}\\n`;\n\n const fullPath = path.join(digestDir, `extract-${tier}.md`);\n const tmpPath = `${fullPath}.tmp`;\n fs.writeFileSync(tmpPath, file, 'utf-8');\n fs.renameSync(tmpPath, fullPath);\n }\n\n /**\n * Append a digest cycle result as a JSON line to trace.jsonl.\n */\n appendTrace(record: DigestCycleResult): void {\n const tracePath = path.join(this.vaultDir, 'digest', 'trace.jsonl');\n appendTraceRecord(tracePath, record as unknown as Record<string, unknown>);\n this.lastCycleTimestampCache = record.timestamp;\n }\n\n /**\n * Read the last cycle timestamp from trace.jsonl.\n * Cached in memory after first read — subsequent calls are O(1).\n */\n getLastCycleTimestamp(): string | null {\n if (this.lastCycleTimestampCache !== undefined) return this.lastCycleTimestampCache;\n\n const tracePath = path.join(this.vaultDir, 'digest', 'trace.jsonl');\n this.lastCycleTimestampCache = readLastTimestamp(tracePath);\n return this.lastCycleTimestampCache;\n }\n\n /**\n * Run a full digest cycle: discover substrate, generate extracts for each tier.\n * Returns the cycle result, or null if no substrate was found.\n */\n async runCycle(opts?: DigestCycleOptions): Promise<DigestCycleResult | null> {\n if (this.cycleInProgress) {\n this.log('debug', 'Cycle already in progress — skipping');\n return null;\n }\n this.cycleInProgress = true;\n\n try {\n // Ensure model is loaded BEFORE pre-pass hooks (e.g., consolidation).\n // Pre-pass hooks share the digest LLM provider — without ensureLoaded first,\n // requests go with just the model name (no instance ID), causing LM Studio\n // to spawn duplicate instances for each concurrent request.\n if (this.llm.ensureLoaded) {\n const { context_window: contextWindow, gpu_kv_cache: gpuKvCache } = this.config.digest.intelligence;\n this.log('debug', 'Verifying digest model', { contextWindow, gpuKvCache });\n await this.llm.ensureLoaded(contextWindow, gpuKvCache);\n }\n\n // Run pre-pass hooks (e.g., consolidation) before discovering substrate\n for (const hook of this.prePassHooks) {\n try {\n await hook.fn();\n } catch (err) {\n this.log('warn', `Pre-pass hook \"${hook.name}\" failed`, { error: (err as Error).message });\n }\n }\n\n return await this.runCycleInternal(opts);\n } finally {\n this.cycleInProgress = false;\n }\n }\n\n private async runCycleInternal(opts?: DigestCycleOptions): Promise<DigestCycleResult | null> {\n\n const startTime = Date.now();\n const fullReprocess = opts?.fullReprocess ?? false;\n const lastTimestamp = fullReprocess ? null : this.getLastCycleTimestamp();\n const substrate = this.discoverSubstrate(lastTimestamp);\n\n this.log('debug', 'Discovering substrate', { lastTimestamp: lastTimestamp ?? 'full reprocess', substrateCount: substrate.length });\n if (substrate.length === 0) {\n this.log('debug', 'No substrate found — skipping cycle');\n return null;\n }\n\n this.log('info', `Starting digest cycle`, { substrateCount: substrate.length, fullReprocess });\n const cycleId = crypto.randomUUID();\n const allEligible = this.getEligibleTiers();\n const eligibleTiers = opts?.tiers\n ? allEligible.filter((t) => opts.tiers!.includes(t))\n : allEligible;\n this.log('debug', `Eligible tiers: [${eligibleTiers.join(', ')}]`);\n const tiersGenerated: number[] = [];\n let totalTokensUsed = 0;\n let model = '';\n\n // Categorize substrate by type for the result\n const typeToKey: Record<string, keyof DigestCycleResult['substrate']> = {\n session: 'sessions',\n spore: 'spores',\n plan: 'plans',\n artifact: 'artifacts',\n 'team-member': 'team',\n };\n const substrateIndex: DigestCycleResult['substrate'] = {\n sessions: [],\n spores: [],\n plans: [],\n artifacts: [],\n team: [],\n };\n for (const note of substrate) {\n const key = typeToKey[note.type];\n if (key) {\n substrateIndex[key].push(note.id);\n }\n }\n\n this.log('debug', 'Substrate breakdown', {\n sessions: substrateIndex.sessions.length,\n spores: substrateIndex.spores.length,\n plans: substrateIndex.plans.length,\n artifacts: substrateIndex.artifacts.length,\n team: substrateIndex.team.length,\n });\n\n // Record the cycle timestamp NOW, before tier processing. This ensures the\n // timestamp advances even if LLM calls fail, preventing the same substrate\n // from being rediscovered on every subsequent timer fire.\n const cycleTimestamp = new Date().toISOString();\n\n const systemPrompt = loadPrompt('digest-system');\n const allSubstrateIds = substrate.map((note) => note.id);\n\n for (const tier of eligibleTiers) {\n const tierPrompt = loadPrompt(`digest-${tier}`);\n const previousExtract = opts?.cleanSlate ? null : this.readPreviousExtract(tier);\n\n // Calculate token budget for substrate:\n // (context_window * safety_margin) - output - system_prompt - tier_prompt - previous_extract\n const contextWindow = this.config.digest.intelligence.context_window;\n const systemPromptTokens = estimateTokens(systemPrompt);\n const tierPromptTokens = estimateTokens(tierPrompt);\n const previousExtractTokens = previousExtract\n ? estimateTokens(previousExtract) + PREVIOUS_EXTRACT_OVERHEAD_TOKENS\n : 0;\n const availableTokens = Math.floor(contextWindow * CONTEXT_SAFETY_MARGIN);\n const substrateBudget = availableTokens - tier - systemPromptTokens - tierPromptTokens - previousExtractTokens;\n\n if (substrateBudget <= 0) continue;\n\n const formattedSubstrate = this.formatSubstrate(substrate, substrateBudget);\n\n // Build user prompt (system prompt sent separately via LlmRequestOptions)\n const promptParts = [tierPrompt];\n\n if (previousExtract) {\n promptParts.push('', '## Previous Synthesis', '', previousExtract);\n }\n\n promptParts.push('', '## New Substrate', '', formattedSubstrate);\n promptParts.push(\n '',\n '---',\n 'Produce your updated synthesis now. Stay within the token budget specified above.',\n );\n\n const userPrompt = promptParts.join('\\n');\n const promptTokens = estimateTokens(systemPrompt + userPrompt);\n this.log('debug', `Tier ${tier}: sending LLM request`, { promptTokens, maxTokens: tier, substrateBudget });\n\n try {\n const tierStart = Date.now();\n const digestConfig = this.config.digest.intelligence;\n const opts: LlmRequestOptions = {\n maxTokens: tier,\n timeoutMs: DIGEST_LLM_REQUEST_TIMEOUT_MS,\n contextLength: contextWindow,\n reasoning: LLM_REASONING_MODE,\n systemPrompt,\n keepAlive: digestConfig.keep_alive ?? undefined,\n };\n const response = await this.llm.summarize(userPrompt, opts);\n const tierDuration = Date.now() - tierStart;\n\n // Strip reasoning tokens if present (some models output chain-of-thought)\n const extractText = stripReasoningTokens(response.text);\n model = response.model;\n const responseTokens = estimateTokens(extractText);\n totalTokensUsed += promptTokens + responseTokens;\n\n this.log('info', `Tier ${tier}: completed`, { durationMs: tierDuration, responseTokens, model: response.model });\n this.writeExtract(tier, extractText, cycleId, response.model, substrate.length, allSubstrateIds, promptTokens + responseTokens);\n tiersGenerated.push(tier);\n } catch (err) {\n this.log('warn', `Tier ${tier}: failed`, { error: (err as Error).message });\n }\n }\n\n // Patch tiers_generated into each extract's frontmatter (not known until all tiers complete)\n if (tiersGenerated.length > 0) {\n const digestDir = path.join(this.vaultDir, 'digest');\n for (const tier of tiersGenerated) {\n const extractPath = path.join(digestDir, `extract-${tier}.md`);\n try {\n const content = fs.readFileSync(extractPath, 'utf-8');\n const fmMatch = content.match(/^---\\n([\\s\\S]*?)\\n---/);\n if (fmMatch) {\n const parsed = YAML.parse(fmMatch[1]) as Record<string, unknown>;\n parsed.tiers_generated = tiersGenerated;\n const fmYaml = YAML.stringify(parsed, { defaultStringType: 'QUOTE_DOUBLE', defaultKeyType: 'PLAIN' }).trim();\n const extractBody = content.slice(fmMatch[0].length);\n const tmpPath = `${extractPath}.tmp`;\n fs.writeFileSync(tmpPath, `---\\n${fmYaml}\\n---${extractBody}`, 'utf-8');\n fs.renameSync(tmpPath, extractPath);\n }\n } catch {\n // Extract file may not exist if that tier failed\n }\n }\n }\n\n const result: DigestCycleResult = {\n cycleId,\n timestamp: cycleTimestamp,\n substrate: substrateIndex,\n tiersGenerated,\n model,\n durationMs: Date.now() - startTime,\n tokensUsed: totalTokensUsed,\n };\n\n this.appendTrace(result);\n\n // Run post-pass hooks after successful digest\n for (const hook of this.postPassHooks) {\n try {\n await hook.fn(result);\n } catch (err) {\n this.log('warn', `Post-pass hook \"${hook.name}\" failed`, { error: (err as Error).message });\n }\n }\n\n return result;\n }\n}\n\n// --- Metabolism (Adaptive Timer) ---\n\nexport type MetabolismState = 'active' | 'cooling' | 'dormant';\n\n/** Milliseconds per second for config conversion. */\nconst MS_PER_SECOND = 1000;\n\nexport class Metabolism {\n state: MetabolismState = 'active';\n currentIntervalMs: number;\n\n private cooldownStep = 0;\n private lastSubstrateTime: number;\n private timer: ReturnType<typeof setTimeout> | null = null;\n private activeIntervalMs: number;\n private cooldownIntervalsMs: number[];\n private dormancyThresholdMs: number;\n\n constructor(config: MycoConfig['digest']['metabolism']) {\n this.activeIntervalMs = config.active_interval * MS_PER_SECOND;\n this.cooldownIntervalsMs = config.cooldown_intervals.map((s) => s * MS_PER_SECOND);\n this.dormancyThresholdMs = config.dormancy_threshold * MS_PER_SECOND;\n this.currentIntervalMs = this.activeIntervalMs;\n this.lastSubstrateTime = Date.now();\n }\n\n /** Reset to active state when new substrate is found. */\n onSubstrateFound(): void {\n this.state = 'active';\n this.cooldownStep = 0;\n this.currentIntervalMs = this.activeIntervalMs;\n this.lastSubstrateTime = Date.now();\n }\n\n /** Advance cooldown when a cycle finds no new substrate. */\n onEmptyCycle(): void {\n if (this.state === 'dormant') return;\n\n this.state = 'cooling';\n if (this.cooldownStep < this.cooldownIntervalsMs.length) {\n this.currentIntervalMs = this.cooldownIntervalsMs[this.cooldownStep];\n this.cooldownStep++;\n }\n\n this.checkDormancy();\n }\n\n /** Enter dormant state if enough time has elapsed since last substrate. */\n checkDormancy(): void {\n const elapsed = Date.now() - this.lastSubstrateTime;\n if (elapsed >= this.dormancyThresholdMs) {\n this.state = 'dormant';\n // Keep the last cooldown interval as the dormant polling rate\n }\n }\n\n /** Return to active from any state, resetting timers and rescheduling immediately. */\n activate(): void {\n this.onSubstrateFound();\n // Reschedule with the new active interval — without this, the old\n // (possibly dormant) timer continues ticking at the wrong rate\n if (this.callback) {\n this.reschedule();\n }\n }\n\n /** Set lastSubstrateTime explicitly (for testing). */\n markLastSubstrate(time: number): void {\n this.lastSubstrateTime = time;\n }\n\n /** Begin scheduling digest cycles with adaptive intervals. */\n start(callback: () => Promise<void>): void {\n this.callback = callback;\n this.reschedule();\n }\n\n /** Stop the timer. */\n stop(): void {\n if (this.timer) {\n clearTimeout(this.timer);\n this.timer = null;\n }\n }\n\n private callback: (() => Promise<void>) | null = null;\n\n private reschedule(): void {\n this.stop();\n if (!this.callback) return;\n const cb = this.callback;\n const schedule = (): void => {\n this.timer = setTimeout(async () => {\n await cb();\n schedule();\n }, this.currentIntervalMs);\n this.timer.unref();\n };\n schedule();\n }\n}\n","/**\n * Shared JSONL trace file utilities.\n *\n * Used by DigestEngine and ConsolidationEngine to read/write append-only\n * trace records with timestamp caching.\n */\n\nimport fs from 'node:fs';\nimport path from 'node:path';\n\n/** Read the last JSON record from a JSONL file. Returns null if file is missing or empty. */\nexport function readLastRecord<T = Record<string, unknown>>(filePath: string): T | null {\n let content: string;\n try {\n content = fs.readFileSync(filePath, 'utf-8').trim();\n } catch {\n return null;\n }\n if (!content) return null;\n const lines = content.split('\\n');\n const lastLine = lines[lines.length - 1];\n try {\n return JSON.parse(lastLine) as T;\n } catch {\n return null;\n }\n}\n\n/** Read the last JSON record's `timestamp` field from a JSONL file. Returns null if file is missing or empty. */\nexport function readLastTimestamp(filePath: string): string | null {\n return readLastRecord<{ timestamp: string }>(filePath)?.timestamp ?? null;\n}\n\n/** Append a JSON record to a JSONL file, creating parent directories if needed. */\nexport function appendTraceRecord(filePath: string, record: Record<string, unknown>): void {\n fs.mkdirSync(path.dirname(filePath), { recursive: true });\n fs.appendFileSync(filePath, JSON.stringify(record) + '\\n', 'utf-8');\n}\n","import { z } from 'zod';\nimport type { LlmProvider } from '../intelligence/llm.js';\nimport { ARTIFACT_TYPES } from '../vault/types.js';\nimport { estimateTokens, CHARS_PER_TOKEN, LLM_REASONING_MODE } from '../constants.js';\nimport type { MycoConfig } from '../config/schema.js';\nimport type { ObservationType, ArtifactType } from '../vault/types.js';\nimport { buildExtractionPrompt, buildSummaryPrompt, buildTitlePrompt, buildClassificationPrompt } from '../prompts/index.js';\nimport { extractJson, stripReasoningTokens } from '../intelligence/response.js';\nimport { TURN_HEADING_PREFIX } from '../obsidian/formatter.js';\n\n/** Estimated token overhead for the extraction prompt template (excluding conversation content). */\nconst EXTRACTION_PROMPT_OVERHEAD_TOKENS = 500;\n\n/** Marker substring in failed summary text. Used by reprocess --failed to detect failures. */\nexport const SUMMARIZATION_FAILED_MARKER = 'summarization failed';\n\nexport interface Observation {\n type: ObservationType;\n title: string;\n content: string;\n tags: string[];\n root_cause?: string;\n fix?: string;\n rationale?: string;\n alternatives_rejected?: string;\n gained?: string;\n sacrificed?: string;\n}\n\nexport interface ProcessorResult {\n summary: string;\n observations: Observation[];\n degraded: boolean;\n}\n\nexport interface ClassifiedArtifact {\n source_path: string;\n artifact_type: ArtifactType;\n title: string;\n tags: string[];\n}\n\nconst ClassificationResponseSchema = z.object({\n artifacts: z.array(z.object({\n source_path: z.string(),\n artifact_type: z.enum(ARTIFACT_TYPES),\n title: z.string(),\n tags: z.array(z.string()).default([]),\n })).default([]),\n});\n\nexport class BufferProcessor {\n private extractionMaxTokens: number;\n private summaryMaxTokens: number;\n private titleMaxTokens: number;\n private classificationMaxTokens: number;\n\n constructor(private backend: LlmProvider, private contextWindow: number = 8192, captureConfig?: MycoConfig['capture']) {\n this.extractionMaxTokens = captureConfig?.extraction_max_tokens ?? 2048;\n this.summaryMaxTokens = captureConfig?.summary_max_tokens ?? 512;\n this.titleMaxTokens = captureConfig?.title_max_tokens ?? 32;\n this.classificationMaxTokens = captureConfig?.classification_max_tokens ?? 1024;\n }\n\n private truncateForContext(data: string, maxTokens: number): string {\n const available = this.contextWindow - maxTokens;\n const dataTokens = estimateTokens(data);\n if (dataTokens <= available) return data;\n const charBudget = available * CHARS_PER_TOKEN;\n return data.slice(0, charBudget);\n }\n\n async process(conversationMarkdown: string, sessionId: string): Promise<ProcessorResult> {\n if (!conversationMarkdown.trim()) {\n return { summary: '', observations: [], degraded: false };\n }\n\n // Truncate from the beginning (keep recent turns) if conversation exceeds budget\n const availableTokens = this.contextWindow - EXTRACTION_PROMPT_OVERHEAD_TOKENS - this.extractionMaxTokens;\n const availableChars = availableTokens * CHARS_PER_TOKEN;\n let truncated = conversationMarkdown;\n if (conversationMarkdown.length > availableChars) {\n truncated = conversationMarkdown.slice(-availableChars);\n // Find first turn boundary to avoid cutting mid-turn\n const turnBoundary = truncated.indexOf(TURN_HEADING_PREFIX);\n if (turnBoundary > 0) {\n truncated = truncated.slice(turnBoundary);\n }\n }\n\n const prompt = buildExtractionPrompt(sessionId, truncated, this.extractionMaxTokens);\n\n try {\n const response = await this.backend.summarize(prompt, {\n maxTokens: this.extractionMaxTokens,\n reasoning: LLM_REASONING_MODE,\n });\n const parsed = extractJson(response.text) as {\n summary: string;\n observations: Observation[];\n };\n return {\n summary: parsed.summary,\n observations: parsed.observations ?? [],\n degraded: false,\n };\n } catch (error) {\n return {\n summary: `LLM processing failed for session ${sessionId}. Error: ${(error as Error).message}`,\n observations: [],\n degraded: true,\n };\n }\n }\n\n async summarizeSession(\n conversationMarkdown: string,\n sessionId: string,\n user?: string,\n ): Promise<{ summary: string; title: string }> {\n const truncatedContent = this.truncateForContext(conversationMarkdown, this.summaryMaxTokens);\n const summaryPrompt = buildSummaryPrompt(sessionId, user ?? 'unknown', truncatedContent, this.summaryMaxTokens);\n\n let summaryText: string;\n try {\n const response = await this.backend.summarize(summaryPrompt, { maxTokens: this.summaryMaxTokens, reasoning: LLM_REASONING_MODE });\n summaryText = stripReasoningTokens(response.text);\n } catch (error) {\n summaryText = `Session ${sessionId} — ${SUMMARIZATION_FAILED_MARKER}: ${(error as Error).message}`;\n }\n\n const titlePrompt = buildTitlePrompt(summaryText, sessionId);\n let title: string;\n try {\n const response = await this.backend.summarize(titlePrompt, { maxTokens: this.titleMaxTokens, reasoning: LLM_REASONING_MODE });\n title = stripReasoningTokens(response.text).trim();\n } catch {\n title = `Session ${sessionId}`;\n }\n\n return { summary: summaryText, title };\n }\n\n async classifyArtifacts(\n candidates: Array<{ path: string; content: string }>,\n sessionId: string,\n ): Promise<ClassifiedArtifact[]> {\n if (candidates.length === 0) return [];\n\n const prompt = this.buildPromptForClassification(candidates, sessionId);\n const response = await this.backend.summarize(prompt, { maxTokens: this.classificationMaxTokens, reasoning: LLM_REASONING_MODE });\n const raw = extractJson(response.text);\n const parsed = ClassificationResponseSchema.parse(raw);\n return parsed.artifacts;\n }\n\n private buildPromptForClassification(\n candidates: Array<{ path: string; content: string }>,\n sessionId: string,\n ): string {\n return buildClassificationPrompt(sessionId, candidates, this.classificationMaxTokens);\n }\n\n}\n","import { formatSporeBody } from '../obsidian/formatter.js';\nimport { sessionNoteId } from './session-id.js';\nimport { indexNote } from '../index/rebuild.js';\nimport type { Observation } from '../daemon/processor.js';\nimport type { VaultWriter } from './writer.js';\nimport type { MycoIndex } from '../index/sqlite.js';\n\nexport interface WrittenNote {\n id: string;\n path: string;\n observation: Observation;\n}\n\nexport function writeObservationNotes(\n observations: Observation[],\n sessionId: string,\n writer: VaultWriter,\n index: MycoIndex,\n vaultDir: string,\n): WrittenNote[] {\n const results: WrittenNote[] = [];\n\n for (const obs of observations) {\n const obsId = `${obs.type}-${sessionId.slice(-6)}-${Date.now()}`;\n const body = formatSporeBody({\n title: obs.title,\n observationType: obs.type,\n content: obs.content,\n sessionId,\n root_cause: obs.root_cause,\n fix: obs.fix,\n rationale: obs.rationale,\n alternatives_rejected: obs.alternatives_rejected,\n gained: obs.gained,\n sacrificed: obs.sacrificed,\n tags: obs.tags,\n });\n const relativePath = writer.writeSpore({\n id: obsId,\n observation_type: obs.type,\n session: sessionNoteId(sessionId),\n tags: obs.tags,\n content: body,\n });\n indexNote(index, vaultDir, relativePath);\n results.push({ id: obsId, path: relativePath, observation: obs });\n }\n\n return results;\n}\n","import fs from 'node:fs';\nimport path from 'node:path';\nimport type { MycoIndex } from '../index/sqlite.js';\nimport type { VectorIndex } from '../index/vectors.js';\nimport type { MycoConfig } from '../config/schema.js';\nimport type { LlmProvider, EmbeddingProvider } from '../intelligence/llm.js';\nimport type { DigestCycleResult, DigestLogFn } from '../daemon/digest.js';\nimport { rebuildIndex, indexNote } from '../index/rebuild.js';\nimport { initFts } from '../index/fts.js';\nimport { generateEmbedding } from '../intelligence/embeddings.js';\nimport { batchExecute, LLM_BATCH_CONCURRENCY, EMBEDDING_BATCH_CONCURRENCY } from '../intelligence/batch.js';\nimport { DigestEngine } from '../daemon/digest.js';\nimport type { DigestCycleOptions } from '../daemon/digest.js';\nimport { BufferProcessor, SUMMARIZATION_FAILED_MARKER } from '../daemon/processor.js';\nimport { VaultWriter } from '../vault/writer.js';\nimport { writeObservationNotes } from '../vault/observations.js';\nimport { sessionNoteId, bareSessionId } from '../vault/session-id.js';\nimport { callout, extractSection, CONVERSATION_HEADING } from '../obsidian/formatter.js';\nimport matter from 'gray-matter';\nimport {\n EMBEDDING_INPUT_LIMIT,\n CURATION_CLUSTER_SIMILARITY,\n SUPERSESSION_MAX_TOKENS,\n LLM_REASONING_MODE,\n} from '../constants.js';\nimport { stripReasoningTokens } from '../intelligence/response.js';\nimport { loadPrompt, formatNoteForPrompt, formatNotesForPrompt } from '../prompts/index.js';\nimport { supersedeSpore, supersededIdsSchema, isActiveSpore } from '../vault/curation.js';\nimport type { PipelineManager } from '../daemon/pipeline.js';\n\nexport interface OperationContext {\n vaultDir: string;\n config: MycoConfig;\n index: MycoIndex;\n vectorIndex?: VectorIndex;\n pipeline?: PipelineManager;\n log?: (level: string, message: string, data?: Record<string, unknown>) => void;\n}\n\n// --- Rebuild ---\n\nexport interface RebuildResult {\n ftsCount: number;\n embeddedCount: number;\n failedCount: number;\n skippedCount: number;\n}\n\n/**\n * Rebuild FTS index and re-embed all active notes.\n * Core logic shared between CLI (`myco rebuild`) and daemon API (`POST /api/rebuild`).\n */\nexport async function runRebuild(\n ctx: OperationContext,\n embeddingProvider: EmbeddingProvider,\n onProgress?: (done: number, total: number) => void,\n): Promise<RebuildResult> {\n const { index, vaultDir } = ctx;\n\n // Phase 1: FTS rebuild\n initFts(index);\n const ftsCount = rebuildIndex(index, vaultDir);\n\n // Phase 2: Vector embeddings\n if (!ctx.vectorIndex) {\n return { ftsCount, embeddedCount: 0, failedCount: 0, skippedCount: 0 };\n }\n\n const allNotes = index.query({});\n // Skip superseded/archived spores\n const activeNotes = allNotes.filter((n) => {\n const status = (n.frontmatter as Record<string, unknown>)?.status as string | undefined;\n return status !== 'superseded' && status !== 'archived';\n });\n const skippedCount = allNotes.length - activeNotes.length;\n\n const vec = ctx.vectorIndex;\n const result = await batchExecute(\n activeNotes,\n async (note) => {\n const text = `${note.title}\\n${note.content}`.slice(0, EMBEDDING_INPUT_LIMIT);\n const emb = await generateEmbedding(embeddingProvider, text);\n vec.upsert(note.id, emb.embedding, {\n type: note.type,\n session_id: (note.frontmatter as Record<string, unknown>)?.session as string ?? '',\n });\n },\n {\n concurrency: EMBEDDING_BATCH_CONCURRENCY,\n onProgress,\n },\n );\n\n // Register embedding results in the pipeline when available\n if (ctx.pipeline) {\n for (const note of activeNotes) {\n ctx.pipeline.register(note.id, note.type, note.path);\n ctx.pipeline.advance(note.id, note.type, 'capture', 'succeeded');\n ctx.pipeline.advance(note.id, note.type, 'embedding', 'succeeded');\n }\n }\n\n return {\n ftsCount,\n embeddedCount: result.succeeded,\n failedCount: result.failed,\n skippedCount,\n };\n}\n\n// --- Digest ---\n\nexport interface DigestOptions {\n tier?: number;\n full?: boolean;\n}\n\n/**\n * Run a single digest cycle.\n * Core logic shared between CLI (`myco digest`) and daemon API (`POST /api/digest`).\n *\n * When a PipelineManager is available in ctx.pipeline and `--full` is set,\n * all pipeline items are reset to digest:pending so the metabolism timer\n * picks them up. Regular (non-full) digest runs the engine directly.\n */\nexport async function runDigest(\n ctx: OperationContext,\n llmProvider: LlmProvider,\n options?: DigestOptions,\n): Promise<DigestCycleResult | null> {\n const { config, vaultDir, index } = ctx;\n const log: DigestLogFn = ctx.log\n ? (level, message, data) => ctx.log!(level, message, data)\n : () => {};\n\n // Pipeline mode for --full: reset digest stages to pending and let\n // the metabolism timer handle the actual digest cycle.\n if (ctx.pipeline && options?.full) {\n const items = ctx.pipeline.listItems({ stage: 'digest', status: 'succeeded' });\n let reset = 0;\n for (const item of items.items) {\n ctx.pipeline.advance(item.id, item.item_type, 'digest', 'pending');\n reset++;\n }\n log('info', `Reset ${reset} item(s) to digest:pending for full reprocessing`);\n // Return null to indicate no immediate cycle was run; the metabolism\n // timer will pick up the pending items on its next tick.\n return null;\n }\n\n const engine = new DigestEngine({\n vaultDir,\n index,\n llmProvider,\n config,\n log,\n });\n\n const opts: DigestCycleOptions = {};\n const isReprocess = options?.full || options?.tier !== undefined;\n\n if (isReprocess) {\n opts.fullReprocess = true;\n opts.cleanSlate = true;\n }\n if (options?.tier !== undefined) {\n const eligible = engine.getEligibleTiers();\n if (!eligible.includes(options.tier)) {\n throw new Error(`Tier ${options.tier} is not eligible. Eligible tiers: [${eligible.join(', ')}]`);\n }\n opts.tiers = [options.tier];\n }\n\n return engine.runCycle(opts);\n}\n\n// --- Curation ---\n\nexport interface CurationDeps {\n vaultDir: string;\n config: MycoConfig;\n index: MycoIndex;\n vectorIndex: VectorIndex;\n llmProvider: LlmProvider;\n embeddingProvider: EmbeddingProvider;\n log?: (level: string, message: string, data?: Record<string, unknown>) => void;\n pipeline?: PipelineManager;\n}\n\n// --- Curation internals ---\n\n/** Max concurrent embedding requests to avoid overwhelming the provider. */\nconst CURATION_EMBEDDING_BATCH_SIZE = 10;\n\ninterface SporeWithEmbedding {\n id: string;\n path: string;\n title: string;\n content: string;\n created: string;\n frontmatter: Record<string, unknown>;\n embedding: number[];\n}\n\ninterface Cluster {\n spores: SporeWithEmbedding[];\n centroid: number[];\n}\n\nfunction cosineSimilarity(a: number[], b: number[]): number {\n let dot = 0, normA = 0, normB = 0;\n for (let i = 0; i < a.length; i++) {\n dot += a[i] * b[i];\n normA += a[i] * a[i];\n normB += b[i] * b[i];\n }\n return dot / (Math.sqrt(normA) * Math.sqrt(normB));\n}\n\nfunction updateCentroid(spores: SporeWithEmbedding[]): number[] {\n if (spores.length === 0) return [];\n const dim = spores[0].embedding.length;\n const centroid = new Array<number>(dim).fill(0);\n for (const s of spores) {\n for (let i = 0; i < dim; i++) {\n centroid[i] += s.embedding[i];\n }\n }\n for (let i = 0; i < dim; i++) {\n centroid[i] /= spores.length;\n }\n return centroid;\n}\n\nfunction clusterSpores(spores: SporeWithEmbedding[]): Cluster[] {\n const clusters: Cluster[] = [];\n for (const spore of spores) {\n let bestCluster: Cluster | null = null;\n let bestSimilarity = -1;\n for (const cluster of clusters) {\n const sim = cosineSimilarity(spore.embedding, cluster.centroid);\n if (sim > bestSimilarity) {\n bestSimilarity = sim;\n bestCluster = cluster;\n }\n }\n if (bestCluster !== null && bestSimilarity >= CURATION_CLUSTER_SIMILARITY) {\n bestCluster.spores.push(spore);\n bestCluster.centroid = updateCentroid(bestCluster.spores);\n } else {\n clusters.push({ spores: [spore], centroid: [...spore.embedding] });\n }\n }\n return clusters;\n}\n\nexport interface CurationResult {\n scanned: number;\n clustersEvaluated: number;\n superseded: number;\n /** True when spores were enqueued via pipeline instead of curated inline. */\n enqueued?: boolean;\n}\n\n/**\n * Run vault curation: embed spores, cluster, ask LLM which are outdated, supersede.\n * Core logic shared between CLI (`myco curate`) and daemon API (`POST /api/curate`).\n *\n * When a PipelineManager is available in deps.pipeline, active spores are\n * registered at consolidation:pending for the pipeline tick to handle.\n * When no pipeline is available, falls back to inline curation.\n */\nexport async function runCuration(\n deps: CurationDeps,\n dryRun: boolean,\n): Promise<CurationResult> {\n const { index, vectorIndex, llmProvider, embeddingProvider, vaultDir } = deps;\n const log = deps.log ?? (() => {});\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 // --- Pipeline mode: enqueue spores for consolidation via pipeline tick ---\n if (deps.pipeline && !dryRun) {\n let enqueued = 0;\n for (const spore of activeSpores) {\n deps.pipeline.register(spore.id, 'spore', spore.path);\n deps.pipeline.advance(spore.id, 'spore', 'capture', 'succeeded');\n deps.pipeline.advance(spore.id, 'spore', 'consolidation', 'pending');\n enqueued++;\n }\n log('info', `Enqueued ${enqueued} spore(s) for pipeline consolidation`);\n return { scanned: activeSpores.length, clustersEvaluated: 0, superseded: 0, enqueued: true };\n }\n\n if (activeSpores.length === 0) {\n return { scanned: 0, clustersEvaluated: 0, superseded: 0 };\n }\n\n // 2. Embed all active spores (batched for concurrency)\n const sporesWithEmbeddings: SporeWithEmbedding[] = [];\n let embedFailures = 0;\n\n for (let i = 0; i < activeSpores.length; i += CURATION_EMBEDDING_BATCH_SIZE) {\n const batch = activeSpores.slice(i, i + CURATION_EMBEDDING_BATCH_SIZE);\n const results = await Promise.allSettled(\n batch.map(async (spore) => {\n const text = spore.content.slice(0, EMBEDDING_INPUT_LIMIT);\n const result = await generateEmbedding(embeddingProvider, text);\n return { spore, embedding: result.embedding };\n }),\n );\n\n for (const result of results) {\n if (result.status === 'fulfilled') {\n const { spore, embedding } = result.value;\n sporesWithEmbeddings.push({\n id: spore.id,\n path: spore.path,\n title: spore.title,\n content: spore.content,\n created: spore.created,\n frontmatter: spore.frontmatter,\n embedding,\n });\n } else {\n embedFailures++;\n }\n }\n }\n\n if (embedFailures > 0) {\n log('warn', `${embedFailures} spore(s) could not be embedded and were skipped`);\n }\n\n // 3. Group by observation_type\n const byType = new Map<string, SporeWithEmbedding[]>();\n for (const spore of sporesWithEmbeddings) {\n const obsType = (spore.frontmatter['observation_type'] as string | undefined) ?? 'unknown';\n if (!byType.has(obsType)) byType.set(obsType, []);\n byType.get(obsType)!.push(spore);\n }\n\n // 4. Cluster within each type group\n const template = loadPrompt('supersession');\n let totalClusters = 0;\n let totalSuperseded = 0;\n\n for (const [obsType, typeSpores] of byType) {\n const clusters = clusterSpores(typeSpores);\n const multiSpore = clusters.filter((c) => c.spores.length >= 2);\n if (multiSpore.length === 0) continue;\n\n log('info', `Type: ${obsType} — ${typeSpores.length} spores, ${multiSpore.length} cluster(s) to evaluate`);\n totalClusters += multiSpore.length;\n\n for (const cluster of multiSpore) {\n const sorted = [...cluster.spores].sort((a, b) => a.created.localeCompare(b.created));\n const newest = sorted[sorted.length - 1];\n const candidates = sorted.slice(0, sorted.length - 1);\n\n // Build supersession prompt\n const newSporeText = formatNoteForPrompt(newest);\n const candidatesText = formatNotesForPrompt(candidates);\n\n const prompt = template\n .replace('{{new_spore}}', newSporeText)\n .replace('{{candidates}}', candidatesText);\n\n // 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 log('warn', `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 log('warn', `Could not parse LLM response for cluster in ${obsType}`);\n continue;\n }\n\n const parsed = supersededIdsSchema.safeParse(rawIds);\n if (!parsed.success) {\n log('warn', `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 if (validIds.length === 0) continue;\n\n for (const id of validIds) {\n const candidate = candidateMap.get(id)!;\n\n if (dryRun) {\n log('info', `[dry-run] Would supersede: ${candidate.title} (${id}) by ${newest.title} (${newest.id})`);\n totalSuperseded++;\n continue;\n }\n\n const wrote = supersedeSpore(id, newest.id, candidate.path, { index, vectorIndex, vaultDir });\n if (!wrote) {\n log('warn', `File not found for ${id}, skipping write`);\n continue;\n }\n\n log('info', `Superseded: ${candidate.title} (${id}) by ${newest.title} (${newest.id})`);\n totalSuperseded++;\n }\n }\n }\n\n return {\n scanned: activeSpores.length,\n clustersEvaluated: totalClusters,\n superseded: totalSuperseded,\n };\n}\n\n// --- Reprocess ---\n\nexport interface ReprocessOptions {\n /** Filter to sessions matching this substring. */\n session?: string;\n /** Filter to sessions from a specific date (YYYY-MM-DD). */\n date?: string;\n /** Only reprocess sessions with failed summaries. */\n failed?: boolean;\n /** Skip LLM calls — re-index and re-embed only. */\n indexOnly?: boolean;\n}\n\nexport interface ReprocessResult {\n sessionsFound: number;\n sessionsProcessed: number;\n observationsExtracted: number;\n summariesRegenerated: number;\n embeddingsQueued: number;\n /** True when sessions were enqueued via pipeline instead of processed inline. */\n enqueued?: boolean;\n}\n\n\n/**\n * Replace the title (first `# ` line) and summary callout in a session note body.\n * Handles both cases: existing callout (replace) and no callout (insert after title).\n */\nexport function updateTitleAndSummary(body: string, newTitle: string, newNarrative: string): string {\n let updated = body.replace(/^# .*/m, `# ${newTitle}`);\n const summaryCallout = callout('abstract', 'Summary', newNarrative);\n const hasExistingCallout = /> \\[!abstract\\] Summary/.test(updated);\n if (hasExistingCallout) {\n updated = updated.replace(/> \\[!abstract\\] Summary\\n(?:> .*\\n?)*/m, summaryCallout + '\\n');\n } else {\n // Insert callout after the title line\n updated = updated.replace(/^(# .*\\n)/m, `$1\\n${summaryCallout}\\n`);\n }\n return updated;\n}\n\n/**\n * Reprocess sessions: re-extract observations, regenerate summaries, re-index.\n * Core logic shared between CLI (`myco reprocess`) and daemon API (`POST /api/reprocess`).\n *\n * When a PipelineManager is available in ctx.pipeline, sessions are registered\n * at extraction:pending for the pipeline tick to handle. When no pipeline is\n * available (standalone CLI), falls back to inline processing.\n */\nexport async function runReprocess(\n ctx: OperationContext,\n llmProvider: LlmProvider | null,\n embeddingProvider: EmbeddingProvider,\n options?: ReprocessOptions,\n onProgress?: (phase: string, done: number, total: number) => void,\n): Promise<ReprocessResult> {\n const { vaultDir, config, index } = ctx;\n const log = ctx.log ?? (() => {});\n\n const sessionFilter = options?.session;\n const dateFilter = options?.date;\n const failedOnly = options?.failed ?? false;\n const skipLlm = options?.indexOnly ?? false;\n\n // Find sessions (shared between pipeline and legacy modes)\n const sessionsDir = path.join(vaultDir, 'sessions');\n if (!fs.existsSync(sessionsDir)) {\n return { sessionsFound: 0, sessionsProcessed: 0, observationsExtracted: 0, summariesRegenerated: 0, embeddingsQueued: 0 };\n }\n\n const sessionFiles: Array<{ relativePath: string; sessionId: string; dateDir: string }> = [];\n for (const dateDir of fs.readdirSync(sessionsDir)) {\n if (dateFilter && dateDir !== dateFilter) continue;\n const datePath = path.join(sessionsDir, dateDir);\n if (!fs.statSync(datePath).isDirectory()) continue;\n for (const file of fs.readdirSync(datePath)) {\n if (!file.startsWith('session-') || !file.endsWith('.md')) continue;\n const sessionId = file.replace('session-', '').replace('.md', '');\n if (sessionFilter && !sessionId.includes(sessionFilter)) continue;\n sessionFiles.push({ relativePath: path.join('sessions', dateDir, file), sessionId, dateDir });\n }\n }\n\n if (sessionFiles.length === 0) {\n return { sessionsFound: 0, sessionsProcessed: 0, observationsExtracted: 0, summariesRegenerated: 0, embeddingsQueued: 0 };\n }\n\n // --- Pipeline mode: enqueue sessions for extraction via pipeline tick ---\n if (ctx.pipeline && !skipLlm) {\n let enqueued = 0;\n\n // Pre-filter for failed-only if requested\n let eligibleFiles = sessionFiles;\n if (failedOnly) {\n eligibleFiles = sessionFiles.filter(({ relativePath }) => {\n const rawContent = fs.readFileSync(path.join(vaultDir, relativePath), 'utf-8');\n return rawContent.includes(SUMMARIZATION_FAILED_MARKER);\n });\n }\n\n for (const { relativePath, sessionId } of eligibleFiles) {\n // Register (idempotent) and reset extraction to pending\n ctx.pipeline.register(sessionId, 'session', relativePath);\n ctx.pipeline.advance(sessionId, 'session', 'capture', 'succeeded');\n ctx.pipeline.advance(sessionId, 'session', 'extraction', 'pending');\n enqueued++;\n }\n\n log('info', `Enqueued ${enqueued} session(s) for pipeline reprocessing`, {\n filters: { session: sessionFilter, date: dateFilter, failed: failedOnly },\n });\n\n return {\n sessionsFound: sessionFiles.length,\n sessionsProcessed: enqueued,\n observationsExtracted: 0,\n summariesRegenerated: 0,\n embeddingsQueued: 0,\n enqueued: true,\n };\n }\n\n // --- Legacy inline mode (no pipeline) ---\n const effectiveLlm = skipLlm ? null : llmProvider;\n const processor = effectiveLlm\n ? new BufferProcessor(effectiveLlm, config.intelligence.llm.context_window, config.capture)\n : null;\n const writer = new VaultWriter(vaultDir);\n\n // Prepare tasks\n interface SessionTask {\n relativePath: string;\n sessionId: string;\n bare: string;\n frontmatter: Record<string, unknown>;\n frontmatterBlock: string;\n body: string;\n conversationSection: string;\n hasFailed: boolean;\n }\n\n const tasks: SessionTask[] = [];\n for (const { relativePath, sessionId } of sessionFiles) {\n const rawContent = fs.readFileSync(path.join(vaultDir, relativePath), 'utf-8');\n\n // Quick pre-screen before expensive parsing when filtering to failed sessions only\n const hasFailed = rawContent.includes(SUMMARIZATION_FAILED_MARKER);\n if (failedOnly && !hasFailed) continue;\n\n const { data: frontmatter, content: body } = matter(rawContent);\n const bare = bareSessionId(sessionId);\n const conversationSection = extractSection(body, CONVERSATION_HEADING);\n const fmEnd = rawContent.indexOf('---', 4);\n const frontmatterBlock = rawContent.slice(0, fmEnd + 3);\n\n tasks.push({ relativePath, sessionId, bare, frontmatter, frontmatterBlock, body, conversationSection, hasFailed });\n }\n\n if (tasks.length === 0) {\n return { sessionsFound: sessionFiles.length, sessionsProcessed: 0, observationsExtracted: 0, summariesRegenerated: 0, embeddingsQueued: 0 };\n }\n\n log('info', `Reprocessing ${tasks.length} session(s)`, { filters: { session: sessionFilter, date: dateFilter, failed: failedOnly, indexOnly: skipLlm } });\n\n // Fire-and-forget embedding helper — pipelines embeddings as data is produced\n // instead of accumulating all jobs in memory for a separate phase.\n let embeddingsQueued = 0;\n const embedPending: Promise<void>[] = [];\n const fireEmbed = (id: string, text: string, metadata: Record<string, string>) => {\n if (!ctx.vectorIndex) return;\n embeddingsQueued++;\n const vec = ctx.vectorIndex;\n const p = generateEmbedding(embeddingProvider, text)\n .then((emb) => { vec.upsert(id, emb.embedding, metadata); })\n .catch((err) => { log('warn', `Embedding failed for ${id}`, { error: (err as Error).message }); });\n embedPending.push(p);\n };\n\n // Phase 1: Extraction + FTS re-indexing + inline embeddings\n let totalObservations = 0;\n\n const extractionResult = await batchExecute(\n tasks,\n async (task) => {\n let obs = 0;\n\n if (processor && task.conversationSection.trim()) {\n const result = await processor.process(task.conversationSection, task.bare);\n if (result.observations.length > 0) {\n writeObservationNotes(result.observations, task.bare, writer, index, vaultDir);\n obs = result.observations.length;\n for (const o of result.observations) {\n fireEmbed(\n `${o.type}-${task.bare.slice(-6)}-${Date.now()}`,\n `${o.title}\\n${o.content}`.slice(0, EMBEDDING_INPUT_LIMIT),\n { type: 'spore', session_id: task.bare },\n );\n }\n }\n }\n\n indexNote(index, vaultDir, task.relativePath);\n\n const embText = `${task.frontmatter.title ?? ''}\\n${task.frontmatter.summary ?? 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package/dist/{chunk-UP4P4OAA.js → chunk-V6BJVYNH.js} RENAMED Viewed

@@ -14,7 +14,7 @@ import {
   SUPERSESSION_MAX_TOKENS,
   SUPERSESSION_VECTOR_FETCH_LIMIT,
   TURN_MAX_FILES_DISPLAYED
-} from "./chunk-J4D4CROB.js";
+} from "./chunk-DYDBF5W6.js";
 import {
   __commonJS,
   __require,
@@ -4420,4 +4420,4 @@ strip-bom-string/index.js:
    * Released under the MIT License.
    *)
 */
-//# sourceMappingURL=chunk-UP4P4OAA.js.map
+//# sourceMappingURL=chunk-V6BJVYNH.js.map

package/dist/{chunk-QN4W3JUA.js → chunk-XH34FX4C.js} RENAMED Viewed

@@ -1,7 +1,7 @@
 import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
 import {
   AgentRegistry
-} from "./chunk-Z74SDEKE.js";
+} from "./chunk-F7GAYVWF.js";
 // src/version.ts
 import fs from "fs";
@@ -40,4 +40,4 @@ function readVersionFrom(dir) {
 export {
   getPluginVersion
 };
-//# sourceMappingURL=chunk-QN4W3JUA.js.map
+//# sourceMappingURL=chunk-XH34FX4C.js.map

package/dist/{chunk-YTFXA4RX.js → chunk-YRIIBPJD.js} RENAMED Viewed

@@ -2,10 +2,10 @@ import { createRequire as __cr } from 'node:module'; const require = __cr(import
 import {
   LmStudioBackend,
   OllamaBackend
-} from "./chunk-7WHF2OIZ.js";
+} from "./chunk-4DYD4HHG.js";
 import {
   AgentRegistry
-} from "./chunk-Z74SDEKE.js";
+} from "./chunk-F7GAYVWF.js";
 // src/cli/shared.ts
 import fs from "fs";
@@ -83,4 +83,4 @@ export {
   VAULT_GITIGNORE,
   configureVaultEnv
 };
-//# sourceMappingURL=chunk-YTFXA4RX.js.map
+//# sourceMappingURL=chunk-YRIIBPJD.js.map

package/dist/{cli-IHILSS6N.js → cli-OJYHLO4Y.js} RENAMED Viewed

@@ -2,14 +2,14 @@
 import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
 import {
   loadEnv
-} from "./chunk-YTFXA4RX.js";
+} from "./chunk-YRIIBPJD.js";
 import "./chunk-SAKJMNSR.js";
-import "./chunk-7WHF2OIZ.js";
+import "./chunk-4DYD4HHG.js";
 import {
   resolveVaultDir
 } from "./chunk-N33KUCFP.js";
-import "./chunk-Z74SDEKE.js";
-import "./chunk-J4D4CROB.js";
+import "./chunk-F7GAYVWF.js";
+import "./chunk-DYDBF5W6.js";
 import "./chunk-PZUWP5VK.js";
 // src/cli.ts
@@ -43,10 +43,10 @@ async function main() {
     process.stdout.write(USAGE);
     return;
   }
-  if (cmd === "init") return (await import("./init-ARQ53JOR.js")).run(args);
-  if (cmd === "detect-providers") return (await import("./detect-providers-XEP4QA3R.js")).run(args);
+  if (cmd === "init") return (await import("./init-3LVKVQ4L.js")).run(args);
+  if (cmd === "detect-providers") return (await import("./detect-providers-LFIVJYQO.js")).run(args);
   if (cmd === "version" || cmd === "--version" || cmd === "-v") {
-    const { getPluginVersion } = await import("./version-36RVCQA6.js");
+    const { getPluginVersion } = await import("./version-XE4GYTBV.js");
     console.log(getPluginVersion());
     return;
   }
@@ -59,31 +59,31 @@ async function main() {
     case "config":
       return (await import("./config-IBS6KOLQ.js")).run(args, vaultDir);
     case "curate":
-      return (await import("./curate-3D4GHKJH.js")).run(args, vaultDir);
+      return (await import("./curate-4CKEMOPV.js")).run(args, vaultDir);
     case "verify":
-      return (await import("./verify-TOWQHPBX.js")).run(args, vaultDir);
+      return (await import("./verify-X272WGBD.js")).run(args, vaultDir);
     case "stats":
-      return (await import("./stats-TTSDXGJV.js")).run(args, vaultDir);
+      return (await import("./stats-QBLIEFWL.js")).run(args, vaultDir);
     case "search":
-      return (await import("./search-7W25SKCB.js")).run(args, vaultDir);
+      return (await import("./search-BQLBW5CS.js")).run(args, vaultDir);
     case "vectors":
-      return (await import("./search-7W25SKCB.js")).runVectors(args, vaultDir);
+      return (await import("./search-BQLBW5CS.js")).runVectors(args, vaultDir);
     case "session":
       return (await import("./session-F326AWCH.js")).run(args, vaultDir);
     case "setup-llm":
-      return (await import("./setup-llm-S5OHQJXK.js")).run(args, vaultDir);
+      return (await import("./setup-llm-QBSTQO7N.js")).run(args, vaultDir);
     case "setup-digest":
-      return (await import("./setup-digest-X5PN27F4.js")).run(args, vaultDir);
+      return (await import("./setup-digest-X735EZSD.js")).run(args, vaultDir);
     case "digest":
-      return (await import("./digest-7HLJXL77.js")).run(args, vaultDir);
+      return (await import("./digest-ZLARHLLY.js")).run(args, vaultDir);
     case "restart":
-      return (await import("./restart-XCMILOL5.js")).run(args, vaultDir);
+      return (await import("./restart-UIP7US4U.js")).run(args, vaultDir);
     case "rebuild":
-      return (await import("./rebuild-Q2ACEB6F.js")).run(args, vaultDir);
+      return (await import("./rebuild-QWVVCBCZ.js")).run(args, vaultDir);
     case "reprocess":
-      return (await import("./reprocess-CDEFGQOV.js")).run(args, vaultDir);
+      return (await import("./reprocess-YG3WLUI2.js")).run(args, vaultDir);
     case "logs":
-      return (await import("./logs-IENORIYR.js")).run(args, vaultDir);
+      return (await import("./logs-6CWVP574.js")).run(args, vaultDir);
     default:
       console.error(`Unknown command: ${cmd}`);
       process.stdout.write(USAGE);
@@ -94,4 +94,4 @@ main().catch((err) => {
   console.error(`myco: ${err.message}`);
   process.exit(1);
 });
-//# sourceMappingURL=cli-IHILSS6N.js.map
+//# sourceMappingURL=cli-OJYHLO4Y.js.map

package/dist/{client-AGFNR2S4.js → client-SS3C5MF6.js} RENAMED Viewed

@@ -1,12 +1,12 @@
 import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
 import {
   DaemonClient
-} from "./chunk-YIQLYIHW.js";
-import "./chunk-QN4W3JUA.js";
-import "./chunk-Z74SDEKE.js";
-import "./chunk-J4D4CROB.js";
+} from "./chunk-4B5RO2YV.js";
+import "./chunk-XH34FX4C.js";
+import "./chunk-F7GAYVWF.js";
+import "./chunk-DYDBF5W6.js";
 import "./chunk-PZUWP5VK.js";
 export {
   DaemonClient
 };
-//# sourceMappingURL=client-AGFNR2S4.js.map
+//# sourceMappingURL=client-SS3C5MF6.js.map

package/dist/{curate-3D4GHKJH.js → curate-4CKEMOPV.js} RENAMED Viewed

@@ -1,27 +1,27 @@
 import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
 import {
   runCuration
-} from "./chunk-4XVKZ3WA.js";
+} from "./chunk-TK7A4RX7.js";
 import {
   VectorIndex
 } from "./chunk-4RMSHZE4.js";
-import "./chunk-UP4P4OAA.js";
+import "./chunk-V6BJVYNH.js";
 import "./chunk-RGVBGTD6.js";
 import {
   createEmbeddingProvider,
   createLlmProvider
-} from "./chunk-NLUE6CYG.js";
+} from "./chunk-54WVLTKD.js";
 import "./chunk-GENQ5QGP.js";
 import "./chunk-6FQISQNA.js";
 import {
   MycoIndex
 } from "./chunk-TWSTAVLO.js";
-import "./chunk-7WHF2OIZ.js";
+import "./chunk-4DYD4HHG.js";
 import {
   loadConfig
 } from "./chunk-HYVT345Y.js";
 import "./chunk-ERG2IEWX.js";
-import "./chunk-J4D4CROB.js";
+import "./chunk-DYDBF5W6.js";
 import "./chunk-PZUWP5VK.js";
 // src/cli/curate.ts
@@ -75,4 +75,4 @@ Curation complete:`);
 export {
   run
 };
-//# sourceMappingURL=curate-3D4GHKJH.js.map
+//# sourceMappingURL=curate-4CKEMOPV.js.map

package/dist/{detect-providers-XEP4QA3R.js → detect-providers-LFIVJYQO.js} RENAMED Viewed

@@ -2,10 +2,10 @@ import { createRequire as __cr } from 'node:module'; const require = __cr(import
 import {
   LmStudioBackend,
   OllamaBackend
-} from "./chunk-7WHF2OIZ.js";
+} from "./chunk-4DYD4HHG.js";
 import {
   PROVIDER_DETECT_TIMEOUT_MS
-} from "./chunk-J4D4CROB.js";
+} from "./chunk-DYDBF5W6.js";
 import "./chunk-PZUWP5VK.js";
 // src/cli/detect-providers.ts
@@ -32,4 +32,4 @@ async function run(_args) {
 export {
   run
 };
-//# sourceMappingURL=detect-providers-XEP4QA3R.js.map
+//# sourceMappingURL=detect-providers-LFIVJYQO.js.map

package/dist/{digest-7HLJXL77.js → digest-ZLARHLLY.js} RENAMED Viewed

@@ -1,28 +1,28 @@
 import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
 import {
   runDigest
-} from "./chunk-4XVKZ3WA.js";
-import "./chunk-UP4P4OAA.js";
+} from "./chunk-TK7A4RX7.js";
+import "./chunk-V6BJVYNH.js";
 import "./chunk-RGVBGTD6.js";
 import {
   createLlmProvider
-} from "./chunk-NLUE6CYG.js";
+} from "./chunk-54WVLTKD.js";
 import "./chunk-GENQ5QGP.js";
 import "./chunk-6FQISQNA.js";
 import {
   MycoIndex
 } from "./chunk-TWSTAVLO.js";
-import "./chunk-YTFXA4RX.js";
+import "./chunk-YRIIBPJD.js";
 import {
   parseIntFlag
 } from "./chunk-SAKJMNSR.js";
-import "./chunk-7WHF2OIZ.js";
+import "./chunk-4DYD4HHG.js";
 import {
   loadConfig
 } from "./chunk-HYVT345Y.js";
 import "./chunk-ERG2IEWX.js";
-import "./chunk-Z74SDEKE.js";
-import "./chunk-J4D4CROB.js";
+import "./chunk-F7GAYVWF.js";
+import "./chunk-DYDBF5W6.js";
 import "./chunk-PZUWP5VK.js";
 // src/cli/digest.ts
@@ -82,4 +82,4 @@ Digest cycle complete:`);
 export {
   run
 };
-//# sourceMappingURL=digest-7HLJXL77.js.map
+//# sourceMappingURL=digest-ZLARHLLY.js.map

package/dist/{init-ARQ53JOR.js → init-3LVKVQ4L.js} RENAMED Viewed

@@ -14,11 +14,11 @@ import {
 import {
   VAULT_GITIGNORE,
   configureVaultEnv
-} from "./chunk-YTFXA4RX.js";
+} from "./chunk-YRIIBPJD.js";
 import {
   parseStringFlag
 } from "./chunk-SAKJMNSR.js";
-import "./chunk-7WHF2OIZ.js";
+import "./chunk-4DYD4HHG.js";
 import {
   MycoConfigSchema,
   require_dist
@@ -26,8 +26,8 @@ import {
 import {
   resolveVaultDir
 } from "./chunk-N33KUCFP.js";
-import "./chunk-Z74SDEKE.js";
-import "./chunk-J4D4CROB.js";
+import "./chunk-F7GAYVWF.js";
+import "./chunk-DYDBF5W6.js";
 import {
   __toESM
 } from "./chunk-PZUWP5VK.js";
@@ -106,4 +106,4 @@ async function run3(args) {
 export {
   run3 as run
 };
-//# sourceMappingURL=init-ARQ53JOR.js.map
+//# sourceMappingURL=init-3LVKVQ4L.js.map

package/dist/{logs-IENORIYR.js → logs-6CWVP574.js} RENAMED Viewed

@@ -3,10 +3,10 @@ import {
   DEFAULT_LOG_TAIL,
   matchesFilter,
   queryLogs
-} from "./chunk-H7PRCVGQ.js";
+} from "./chunk-F7PGDD2X.js";
 import {
   LEVEL_ORDER
-} from "./chunk-QLUE3BUL.js";
+} from "./chunk-O6TBHGVO.js";
 import {
   formatLogLine,
   parseIntFlag,
@@ -81,4 +81,4 @@ function run(args, vaultDir) {
 export {
   run
 };
-//# sourceMappingURL=logs-IENORIYR.js.map
+//# sourceMappingURL=logs-6CWVP574.js.map