@goondocks/myco 0.14.2 → 0.14.3

package/dist/executor-YX2MA4T3.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/agent/executor.ts","../src/agent/tools.ts","../src/db/queries/agent-state.ts","../src/agent/context.ts","../src/agent/orchestrator.ts","../src/intelligence/response.ts","../src/agent/context-queries.ts","../src/agent/provider.ts"],"sourcesContent":["/**\n * Agent executor.\n *\n * Orchestrates a single agent run:\n *   1. Initializes the database for the vault.\n *   2. Resolves effective config (definition + agent DB overrides + task).\n *   3. Guards against concurrent runs for the same agent.\n *   4. Creates a run record in the database.\n *   5. Builds the task prompt (vault context + task + optional instruction).\n *   6. Executes the Claude Agent SDK query — single call for flat tasks,\n *      wave-based parallel execution for phased tasks.\n *   7. Records cost/token data and marks the run completed or failed.\n */\n\nimport crypto from 'node:crypto';\nimport { resolve } from 'node:path';\nimport { epochSeconds, DEFAULT_AGENT_ID, MS_PER_SECOND, PHASE_SUMMARY_MAX_CHARS } from '@myco/constants.js';\nimport { errorMessage as toErrorMessage } from '@myco/utils/error-message.js';\nimport { initDatabase, vaultDbPath, getDatabase } from '@myco/db/client.js';\nimport { createSchema } from '@myco/db/schema.js';\nimport { getAgent } from '@myco/db/queries/agents.js';\nimport { getTask, getDefaultTask } from '@myco/db/queries/tasks.js';\nimport {\n  insertRun,\n  updateRunStatus,\n  getRunningRunForTask,\n  STATUS_RUNNING,\n  STATUS_COMPLETED,\n  STATUS_FAILED,\n} from '@myco/db/queries/runs.js';\nimport {\n  resolveDefinitionsDir,\n  loadAgentDefinition,\n  loadSystemPrompt,\n  resolveEffectiveConfig,\n} from './loader.js';\nimport { loadAllTasks } from './registry.js';\nimport { createVaultToolServer, createScopedVaultToolServer } from './tools.js';\nimport { buildVaultContext } from './context.js';\nimport { composeOrchestratorPrompt, parseOrchestratorPlan, applyDirectives, DEFAULT_ORCHESTRATOR_MAX_TURNS } from './orchestrator.js';\nimport { executeContextQueries } from './context-queries.js';\nimport { buildPhaseEnv } from './provider.js';\nimport { loadConfig } from '@myco/config/loader.js';\nimport type { ContextQueryResult } from './context-queries.js';\nimport type { ProviderConfig } from './types.js';\nimport type {\n  RunOptions,\n  AgentRunResult,\n  EffectiveConfig,\n  PhaseDefinition,\n  PhaseResult,\n} from './types.js';\n\n// ---------------------------------------------------------------------------\n// Constants\n// ---------------------------------------------------------------------------\n\n/** Run status returned when a concurrent run is already active. */\nconst STATUS_SKIPPED = 'skipped';\n\n/** Reason string when skipping due to concurrency guard. */\nconst SKIP_REASON_ALREADY_RUNNING = 'already_running';\n\n/** Section header for vault context in the composed prompt. */\nconst PROMPT_SECTION_TASK = '## Task: ';\n\n/** Section header for user instruction in the composed prompt. */\nconst PROMPT_SECTION_INSTRUCTION = '## User Instruction';\n\n/** Separator between prompt sections. */\nconst PROMPT_SECTION_SEPARATOR = '\\n\\n';\n\n/** MCP server name for the vault tool server. */\nconst MCP_SERVER_NAME = 'myco-vault';\n\n/** Whether to persist the agent session to disk. */\nconst PERSIST_SESSION = true;\n\n/** Header for prior phase context in phased prompts. */\nconst PROMPT_SECTION_PRIOR_PHASES = '## Prior Phase Results';\n\n/** Header for the current phase in phased prompts. */\nconst PROMPT_SECTION_CURRENT_PHASE = '## Current Phase: ';\n\n// ---------------------------------------------------------------------------\n// Prompt composition\n// ---------------------------------------------------------------------------\n\n/**\n * Build the full task prompt from vault context, task definition, and\n * optional user instruction.\n *\n * Task prompts support template variables:\n * - `{{session_id}}` — replaced with the session ID from instruction (if present)\n * - `{{instruction}}` — the raw user instruction text\n */\nexport function composeTaskPrompt(\n  vaultContext: string,\n  taskDisplayName: string,\n  taskPrompt: string,\n  instruction?: string,\n): string {\n  // Extract session_id from instruction if it contains one (UUID pattern)\n  const sessionIdMatch = instruction?.match(/\\b([0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12})\\b/i);\n  const sessionId = sessionIdMatch?.[1] ?? '';\n\n  // Template variable substitution in task prompt\n  let resolvedPrompt = taskPrompt;\n  resolvedPrompt = resolvedPrompt.replace(/\\{\\{session_id\\}\\}/g, sessionId);\n  resolvedPrompt = resolvedPrompt.replace(/\\{\\{instruction\\}\\}/g, instruction ?? '');\n\n  const parts = [\n    vaultContext,\n    `${PROMPT_SECTION_TASK}${taskDisplayName}\\n${resolvedPrompt}`,\n  ];\n\n  if (instruction) {\n    parts.push(`${PROMPT_SECTION_INSTRUCTION}\\n${instruction}`);\n  }\n\n  return parts.join(PROMPT_SECTION_SEPARATOR);\n}\n\n/**\n * Build the prompt for a single phase in a phased execution.\n *\n * Includes vault context, the task overview, prior phase summaries,\n * and the current phase instructions.\n */\nexport function composePhasePrompt(\n  vaultContext: string,\n  taskDisplayName: string,\n  taskOverview: string,\n  phase: PhaseDefinition,\n  priorPhaseResults: PhaseResult[],\n  instruction?: string,\n): string {\n  const parts = [\n    vaultContext,\n    `${PROMPT_SECTION_TASK}${taskDisplayName}\\n${taskOverview}`,\n  ];\n\n  if (instruction) {\n    parts.push(`${PROMPT_SECTION_INSTRUCTION}\\n${instruction}`);\n  }\n\n  // Include prior phase results as context (unless the phase opts out)\n  if (priorPhaseResults.length > 0 && !phase.skipPriorContext) {\n    const summaries = priorPhaseResults.map((pr) => {\n      const truncated = pr.summary.length > PHASE_SUMMARY_MAX_CHARS\n        ? pr.summary.slice(0, PHASE_SUMMARY_MAX_CHARS) + '...'\n        : pr.summary;\n      return `### ${pr.name} (${pr.status})\\n${truncated}`;\n    });\n    parts.push(`${PROMPT_SECTION_PRIOR_PHASES}\\n${summaries.join('\\n\\n')}`);\n  }\n\n  // Current phase instructions\n  parts.push(`${PROMPT_SECTION_CURRENT_PHASE}${phase.name}\\n${phase.prompt}`);\n\n  return parts.join(PROMPT_SECTION_SEPARATOR);\n}\n\n// ---------------------------------------------------------------------------\n// Ollama model pre-loading\n// ---------------------------------------------------------------------------\n\n/** Timeout for Ollama model pre-load request (ms). */\nconst OLLAMA_PRELOAD_TIMEOUT_MS = 30_000;\n\n/**\n * Ensure an Ollama model variant exists with the desired context length.\n *\n * The Anthropic-compatible endpoint (/v1/messages) always loads models at\n * default context — it ignores /api/chat preloads and API-created params.\n * The only reliable way is `ollama create` with a Modelfile containing\n * `PARAMETER num_ctx`. Creates a variant named `{model}-ctx{contextLength}`.\n *\n * Returns the variant model name to use.\n */\nasync function ensureOllamaContextVariant(\n  model: string,\n  contextLength: number,\n): Promise<string> {\n  const { execFileSync } = await import('node:child_process');\n  const { writeFileSync, unlinkSync } = await import('node:fs');\n  const { tmpdir } = await import('node:os');\n  const { join } = await import('node:path');\n\n  const baseName = model.replace(/:latest$/, '');\n  const variantName = `${baseName}-ctx${contextLength}`;\n\n  try {\n    // Check if variant already exists\n    execFileSync('ollama', ['show', variantName], { stdio: 'ignore' });\n    return variantName;\n  } catch {\n    // Doesn't exist — create it\n  }\n\n  try {\n    const modelfilePath = join(tmpdir(), `myco-modelfile-${Date.now()}`);\n    writeFileSync(modelfilePath, `FROM ${model}\\nPARAMETER num_ctx ${contextLength}\\n`);\n    execFileSync('ollama', ['create', variantName, '-f', modelfilePath], {\n      stdio: 'ignore',\n      timeout: OLLAMA_PRELOAD_TIMEOUT_MS,\n    });\n    try { unlinkSync(modelfilePath); } catch { /* cleanup best-effort */ }\n    return variantName;\n  } catch {\n    return model; // Fall back to original\n  }\n}\n\n// ---------------------------------------------------------------------------\n// Wave computation (Kahn's algorithm)\n// ---------------------------------------------------------------------------\n\n/**\n * Compute execution waves from phase dependency graph.\n *\n * Uses Kahn's algorithm to topologically sort phases into waves.\n * Phases in the same wave have no dependencies on each other and\n * can execute in parallel via Promise.allSettled().\n *\n * @throws Error if circular dependencies are detected.\n */\nexport function computeWaves(phases: PhaseDefinition[]): PhaseDefinition[][] {\n  const nameToPhase = new Map(phases.map(p => [p.name, p]));\n  const inDegree = new Map<string, number>();\n  const dependents = new Map<string, string[]>(); // dependency → phases that depend on it\n\n  // Initialize\n  for (const phase of phases) {\n    inDegree.set(phase.name, 0);\n    dependents.set(phase.name, []);\n  }\n\n  // Build adjacency — skip dependencies on phases not in the set\n  // (they may have been removed by orchestrator directives)\n  for (const phase of phases) {\n    const deps = phase.dependsOn ?? [];\n    for (const dep of deps) {\n      if (!nameToPhase.has(dep)) continue; // skipped/removed phase — treat as satisfied\n      inDegree.set(phase.name, (inDegree.get(phase.name) ?? 0) + 1);\n      dependents.get(dep)!.push(phase.name);\n    }\n  }\n\n  // Collect waves\n  const waves: PhaseDefinition[][] = [];\n  const completed = new Set<string>();\n\n  while (completed.size < phases.length) {\n    // Find all phases with zero unsatisfied deps\n    const wave: PhaseDefinition[] = [];\n    for (const phase of phases) {\n      if (completed.has(phase.name)) continue;\n      if ((inDegree.get(phase.name) ?? 0) === 0) {\n        wave.push(phase);\n      }\n    }\n\n    if (wave.length === 0) {\n      const remaining = phases.filter(p => !completed.has(p.name)).map(p => p.name);\n      throw new Error(`Circular dependency detected among phases: ${remaining.join(', ')}`);\n    }\n\n    waves.push(wave);\n\n    // Mark wave as completed and decrement dependents' in-degrees\n    for (const phase of wave) {\n      completed.add(phase.name);\n      for (const dependent of (dependents.get(phase.name) ?? [])) {\n        inDegree.set(dependent, (inDegree.get(dependent) ?? 0) - 1);\n      }\n    }\n  }\n\n  return waves;\n}\n\n// ---------------------------------------------------------------------------\n// Session ID generation\n// ---------------------------------------------------------------------------\n\n/**\n * Generate a deterministic session ID (UUID format) for a phase.\n * Derived from run ID + phase name so the same run always produces\n * the same session IDs.\n */\nfunction phaseSessionId(runId: string, phaseName: string): string {\n  const hash = crypto.createHash('sha256').update(`${runId}-${phaseName}`).digest('hex');\n  // Format as UUID: 8-4-4-4-12\n  return [\n    hash.slice(0, 8),\n    hash.slice(8, 12),\n    hash.slice(12, 16),\n    hash.slice(16, 20),\n    hash.slice(20, 32),\n  ].join('-');\n}\n\n// ---------------------------------------------------------------------------\n// Single-phase execution helper\n// ---------------------------------------------------------------------------\n\n/**\n * Execute a single phase query.\n *\n * Isolated helper that runs one query() call with scoped tools,\n * provider env, and phase-specific config.\n */\nasync function executePhase(\n  query: typeof import('@anthropic-ai/claude-agent-sdk').query,\n  phasePrompt: string,\n  phaseModel: string,\n  systemPrompt: string,\n  toolServer: ReturnType<typeof createScopedVaultToolServer>,\n  phase: PhaseDefinition,\n  env: Record<string, string | undefined> | undefined,\n  sessionId?: string,\n  abortController?: AbortController,\n): Promise<PhaseResult> {\n  let phaseCost = 0;\n  let phaseTokens = 0;\n  let phaseTurns = 0;\n  let phaseSummary = '';\n\n  try {\n    for await (const message of query({\n      prompt: phasePrompt,\n      options: {\n        model: phaseModel,\n        systemPrompt,\n        mcpServers: { [MCP_SERVER_NAME]: toolServer },\n        strictMcpConfig: true,\n        maxTurns: phase.maxTurns,\n        permissionMode: 'bypassPermissions',\n        allowDangerouslySkipPermissions: true,\n        persistSession: PERSIST_SESSION,\n        env,\n        tools: [],\n        ...(sessionId ? { sessionId } : {}),\n        ...(abortController ? { abortController } : {}),\n      },\n    })) {\n      if (message.type === 'result') {\n        phaseCost = message.total_cost_usd ?? 0;\n        phaseTokens =\n          (message.usage.input_tokens ?? 0) + (message.usage.output_tokens ?? 0);\n        phaseTurns = message.num_turns ?? 0;\n        if ('result' in message && typeof message.result === 'string') {\n          phaseSummary = message.result;\n        }\n      }\n    }\n\n    if (phase.required && phaseTurns === 0) {\n      console.warn(`[agent] Required phase \"${phase.name}\" produced 0 turns`);\n    }\n\n    return {\n      name: phase.name,\n      status: 'completed',\n      turnsUsed: phaseTurns,\n      tokensUsed: phaseTokens,\n      costUsd: phaseCost,\n      summary: phaseSummary,\n    };\n  } catch (err) {\n    return {\n      name: phase.name,\n      status: 'failed',\n      turnsUsed: phaseTurns,\n      tokensUsed: phaseTokens,\n      costUsd: phaseCost,\n      summary: `Error: ${toErrorMessage(err)}`,\n    };\n  }\n}\n\n// ---------------------------------------------------------------------------\n// Single-query execution (non-phased tasks)\n// ---------------------------------------------------------------------------\n\n/**\n * Execute a single query() call for non-phased tasks.\n *\n * @returns tokens used, cost, and status.\n */\nasync function executeSingleQuery(\n  config: EffectiveConfig,\n  systemPrompt: string,\n  taskPrompt: string,\n  agentId: string,\n  runId: string,\n  provider?: ProviderConfig,\n  embeddingManager?: RunOptions['embeddingManager'],\n  abortController?: AbortController,\n  vaultDir?: string,\n): Promise<{ tokensUsed: number; costUsd: number }> {\n  const { query } = await import('@anthropic-ai/claude-agent-sdk');\n  const toolServer = createVaultToolServer(agentId, runId, { embeddingManager, vaultDir });\n  const baseEnv = buildPhaseEnv(provider);\n  const env = { ...(baseEnv ?? process.env), MYCO_AGENT_SESSION: '1' };\n  // Model priority: provider model override → task YAML model\n  const effectiveModel = provider?.model ?? config.model;\n\n  let resultCostUsd = 0;\n  let resultTokens = 0;\n\n  for await (const message of query({\n    prompt: taskPrompt,\n    options: {\n      model: effectiveModel,\n      systemPrompt,\n      mcpServers: { [MCP_SERVER_NAME]: toolServer },\n      strictMcpConfig: true,\n      maxTurns: config.maxTurns,\n      permissionMode: 'bypassPermissions',\n      allowDangerouslySkipPermissions: true,\n      persistSession: PERSIST_SESSION,\n      env,\n      tools: [],\n      ...(abortController ? { abortController } : {}),\n    },\n  })) {\n    if (message.type === 'result') {\n      resultCostUsd = message.total_cost_usd ?? 0;\n      resultTokens =\n        (message.usage.input_tokens ?? 0) + (message.usage.output_tokens ?? 0);\n    }\n  }\n\n  return { tokensUsed: resultTokens, costUsd: resultCostUsd };\n}\n\n// ---------------------------------------------------------------------------\n// Phased execution (wave-based parallel)\n// ---------------------------------------------------------------------------\n\n/**\n * Execute a phased task — wave-based parallel query() calls.\n *\n * Phases are sorted into waves via `computeWaves()`. Phases within the same\n * wave execute concurrently via `Promise.allSettled()`. Each phase gets:\n * - Scoped tools (only the tools listed in the phase definition)\n * - Its own turn budget (maxTurns)\n * - Optional model override (falls back to task/agent model)\n * - Isolated provider env (via SDK `env` option — no process.env mutation)\n * - Context from prior wave results\n * - Deterministic session ID derived from run ID + phase name\n *\n * The executor controls the loop — the LLM cannot skip phases.\n */\nasync function executePhasedQuery(\n  config: EffectiveConfig,\n  systemPrompt: string,\n  vaultContext: string,\n  agentId: string,\n  runId: string,\n  taskProviderOverride?: ProviderConfig,\n  phaseProviderOverrides?: Record<string, { provider?: ProviderConfig; maxTurns?: number }>,\n  instruction?: string,\n  embeddingManager?: RunOptions['embeddingManager'],\n  abortController?: AbortController,\n  projectRoot?: string,\n  vaultDir?: string,\n): Promise<{ tokensUsed: number; costUsd: number; phases: PhaseResult[] }> {\n  const { query } = await import('@anthropic-ai/claude-agent-sdk');\n\n  const phases = config.phases!;\n  const phaseResults: PhaseResult[] = [];\n  let totalTokens = 0;\n  let totalCost = 0;\n  let runningTurnCount = 0;\n\n  // ---------------------------------------------------------------------------\n  // Orchestrator planning (opt-in via config.orchestrator.enabled)\n  // ---------------------------------------------------------------------------\n\n  let effectivePhases = [...phases];\n\n  if (config.orchestrator?.enabled) {\n    // 1. Run context queries (if any)\n    const contextQueries = config.contextQueries\n      ? Object.values(config.contextQueries).flat()\n      : [];\n    const contextResults: ContextQueryResult[] = contextQueries.length > 0\n      ? await executeContextQueries(agentId, contextQueries)\n      : [];\n\n    // 2. Compose orchestrator prompt\n    const orchestratorPrompt = composeOrchestratorPrompt(vaultContext, phases, contextResults);\n    const orchestratorModel = config.orchestrator.model ?? config.model;\n    const orchestratorMaxTurns = config.orchestrator.maxTurns ?? DEFAULT_ORCHESTRATOR_MAX_TURNS;\n\n    // 3. Call orchestrator (no tools — planning only)\n    let planResponse = '';\n    for await (const message of query({\n      prompt: orchestratorPrompt,\n      options: {\n        model: orchestratorModel,\n        maxTurns: orchestratorMaxTurns,\n        permissionMode: 'bypassPermissions',\n        allowDangerouslySkipPermissions: true,\n        persistSession: PERSIST_SESSION,\n        tools: [],\n      },\n    })) {\n      if (message.type === 'result' && 'result' in message && typeof message.result === 'string') {\n        planResponse = message.result;\n      }\n    }\n\n    // 4. Parse plan and apply directives\n    const plan = parseOrchestratorPlan(planResponse, phases);\n    effectivePhases = applyDirectives(phases, plan.phases);\n  }\n\n  // ---------------------------------------------------------------------------\n  // Wave-based phase execution\n  // ---------------------------------------------------------------------------\n\n  // Build a map from phase name to its YAML declaration order for stable output\n  const declarationOrder = new Map(phases.map((p, i) => [p.name, i]));\n\n  const waves = computeWaves(effectivePhases);\n\n  for (const wave of waves) {\n    const executions = wave.map((phase, indexInWave) => {\n      const phasePrompt = composePhasePrompt(\n        vaultContext,\n        config.taskDisplayName,\n        config.taskPrompt,\n        phase,\n        phaseResults,\n        instruction,\n      );\n\n      // Apply myco.yaml per-phase overrides (maxTurns, provider)\n      const phaseOverride = phaseProviderOverrides?.[phase.name];\n      const effectiveMaxTurns = phaseOverride?.maxTurns ?? phase.maxTurns;\n\n      // Model priority: phase YAML → myco.yaml phase provider → myco.yaml task provider → task YAML\n      const phaseModel = phase.model ?? phaseOverride?.provider?.model ?? taskProviderOverride?.model ?? config.model;\n      const toolServer = createScopedVaultToolServer(\n        agentId,\n        runId,\n        phase.tools,\n        {\n          turnOffset: runningTurnCount + (indexInWave * effectiveMaxTurns),\n          embeddingManager,\n          projectRoot,\n          vaultDir,\n        },\n      );\n\n      // Provider priority: phase YAML → myco.yaml phase → myco.yaml task → task YAML execution → default\n      const phaseProvider = phase.provider ?? phaseOverride?.provider ?? taskProviderOverride ?? config.execution?.provider;\n      const baseEnv = buildPhaseEnv(phaseProvider);\n      const env = { ...(baseEnv ?? process.env), MYCO_AGENT_SESSION: '1' };\n      const sessionId = phaseSessionId(runId, phase.name);\n\n      // Pass effective maxTurns to executePhase via a modified phase object\n      const effectivePhase = effectiveMaxTurns !== phase.maxTurns\n        ? { ...phase, maxTurns: effectiveMaxTurns }\n        : phase;\n\n      return executePhase(query, phasePrompt, phaseModel, systemPrompt, toolServer, effectivePhase, env, sessionId, abortController);\n    });\n\n    const settled = await Promise.allSettled(executions);\n\n    // Map settled results to PhaseResult[]\n    const waveResults: PhaseResult[] = settled.map((outcome, i) => {\n      if (outcome.status === 'fulfilled') {\n        return outcome.value;\n      }\n      // Promise.allSettled rejected — shouldn't happen since executePhase catches,\n      // but handle defensively\n      return {\n        name: wave[i].name,\n        status: 'failed' as const,\n        turnsUsed: 0,\n        tokensUsed: 0,\n        costUsd: 0,\n        summary: `Error: ${toErrorMessage(outcome.reason)}`,\n      };\n    });\n\n    // Sort by YAML declaration order for stable output\n    waveResults.sort((a, b) =>\n      (declarationOrder.get(a.name) ?? 0) - (declarationOrder.get(b.name) ?? 0),\n    );\n\n    // Accumulate results and totals\n    for (const result of waveResults) {\n      phaseResults.push(result);\n      totalTokens += result.tokensUsed;\n      totalCost += result.costUsd;\n      runningTurnCount += result.turnsUsed;\n    }\n\n    // If any required phase in this wave failed, stop the pipeline\n    const shouldStop = wave.some((phase, i) => {\n      if (!phase.required) return false;\n      const outcome = settled[i];\n      if (outcome.status === 'rejected') return true;\n      return outcome.value.status === 'failed';\n    });\n\n    if (shouldStop) {\n      break;\n    }\n  }\n\n  return { tokensUsed: totalTokens, costUsd: totalCost, phases: phaseResults };\n}\n\n// ---------------------------------------------------------------------------\n// Public API\n// ---------------------------------------------------------------------------\n\n/**\n * Run an agent against a vault.\n *\n * For tasks with a `phases` array, uses wave-based parallel execution\n * (phases sorted into dependency waves via Kahn's algorithm). For tasks\n * without phases, uses a single query() call.\n *\n * @param vaultDir — absolute path to the vault directory.\n * @param options — optional overrides for agent, task, and instruction.\n * @returns the run result with status, token usage, and cost.\n */\nexport async function runAgent(\n  vaultDir: string,\n  options?: RunOptions,\n): Promise<AgentRunResult> {\n  // 1. Init DB (idempotent — returns existing instance if already open)\n  const db = initDatabase(vaultDbPath(vaultDir));\n  createSchema(db);\n\n  const agentId = options?.agentId ?? DEFAULT_AGENT_ID;\n\n  // 2. Concurrency guard — block duplicate runs of the SAME task, not all tasks.\n  // Different tasks (e.g., full-intelligence and skill-generate) can run concurrently.\n  // When no task is specified, resolve the effective task name first so the guard applies.\n  const requestedTask = options?.task;\n  {\n    const effectiveTask = requestedTask\n      ?? getDefaultTask(agentId)?.id;\n    if (effectiveTask) {\n      const runningId = getRunningRunForTask(agentId, effectiveTask);\n      if (runningId) {\n        return {\n          runId: runningId,\n          status: STATUS_SKIPPED,\n          reason: SKIP_REASON_ALREADY_RUNNING,\n        };\n      }\n    }\n  }\n\n  // 3. Resolve config\n  const definitionsDir = resolveDefinitionsDir();\n  const definition = loadAgentDefinition(definitionsDir);\n\n  // Load agent and task — both are sync DB lookups\n  const agentRow = getAgent(agentId);\n  const taskRow = options?.task\n    ? getTask(options.task)\n    : getDefaultTask(agentId);\n\n  // Structural fields (phases, execution, contextQueries) come from the registry\n  // (built-in YAML merged with user vault tasks) rather than the DB flat columns.\n  const allTasks = loadAllTasks(definitionsDir, vaultDir);\n  const taskName = taskRow?.id ?? options?.task;\n  const yamlTask = taskName ? allTasks.get(taskName) : undefined;\n\n  const taskOverrides = taskRow\n    ? {\n        name: taskRow.id,\n        displayName: taskRow.display_name ?? taskRow.id,\n        description: taskRow.description ?? '',\n        agent: taskRow.agent_id,\n        prompt: taskRow.prompt,\n        isDefault: taskRow.is_default === 1,\n        ...(taskRow.tool_overrides\n          ? { toolOverrides: JSON.parse(taskRow.tool_overrides) as string[] }\n          : {}),\n        // Scalar config from YAML (model, turns, timeout) — DB doesn't store these\n        ...(yamlTask?.model ? { model: yamlTask.model } : {}),\n        ...(yamlTask?.maxTurns ? { maxTurns: yamlTask.maxTurns } : {}),\n        ...(yamlTask?.timeoutSeconds ? { timeoutSeconds: yamlTask.timeoutSeconds } : {}),\n        // Structural config from YAML\n        ...(yamlTask?.phases ? { phases: yamlTask.phases } : {}),\n        ...(yamlTask?.execution ? { execution: yamlTask.execution } : {}),\n        ...(yamlTask?.contextQueries ? { contextQueries: yamlTask.contextQueries } : {}),\n        ...(yamlTask?.orchestrator ? { orchestrator: yamlTask.orchestrator } : {}),\n      }\n    : undefined;\n\n  const config = resolveEffectiveConfig(definition, agentRow, taskOverrides);\n\n  // Load myco.yaml for provider overrides (global, per-task, per-phase)\n  let taskProviderOverride: ProviderConfig | undefined;\n  let phaseProviderOverrides: Record<string, { provider?: ProviderConfig; maxTurns?: number }> = {};\n  try {\n    const mycoConfig = loadConfig(vaultDir);\n\n    // Helper to convert myco.yaml snake_case provider to runtime camelCase\n    // API keys are NOT stored in myco.yaml — they flow via env vars (settings.json → hooks → daemon)\n    const toProviderConfig = (p: { type: 'cloud' | 'ollama' | 'lmstudio'; base_url?: string; model?: string; context_length?: number }): ProviderConfig => ({\n      type: p.type, baseUrl: p.base_url, model: p.model, contextLength: p.context_length,\n    });\n\n    // Per-task override takes priority over global\n    const taskConfig = taskName ? mycoConfig.agent.tasks?.[taskName] : undefined;\n    const globalProvider = mycoConfig.agent.provider;\n\n    if (taskConfig?.provider) {\n      taskProviderOverride = toProviderConfig(taskConfig.provider);\n    } else if (globalProvider) {\n      taskProviderOverride = toProviderConfig(globalProvider);\n    }\n\n    // Per-phase overrides from myco.yaml\n    if (taskConfig?.phases) {\n      for (const [phaseName, phaseConfig] of Object.entries(taskConfig.phases)) {\n        phaseProviderOverrides[phaseName] = {\n          ...(phaseConfig.provider ? { provider: toProviderConfig(phaseConfig.provider) } : {}),\n          ...(phaseConfig.maxTurns != null ? { maxTurns: phaseConfig.maxTurns } : {}),\n        };\n      }\n    }\n  } catch {\n    // Config load failure is non-fatal — proceed without overrides\n  }\n\n  // 4. Create run record\n  const runId = options?.resumeRunId ?? crypto.randomUUID();\n  const now = epochSeconds();\n\n  if (!options?.resumeRunId) {\n    insertRun({\n      id: runId,\n      agent_id: agentId,\n      task: config.taskName,\n      instruction: options?.instruction ?? null,\n      status: STATUS_RUNNING,\n      started_at: now,\n    });\n  }\n\n  // 5. Build prompt components\n  const systemPrompt = loadSystemPrompt(definitionsDir, config.systemPromptPath);\n  const vaultContext = buildVaultContext(agentId);\n\n  // 6. Build run metadata for audit trail\n  const effectiveProvider = taskProviderOverride ?? config.execution?.provider;\n  const effectiveModel = effectiveProvider?.model ?? config.model;\n  const runMeta = {\n    model: effectiveModel,\n    provider: effectiveProvider?.type ?? 'cloud',\n    ...(effectiveProvider?.baseUrl ? { baseUrl: effectiveProvider.baseUrl } : {}),\n  };\n\n  // 7. Ensure Ollama model has correct context length (creates variant if needed)\n  if (effectiveProvider?.type === 'ollama' && effectiveProvider.contextLength && effectiveProvider.model) {\n    const variantModel = await ensureOllamaContextVariant(\n      effectiveProvider.model,\n      effectiveProvider.contextLength,\n    );\n    // Override the model name so the SDK uses the context-aware variant\n    taskProviderOverride = { ...taskProviderOverride!, model: variantModel };\n  }\n\n  // 8. Execute — phased or single query\n  // Create abort controller for task-level timeout enforcement\n  const taskAbortController = new AbortController();\n  const timeoutMs = config.timeoutSeconds * MS_PER_SECOND;\n  const timeoutId = setTimeout(() => {\n    console.warn(`[agent] Run ${runId} exceeded timeout (${config.timeoutSeconds}s), aborting`);\n    taskAbortController.abort();\n  }, timeoutMs);\n  timeoutId.unref?.();\n\n  let phaseResults: PhaseResult[] | undefined;\n  try {\n    let tokensUsed: number;\n    let costUsd: number;\n\n    if (config.phases && config.phases.length > 0) {\n      // Phased execution: wave-based parallel query() per phase with scoped tools\n      const projectRoot = resolve(vaultDir, '..');\n      const result = await executePhasedQuery(\n        config,\n        systemPrompt,\n        vaultContext,\n        agentId,\n        runId,\n        taskProviderOverride,\n        phaseProviderOverrides,\n        options?.instruction,\n        options?.embeddingManager,\n        taskAbortController,\n        projectRoot,\n        vaultDir,\n      );\n      tokensUsed = result.tokensUsed;\n      costUsd = result.costUsd;\n      phaseResults = result.phases;\n    } else {\n      // Single-query execution (backward compatible)\n      const taskPrompt = composeTaskPrompt(\n        vaultContext,\n        config.taskDisplayName,\n        config.taskPrompt,\n        options?.instruction,\n      );\n\n      // Provider priority for single-query: myco.yaml task override → task execution config → default\n      const singleProvider = taskProviderOverride ?? config.execution?.provider;\n\n      const result = await executeSingleQuery(\n        config,\n        systemPrompt,\n        taskPrompt,\n        agentId,\n        runId,\n        singleProvider,\n        options?.embeddingManager,\n        taskAbortController,\n        vaultDir,\n      );\n      tokensUsed = result.tokensUsed;\n      costUsd = result.costUsd;\n    }\n\n    clearTimeout(timeoutId);\n    const completedAt = epochSeconds();\n    updateRunStatus(runId, STATUS_COMPLETED, {\n      completed_at: completedAt,\n      tokens_used: tokensUsed,\n      cost_usd: costUsd,\n      actions_taken: JSON.stringify({ ...runMeta, ...(phaseResults ? { phases: phaseResults } : {}) }),\n    });\n\n    return {\n      runId,\n      status: STATUS_COMPLETED,\n      tokensUsed,\n      costUsd,\n      ...(phaseResults ? { phases: phaseResults } : {}),\n    };\n  } catch (err) {\n    clearTimeout(timeoutId);\n    // 7. Error handling — mark run as failed, preserve phase results\n    // Aggressively extract error info — the SDK may throw non-Error objects\n    let errorMessage: string;\n    if (err instanceof Error) {\n      errorMessage = err.message || err.constructor.name || 'Error (no message)';\n      if (err.stack) errorMessage += `\\n${err.stack.split('\\n').slice(0, 3).join('\\n')}`;\n    } else if (typeof err === 'string') {\n      errorMessage = err || 'Empty string error';\n    } else {\n      try { errorMessage = JSON.stringify(err); } catch { errorMessage = 'Unserializable error'; }\n    }\n    const failedAt = epochSeconds();\n\n    // Log to stderr (daemon may capture) and to structured log\n    console.error(`[agent] Run ${runId} failed: ${errorMessage}`);\n\n    try {\n      updateRunStatus(runId, STATUS_FAILED, {\n        completed_at: failedAt,\n        error: errorMessage,\n        // Preserve phase results collected before the failure\n        actions_taken: JSON.stringify({ ...runMeta, ...(phaseResults ? { phases: phaseResults } : {}) }),\n      });\n    } catch (dbErr) {\n      // DB failure in error path — log it but don't mask the original error\n      console.error(`[agent] Failed to save error to DB:`, dbErr);\n    }\n\n    return {\n      runId,\n      status: STATUS_FAILED,\n      error: errorMessage,\n      ...(phaseResults ? { phases: phaseResults } : {}),\n    };\n  }\n}\n","/**\n * Vault MCP tool server for the agent.\n *\n * Creates 21 tools that expose SQLite query helpers to the agent\n * via the Claude Agent SDK. Tools are grouped into:\n * - Read tools: vault_unprocessed, vault_spores, vault_sessions, vault_search_fts,\n *               vault_search_semantic, vault_state, vault_entities, vault_edges,\n *               vault_read_digest\n * - Write tools: vault_create_spore, vault_create_entity, vault_create_edge,\n *                vault_resolve_spore, vault_update_session, vault_set_state,\n *                vault_write_digest, vault_mark_processed\n * - Observability: vault_report\n *\n * `agentId` and `runId` are captured in closures — tools inject them\n * automatically so the agent cannot impersonate another agent.\n */\n\nimport crypto from 'node:crypto';\nimport { writeFileSync, mkdirSync, rmSync } from 'node:fs';\nimport { resolve } from 'node:path';\nimport { z } from 'zod/v4';\nimport { tool, createSdkMcpServer } from '@anthropic-ai/claude-agent-sdk';\nimport { epochSeconds, SEARCH_SIMILARITY_THRESHOLD, TEAM_SOURCE_PREFIX, DEFAULT_LIST_LIMIT } from '@myco/constants.js';\nimport { getPluginVersion } from '@myco/version.js';\nimport { getDatabase } from '@myco/db/client.js';\nimport { getUnprocessedBatches, markBatchProcessed } from '@myco/db/queries/batches.js';\nimport { listSpores, insertSpore, updateSporeStatus, DEFAULT_IMPORTANCE } from '@myco/db/queries/spores.js';\nimport { listSessions, updateSession } from '@myco/db/queries/sessions.js';\nimport { getStatesForAgent, setState } from '@myco/db/queries/agent-state.js';\nimport { insertReport } from '@myco/db/queries/reports.js';\nimport { insertTurn } from '@myco/db/queries/turns.js';\nimport { EMBEDDABLE_TABLES, type EmbeddableTable } from '@myco/db/queries/embeddings.js';\nimport { fullTextSearch } from '@myco/db/queries/search.js';\nimport { insertEntity, listEntities } from '@myco/db/queries/entities.js';\nimport { insertGraphEdge, listGraphEdges } from '@myco/db/queries/graph-edges.js';\nimport { createSporeLineage } from '@myco/db/queries/lineage.js';\nimport { insertResolutionEvent } from '@myco/db/queries/resolution-events.js';\nimport { upsertDigestExtract, listDigestExtracts } from '@myco/db/queries/digest-extracts.js';\nimport {\n  insertCandidate, getCandidate, listCandidates, updateCandidate,\n} from '@myco/db/queries/skill-candidates.js';\nimport {\n  insertSkillRecord, getSkillRecord, getSkillRecordByName,\n  listSkillRecords, updateSkillRecord,\n} from '@myco/db/queries/skill-records.js';\nimport { insertLineage } from '@myco/db/queries/skill-lineage.js';\nimport { deleteCandidate } from '@myco/db/queries/skill-candidates.js';\nimport { deleteSkillRecordCascade } from '@myco/db/queries/skill-records.js';\nimport type { EmbeddingManager } from '@myco/daemon/embedding/index.js';\nimport type { TeamSyncClient } from '@myco/daemon/team-sync.js';\nimport { notify } from '@myco/notifications/notify.js';\n\n// ---------------------------------------------------------------------------\n// Constants\n// ---------------------------------------------------------------------------\n\n/** Default limit for unprocessed batches query. */\nconst DEFAULT_UNPROCESSED_LIMIT = 50;\n\n/** Default limit for spore listing. */\nconst DEFAULT_SPORES_LIMIT = 50;\n\n/** Default limit for session listing. */\nconst DEFAULT_SESSIONS_LIMIT = 20;\n\n/** Default limit for similarity search results. */\nconst DEFAULT_SEARCH_LIMIT = 10;\n\n/** Default embeddable table for search. */\nconst DEFAULT_SEARCH_TABLE: EmbeddableTable = 'spores';\n\n/** Default limit for entity listing. */\nconst DEFAULT_ENTITIES_LIMIT = 50;\n\n/** Default limit for edge listing. */\nconst DEFAULT_EDGES_LIMIT = 50;\n\n// ---------------------------------------------------------------------------\n// Helpers\n// ---------------------------------------------------------------------------\n\n/** Format a value as a JSON text content block for tool output. */\nfunction textResult(data: unknown): { content: Array<{ type: 'text'; text: string }> } {\n  return { content: [{ type: 'text' as const, text: JSON.stringify(data) }] };\n}\n\n// ---------------------------------------------------------------------------\n// Skill content validation (module-scope — avoids re-creation per server instantiation)\n// ---------------------------------------------------------------------------\n\n/** Maximum lines for a generated skill. */\nexport const MAX_SKILL_LINES = 500;\n\n/** Required frontmatter fields for Myco-managed skills. */\nexport const REQUIRED_FRONTMATTER_FIELDS = ['name', 'description', 'managed_by', 'user-invocable', 'allowed-tools'] as const;\n\n/**\n * Validate skill content before writing. Returns an array of issues\n * (empty = valid). This is a deterministic quality gate — the agent\n * must fix all issues before the skill is accepted.\n */\nexport function validateSkillContent(content: string, dirName: string): string[] {\n  const issues: string[] = [];\n\n  // Check for frontmatter delimiters\n  const fmMatch = content.match(/^---\\n([\\s\\S]*?)\\n---/);\n  if (!fmMatch) {\n    issues.push('Missing YAML frontmatter (must start with --- and end with ---)');\n    return issues; // Can't check fields without frontmatter\n  }\n\n  const frontmatter = fmMatch[1];\n\n  // Check required fields\n  for (const field of REQUIRED_FRONTMATTER_FIELDS) {\n    if (!frontmatter.includes(`${field}:`)) {\n      issues.push(`Missing required frontmatter field: ${field}`);\n    }\n  }\n\n  // Check myco: prefix on name\n  const nameMatch = frontmatter.match(/^name:\\s*(.+)$/m);\n  if (nameMatch && !nameMatch[1].trim().startsWith('myco:')) {\n    issues.push(`Skill name must start with \"myco:\" prefix. Got: \"${nameMatch[1].trim()}\"`);\n  }\n\n  // Check managed_by: myco\n  const managedMatch = frontmatter.match(/^managed_by:\\s*(.+)$/m);\n  if (managedMatch && managedMatch[1].trim() !== 'myco') {\n    issues.push(`managed_by must be \"myco\". Got: \"${managedMatch[1].trim()}\"`);\n  }\n\n  // Check allowed-tools values — must be Claude Code tool names, not vault agent tools.\n  // These skills run in developer Claude Code sessions, not the agent pipeline.\n  const allowedToolsMatch = frontmatter.match(/^allowed-tools:\\s*(.+)$/m);\n  if (allowedToolsMatch) {\n    const toolsValue = allowedToolsMatch[1].trim();\n    // Reject vault_* tool names — common LLM mistake of copying its own tool context\n    if (toolsValue.includes('vault_')) {\n      issues.push(\n        'allowed-tools contains vault agent tool names (vault_*). ' +\n        'Skills run in Claude Code sessions — use Claude Code tool names instead: ' +\n        'Read, Edit, Write, Bash, Grep, Glob'\n      );\n    }\n  }\n  // Also check YAML list format (- vault_search_fts etc.)\n  const listToolLines = frontmatter.match(/^\\s+-\\s+vault_\\w+/gm);\n  if (listToolLines) {\n    issues.push(\n      'allowed-tools contains vault agent tool names (vault_*). ' +\n      'Skills run in Claude Code sessions — use Claude Code tool names instead: ' +\n      'Read, Edit, Write, Bash, Grep, Glob'\n    );\n  }\n\n  // Check line count\n  const lineCount = content.split('\\n').length;\n  if (lineCount > MAX_SKILL_LINES) {\n    issues.push(`Skill is ${lineCount} lines (max ${MAX_SKILL_LINES})`);\n  }\n\n  return issues;\n}\n\n// ---------------------------------------------------------------------------\n// Tool definitions factory\n// ---------------------------------------------------------------------------\n\n/** Total number of vault tools defined. */\nexport const VAULT_TOOL_COUNT = 21;\n\n/** Options for createVaultTools beyond the required agentId and runId. */\nexport interface VaultToolOptions {\n  turnOffset?: number;\n  embeddingManager?: EmbeddingManager;\n  teamClient?: TeamSyncClient | null;\n  machineId?: string;\n  projectRoot?: string;\n  vaultDir?: string;\n}\n\n/**\n * Create the 21 vault tool definitions for the agent (includes 3 skill tools:\n * vault_skill_candidates, vault_skill_records, vault_write_skill).\n *\n * Exposed for testing (call handler directly) and for the MCP server factory.\n */\nexport function createVaultTools(agentId: string, runId: string, options?: VaultToolOptions) {\n  const { turnOffset = 0, embeddingManager, teamClient, machineId, projectRoot, vaultDir } = options ?? {};\n  /** Turn number counter — incremented per tool call (read and write) within a run. */\n  let turnCounter = turnOffset;\n\n  /**\n   * Record a turn in the audit trail.\n   * Called for ALL tool invocations (read and write) for full visibility.\n   * Fire-and-forget — does not block the tool response.\n   */\n  function recordTurn(toolName: string, toolInput: unknown): void {\n    turnCounter++;\n    try {\n      insertTurn({\n        run_id: runId,\n        agent_id: agentId,\n        turn_number: turnCounter,\n        tool_name: toolName,\n        tool_input: JSON.stringify(toolInput),\n        started_at: epochSeconds(),\n      });\n    } catch {\n      /* audit trail is best-effort */\n    }\n  }\n\n  // -------------------------------------------------------------------------\n  // Read tools\n  // -------------------------------------------------------------------------\n\n  const vaultUnprocessed = tool(\n    'vault_unprocessed',\n    'Get unprocessed prompt batches, ordered by id ASC. Supports cursor-based pagination.',\n    {\n      after_id: z.number().optional().describe('Return batches with id greater than this'),\n      limit: z.number().optional().describe('Maximum number of batches to return'),\n    },\n    async (args) => {\n      recordTurn('vault_unprocessed', args);\n      const batches = getUnprocessedBatches({\n        after_id: args.after_id,\n        limit: args.limit ?? DEFAULT_UNPROCESSED_LIMIT,\n      });\n      return textResult(batches);\n    },\n    { annotations: { readOnlyHint: true } },\n  );\n\n  const vaultSpores = tool(\n    'vault_spores',\n    'List spores with optional filters (agent, observation type, status, session).',\n    {\n      agent_id: z.string().optional().describe('Filter by agent ID'),\n      observation_type: z.string().optional().describe('Filter by observation type (e.g., gotcha, decision)'),\n      status: z.enum(['active', 'superseded', 'archived']).optional().describe('Filter by status'),\n      session_id: z.string().optional().describe('Filter by session ID'),\n      limit: z.number().optional().describe('Maximum number of spores to return'),\n    },\n    async (args) => {\n      recordTurn('vault_spores', args);\n      const spores = listSpores({\n        agent_id: args.agent_id,\n        observation_type: args.observation_type,\n        status: args.status,\n        session_id: args.session_id,\n        limit: args.limit ?? DEFAULT_SPORES_LIMIT,\n      });\n      return textResult(spores);\n    },\n    { annotations: { readOnlyHint: true } },\n  );\n\n  const vaultSessions = tool(\n    'vault_sessions',\n    'List sessions with optional status filter, ordered by created_at DESC.',\n    {\n      limit: z.number().optional().describe('Maximum number of sessions to return'),\n      status: z.string().optional().describe('Filter by status (active, completed)'),\n    },\n    async (args) => {\n      recordTurn('vault_sessions', args);\n      const sessions = listSessions({\n        limit: args.limit ?? DEFAULT_SESSIONS_LIMIT,\n        status: args.status,\n      });\n      return textResult(sessions);\n    },\n    { annotations: { readOnlyHint: true } },\n  );\n\n  const vaultSearchFts = tool(\n    'vault_search_fts',\n    'Full-text search across sessions, spores, prompt batches, and activities using FTS5. Best for finding exact keywords, file paths, function names, and specific text. Searches: session titles/summaries, spore content, user prompts, AI response summaries, tool calls.',\n    {\n      query: z.string().describe('Search query text'),\n      type: z.string().optional().describe('Restrict to a result type (session, spore, prompt_batch, activity)'),\n      limit: z.number().optional().describe('Maximum number of results to return'),\n    },\n    async (args) => {\n      recordTurn('vault_search_fts', args);\n      try {\n        const results = fullTextSearch(args.query, {\n          type: args.type,\n          limit: args.limit ?? DEFAULT_SEARCH_LIMIT,\n        });\n        return textResult({ results });\n      } catch {\n        return textResult({ results: [], message: 'Search unavailable' });\n      }\n    },\n    { annotations: { readOnlyHint: true } },\n  );\n\n  const vaultSearchSemantic = tool(\n    'vault_search_semantic',\n    'Semantic similarity search across embedded vault content (spores, sessions, plans, artifacts). Best for finding conceptually related content. Returns results ranked by similarity score.',\n    {\n      query: z.string().describe('Search query text'),\n      namespace: z.string().optional().describe('Restrict to a content type: spores, sessions, plans, artifacts. Omit to search all.'),\n      limit: z.number().optional().describe('Maximum results to return'),\n    },\n    async (args) => {\n      recordTurn('vault_search_semantic', args);\n      if (!embeddingManager) {\n        return textResult({ results: [], message: 'Embedding provider unavailable' });\n      }\n      try {\n        const queryVector = await embeddingManager.embedQuery(args.query);\n        if (!queryVector) {\n          return textResult({ results: [], message: 'Embedding provider unavailable' });\n        }\n        const searchLimit = args.limit ?? DEFAULT_SEARCH_LIMIT;\n\n        // Fire local and team search in parallel\n        const [localResults, teamResults] = await Promise.all([\n          Promise.resolve(\n            embeddingManager.searchVectors(queryVector, {\n              namespace: args.namespace,\n              limit: searchLimit,\n              threshold: SEARCH_SIMILARITY_THRESHOLD,\n            }).map((r) => ({ ...r, source: 'local' as const })),\n          ),\n          teamClient\n            ? teamClient.search(args.query, { limit: searchLimit })\n                .then((res) => res.results.map((r) => ({ ...r, source: `${TEAM_SOURCE_PREFIX}${r.machine_id}` })))\n                .catch(() => [] as Array<Record<string, unknown>>)\n            : Promise.resolve([] as Array<Record<string, unknown>>),\n        ]);\n\n        // Deduplicate: skip team results from this machine (we already have them locally)\n        const dedupedTeam = machineId\n          ? teamResults.filter((r) => (r as Record<string, unknown>).machine_id !== machineId)\n          : teamResults;\n\n        // Merge by similarity/score (normalize to common key), slice to limit\n        const merged = [\n          ...localResults.map((r) => ({ ...r, score: r.similarity })),\n          ...dedupedTeam,\n        ]\n          .sort((a, b) => ((b.score as number) ?? 0) - ((a.score as number) ?? 0))\n          .slice(0, searchLimit);\n\n        return textResult({ results: merged });\n      } catch {\n        return textResult({ results: [], message: 'Semantic search unavailable' });\n      }\n    },\n    { annotations: { readOnlyHint: true } },\n  );\n\n  const vaultState = tool(\n    'vault_state',\n    'Get all state key-value pairs for the current agent.',\n    {},\n    async () => {\n      recordTurn('vault_state', {});\n      const states = getStatesForAgent(agentId);\n      return textResult(states);\n    },\n    { annotations: { readOnlyHint: true } },\n  );\n\n  const vaultEntities = tool(\n    'vault_entities',\n    'List knowledge graph entities with optional filters.',\n    {\n      type: z.enum(['component', 'concept', 'person']).optional().describe('Filter by entity type'),\n      name: z.string().optional().describe('Filter by entity name (exact match)'),\n      limit: z.number().optional().describe('Maximum entities to return'),\n    },\n    async (args) => {\n      recordTurn('vault_entities', args);\n      const entities = listEntities({\n        agent_id: agentId,\n        type: args.type,\n        name: args.name,\n        limit: args.limit ?? DEFAULT_ENTITIES_LIMIT,\n      });\n      return textResult(entities);\n    },\n    { annotations: { readOnlyHint: true } },\n  );\n\n  const vaultEdges = tool(\n    'vault_edges',\n    'List knowledge graph edges with optional filters. Use to check existing relationships before creating new ones.',\n    {\n      source_id: z.string().optional().describe('Filter by source node ID'),\n      target_id: z.string().optional().describe('Filter by target node ID'),\n      type: z.string().optional().describe('Filter by edge type (REFERENCES, DEPENDS_ON, AFFECTS, etc.)'),\n      limit: z.number().optional().describe('Maximum edges to return'),\n    },\n    async (args) => {\n      recordTurn('vault_edges', args);\n      const edges = listGraphEdges({\n        sourceId: args.source_id,\n        targetId: args.target_id,\n        type: args.type,\n        agentId: agentId,\n        limit: args.limit ?? DEFAULT_EDGES_LIMIT,\n      });\n      return textResult(edges);\n    },\n    { annotations: { readOnlyHint: true } },\n  );\n\n  // -------------------------------------------------------------------------\n  // Write tools\n  // -------------------------------------------------------------------------\n\n  const vaultCreateSpore = tool(\n    'vault_create_spore',\n    'Create a new spore (observation) in the vault. The agent_id is set automatically.',\n    {\n      observation_type: z.string().describe('Type of observation (gotcha, decision, discovery, trade-off, bug_fix, etc.)'),\n      content: z.string().describe('The observation content in markdown'),\n      session_id: z.string().optional().describe('Associated session ID'),\n      prompt_batch_id: z.number().optional().describe('Associated prompt batch ID'),\n      importance: z.number().optional().describe('Importance score 1-10 (default 5)'),\n      tags: z.array(z.string()).optional().describe('Tags for categorization'),\n      context: z.string().optional().describe('Additional context about the observation'),\n      file_path: z.string().optional().describe('Related file path'),\n      properties: z.string().optional().describe('JSON metadata (e.g., {\"consolidated_from\": [...]} for wisdom spores)'),\n    },\n    async (args) => {\n      const id = crypto.randomUUID();\n      const now = epochSeconds();\n\n      const spore = insertSpore({\n        id,\n        agent_id: agentId,\n        machine_id: machineId,\n        observation_type: args.observation_type,\n        content: args.content,\n        session_id: args.session_id ?? null,\n        prompt_batch_id: args.prompt_batch_id ?? null,\n        importance: args.importance ?? DEFAULT_IMPORTANCE,\n        tags: args.tags ? JSON.stringify(args.tags) : null,\n        context: args.context ?? null,\n        file_path: args.file_path ?? null,\n        properties: args.properties ?? null,\n        created_at: now,\n      });\n\n      // Best-effort: structural lineage edges (FROM_SESSION, EXTRACTED_FROM, DERIVED_FROM)\n      try { createSporeLineage(spore); } catch { /* lineage best-effort */ }\n\n      embeddingManager?.onContentWritten('spores', spore.id, args.content, {\n        status: 'active',\n        observation_type: args.observation_type,\n        session_id: args.session_id,\n      }).catch(() => {});\n\n      // Spore notifications are batched post-run (daemon emits summary after agent completes)\n      recordTurn('vault_create_spore', args);\n      return textResult(spore);\n    },\n  );\n\n  const vaultCreateEntity = tool(\n    'vault_create_entity',\n    'Create or update an entity in the knowledge graph. Uses UPSERT on (agent_id, type, name).',\n    {\n      type: z.enum(['component', 'concept', 'person']).describe('Entity type'),\n      name: z.string().describe('Entity name (unique within agent + type)'),\n      properties: z.record(z.string(), z.unknown()).optional().describe('Additional properties as key-value pairs'),\n    },\n    async (args) => {\n      const id = crypto.randomUUID();\n      const now = epochSeconds();\n      const props = args.properties ? JSON.stringify(args.properties) : null;\n\n      const entity = insertEntity({\n        id,\n        agent_id: agentId,\n        machine_id: machineId,\n        type: args.type,\n        name: args.name,\n        properties: props,\n        first_seen: now,\n        last_seen: now,\n      });\n\n      recordTurn('vault_create_entity', args);\n      return textResult(entity);\n    },\n  );\n\n  const vaultCreateEdge = tool(\n    'vault_create_edge',\n    'Create a semantic edge in the knowledge graph. Lineage edges (FROM_SESSION, EXTRACTED_FROM, HAS_BATCH, DERIVED_FROM) are created automatically — do NOT create those.',\n    {\n      source_id: z.string().describe('Source node ID'),\n      source_type: z.enum(['session', 'batch', 'spore', 'entity']).describe('Source node type'),\n      target_id: z.string().describe('Target node ID'),\n      target_type: z.enum(['session', 'batch', 'spore', 'entity']).describe('Target node type'),\n      type: z.enum(['RELATES_TO', 'SUPERSEDED_BY', 'REFERENCES', 'DEPENDS_ON', 'AFFECTS']).describe('Semantic edge type'),\n      session_id: z.string().optional().describe('Session where this relationship was observed'),\n      confidence: z.number().optional().describe('Confidence score 0-1 (default 1.0)'),\n      properties: z.record(z.string(), z.unknown()).optional().describe('Additional properties as key-value pairs'),\n    },\n    async (args) => {\n      const now = epochSeconds();\n      const props = args.properties ? JSON.stringify(args.properties) : undefined;\n\n      const edge = insertGraphEdge({\n        agent_id: agentId,\n        machine_id: machineId,\n        source_id: args.source_id,\n        source_type: args.source_type,\n        target_id: args.target_id,\n        target_type: args.target_type,\n        type: args.type,\n        session_id: args.session_id,\n        confidence: args.confidence,\n        properties: props,\n        created_at: now,\n      });\n\n      recordTurn('vault_create_edge', args);\n      return textResult(edge);\n    },\n  );\n\n  const vaultResolveSpore = tool(\n    'vault_resolve_spore',\n    'Resolve a spore by updating its status and recording a resolution event.',\n    {\n      spore_id: z.string().describe('ID of the spore to resolve'),\n      action: z.enum(['supersede', 'archive', 'merge', 'split', 'consolidate']).describe('Resolution action'),\n      new_spore_id: z.string().optional().describe('ID of the replacement spore (for supersede/merge)'),\n      reason: z.string().optional().describe('Explanation for the resolution'),\n      session_id: z.string().optional().describe('Session where this resolution occurred'),\n    },\n    async (args) => {\n      const now = epochSeconds();\n\n      // Update spore status\n      const statusMap: Record<string, string> = {\n        supersede: 'superseded',\n        archive: 'archived',\n        merge: 'merged',\n        split: 'split',\n        consolidate: 'consolidated',\n      };\n      const newStatus = statusMap[args.action] ?? args.action;\n      const updatedSpore = updateSporeStatus(args.spore_id, newStatus, now);\n\n      // Record resolution event\n      const eventId = crypto.randomUUID();\n      insertResolutionEvent({\n        id: eventId,\n        agent_id: agentId,\n        machine_id: machineId,\n        spore_id: args.spore_id,\n        action: args.action,\n        new_spore_id: args.new_spore_id ?? null,\n        reason: args.reason ?? null,\n        session_id: args.session_id ?? null,\n        created_at: now,\n      });\n\n      if (newStatus !== 'active') {\n        try { embeddingManager?.onStatusChanged('spores', args.spore_id, newStatus); } catch { /* best-effort */ }\n      }\n\n      recordTurn('vault_resolve_spore', args);\n      return textResult({ spore: updatedSpore, resolution_event_id: eventId });\n    },\n  );\n\n  const vaultUpdateSession = tool(\n    'vault_update_session',\n    'Update a session title and/or summary. When generating for the first time, provide BOTH title and summary. Title should be under 80 characters and reflect the full session scope.',\n    {\n      session_id: z.string().describe('Session ID to update'),\n      title: z.string().optional().describe('New session title'),\n      summary: z.string().optional().describe('New session summary'),\n    },\n    async (args) => {\n      const updates: Record<string, unknown> = {};\n      if (args.title !== undefined) updates.title = args.title;\n      if (args.summary !== undefined) updates.summary = args.summary;\n\n      const session = updateSession(args.session_id, updates);\n\n      if (args.summary) {\n        embeddingManager?.onContentWritten('sessions', args.session_id, args.summary, {}).catch(() => {});\n      }\n\n      recordTurn('vault_update_session', args);\n      return textResult(session);\n    },\n  );\n\n  const vaultSetState = tool(\n    'vault_set_state',\n    'Set a key-value state pair for the current agent. Used for bookmarks, cursors, and preferences.',\n    {\n      key: z.string().describe('State key (e.g., last_processed_batch_id, cursor)'),\n      value: z.string().describe('State value (stored as text)'),\n    },\n    async (args) => {\n      const now = epochSeconds();\n      const state = setState(agentId, args.key, args.value, now);\n\n      recordTurn('vault_set_state', args);\n      return textResult(state);\n    },\n  );\n\n  const vaultReadDigest = tool(\n    'vault_read_digest',\n    'Read current digest extracts. Without a tier parameter, returns a summary of all tiers (content length, generation time). With a tier parameter, returns the full content for that specific tier.',\n    {\n      tier: z.number().optional().describe('Specific tier to read in full (e.g., 1500, 5000, 10000). Omit to get summary of all tiers.'),\n    },\n    async (args) => {\n      recordTurn('vault_read_digest', args);\n      const extracts = listDigestExtracts(agentId);\n\n      if (args.tier !== undefined) {\n        const extract = extracts.find(e => e.tier === args.tier);\n        if (!extract) return textResult({ tier: args.tier, content: null, message: 'No digest at this tier' });\n        return textResult({ tier: extract.tier, content: extract.content, generated_at: extract.generated_at });\n      }\n\n      // Summary mode — return metadata for all tiers\n      return textResult(extracts.map(e => ({\n        tier: e.tier,\n        content_length: e.content.length,\n        generated_at: e.generated_at,\n      })));\n    },\n    { annotations: { readOnlyHint: true } },\n  );\n\n  const vaultWriteDigest = tool(\n    'vault_write_digest',\n    'Write or update a digest extract at a specific token tier. Uses UPSERT on (agent_id, tier).',\n    {\n      tier: z.number().describe('Token budget tier (e.g., 1500, 5000, 10000)'),\n      content: z.string().describe('The digest extract content in markdown'),\n    },\n    async (args) => {\n      const now = epochSeconds();\n\n      const extract = upsertDigestExtract({\n        agent_id: agentId,\n        tier: args.tier,\n        content: args.content,\n        generated_at: now,\n      });\n\n      // Digest notifications are batched post-run (daemon emits summary after agent completes)\n      recordTurn('vault_write_digest', args);\n      return textResult(extract);\n    },\n  );\n\n  const vaultMarkProcessed = tool(\n    'vault_mark_processed',\n    'Mark a prompt batch as processed so it is not returned by vault_unprocessed.',\n    {\n      batch_id: z.number().describe('ID of the prompt batch to mark as processed'),\n    },\n    async (args) => {\n      const batch = markBatchProcessed(args.batch_id);\n\n      recordTurn('vault_mark_processed', args);\n      return textResult(batch);\n    },\n  );\n\n  // -------------------------------------------------------------------------\n  // Observability tool\n  // -------------------------------------------------------------------------\n\n  const vaultReport = tool(\n    'vault_report',\n    'Record an observability report for the current run. Use action \"skip\" when skipping expected operations (e.g., not updating a session summary) with reasoning in the summary field.',\n    {\n      action: z.string().describe('Action name (e.g., extract, consolidate, digest, skip)'),\n      summary: z.string().describe('Human-readable summary of what was done'),\n      details: z.record(z.string(), z.unknown()).optional().describe('Structured details as key-value pairs'),\n    },\n    async (args) => {\n      recordTurn('vault_report', args);\n      const now = epochSeconds();\n\n      const report = insertReport({\n        run_id: runId,\n        agent_id: agentId,\n        action: args.action,\n        summary: args.summary,\n        details: args.details ? JSON.stringify(args.details) : null,\n        created_at: now,\n      });\n\n      return textResult(report);\n    },\n  );\n\n  // -------------------------------------------------------------------------\n  // Skill lifecycle tools\n  // -------------------------------------------------------------------------\n\n  const vaultSkillCandidates = tool(\n    'vault_skill_candidates',\n    'Manage skill candidates (identified topics that may become skills). Supports list, get, create, and update actions.',\n    {\n      action: z.enum(['list', 'get', 'create', 'update', 'delete']).describe('Action to perform'),\n      id: z.string().optional().describe('Candidate ID (required for get/update)'),\n      topic: z.string().optional().describe('Skill topic (required for create)'),\n      rationale: z.string().optional().describe('Why this should be a skill (required for create)'),\n      confidence: z.number().optional().describe('Confidence score 0-1'),\n      status: z.enum(['identified', 'approved', 'generated', 'dismissed']).optional().describe('Candidate status. Only these values are valid.'),\n      source_ids: z.string().optional().describe('JSON array of source spore/entity IDs'),\n      skill_id: z.string().optional().describe('Associated skill record ID (after materialization)'),\n      limit: z.number().optional().describe('Maximum candidates to return (for list)'),\n    },\n    async (args) => {\n      recordTurn('vault_skill_candidates', args);\n\n      switch (args.action) {\n        case 'list': {\n          const candidates = listCandidates({\n            agent_id: agentId,\n            status: args.status,\n            limit: args.limit ?? DEFAULT_LIST_LIMIT,\n          });\n          return textResult(candidates);\n        }\n\n        case 'get': {\n          if (!args.id) return textResult({ error: 'id is required for get action' });\n          const candidate = getCandidate(args.id);\n          if (!candidate) return textResult({ error: `Candidate not found: ${args.id}` });\n          return textResult(candidate);\n        }\n\n        case 'create': {\n          if (!args.topic || !args.rationale) {\n            return textResult({ error: 'topic and rationale are required for create action' });\n          }\n          const now = epochSeconds();\n          const candidate = insertCandidate({\n            id: crypto.randomUUID(),\n            agent_id: agentId,\n            machine_id: machineId,\n            topic: args.topic,\n            rationale: args.rationale,\n            confidence: args.confidence,\n            status: args.status,\n            source_ids: args.source_ids,\n            created_at: now,\n            updated_at: now,\n          });\n          notify(vaultDir, {\n            domain: 'skills',\n            type: 'skill.surveyed',\n            title: `Skill candidate: ${args.topic}`,\n            message: args.rationale.slice(0, 120),\n            link: '/skills?tab=candidates',\n            metadata: { candidateId: candidate.id, topic: args.topic },\n          });\n          return textResult(candidate);\n        }\n\n        case 'update': {\n          if (!args.id) return textResult({ error: 'id is required for update action' });\n          const now = epochSeconds();\n          const updated = updateCandidate(args.id, {\n            ...(args.topic !== undefined ? { topic: args.topic } : {}),\n            ...(args.rationale !== undefined ? { rationale: args.rationale } : {}),\n            ...(args.confidence !== undefined ? { confidence: args.confidence } : {}),\n            ...(args.status !== undefined ? { status: args.status } : {}),\n            ...(args.source_ids !== undefined ? { source_ids: args.source_ids } : {}),\n            ...(args.skill_id !== undefined ? { skill_id: args.skill_id } : {}),\n            updated_at: now,\n          });\n          if (!updated) return textResult({ error: `Candidate not found: ${args.id}` });\n          return textResult(updated);\n        }\n\n        case 'delete': {\n          if (!args.id) return textResult({ error: 'id is required for delete action' });\n          const deleted = deleteCandidate(args.id);\n          if (!deleted) return textResult({ error: `Candidate not found: ${args.id}` });\n          return textResult({ deleted: true, id: args.id });\n        }\n\n        default:\n          return textResult({ error: `Unknown action: ${args.action}` });\n      }\n    },\n  );\n\n  const vaultSkillRecords = tool(\n    'vault_skill_records',\n    'Read, update, and delete skill records (materialized skills on disk). Supports list, get, update, and delete actions.',\n    {\n      action: z.enum(['list', 'get', 'update', 'delete']).describe('Action to perform'),\n      id: z.string().optional().describe('Skill record ID or name (required for get/update/delete)'),\n      status: z.enum(['active', 'stale', 'retired']).optional().describe('Filter by status'),\n      generation: z.number().optional().describe('New generation number (for update)'),\n      source_ids: z.string().optional().describe('JSON array of source IDs (for update)'),\n      description: z.string().optional().describe('Updated description (for update)'),\n      limit: z.number().optional().describe('Maximum records to return (for list)'),\n    },\n    async (args) => {\n      recordTurn('vault_skill_records', args);\n\n      switch (args.action) {\n        case 'list': {\n          const records = listSkillRecords({\n            agent_id: agentId,\n            status: args.status,\n            limit: args.limit ?? DEFAULT_LIST_LIMIT,\n          });\n          return textResult(records);\n        }\n\n        case 'get': {\n          if (!args.id) return textResult({ error: 'id is required for get action' });\n          const record = getSkillRecord(args.id) ?? getSkillRecordByName(args.id);\n          if (!record) return textResult({ error: `Skill record not found: ${args.id}` });\n          return textResult(record);\n        }\n\n        case 'update': {\n          if (!args.id) return textResult({ error: 'id is required for update action' });\n          // Resolve by id or name\n          const existing = getSkillRecord(args.id) ?? getSkillRecordByName(args.id);\n          if (!existing) return textResult({ error: `Skill record not found: ${args.id}` });\n\n          const now = epochSeconds();\n          const updated = updateSkillRecord(existing.id, {\n            ...(args.status !== undefined ? { status: args.status } : {}),\n            ...(args.generation !== undefined ? { generation: args.generation } : {}),\n            ...(args.source_ids !== undefined ? { source_ids: args.source_ids } : {}),\n            ...(args.description !== undefined ? { description: args.description } : {}),\n            updated_at: now,\n          });\n          if (!updated) return textResult({ error: `Failed to update skill record: ${existing.id}` });\n          return textResult(updated);\n        }\n\n        case 'delete': {\n          if (!args.id) return textResult({ error: 'id is required for delete action' });\n          const result = deleteSkillRecordCascade(args.id);\n          if (!result) return textResult({ error: `Skill record not found: ${args.id}` });\n          // Disk + symlink cleanup (best-effort)\n          const root = projectRoot ?? process.cwd();\n          if (!/[/\\\\]|\\.\\./.test(result.name)) {\n            const skillDir = resolve(root, '.agents', 'skills', result.name);\n            try { rmSync(skillDir, { recursive: true, force: true }); } catch (err) {\n              console.warn('[vault_skill_records] Failed to remove skill directory:', err instanceof Error ? err.message : err);\n            }\n            try {\n              const { syncSkillSymlinks } = await import('../symbionts/installer.js');\n              syncSkillSymlinks(root, result.name, { remove: true });\n            } catch (err) {\n              console.warn('[vault_skill_records] Failed to remove symlinks:', err instanceof Error ? err.message : err);\n            }\n          }\n          return textResult({ deleted: true, id: result.id, name: result.name });\n        }\n\n        default:\n          return textResult({ error: `Unknown action: ${args.action}` });\n      }\n    },\n  );\n\n  const vaultWriteSkill = tool(\n    'vault_write_skill',\n    'Write a SKILL.md file to disk and create or update the corresponding skill record and lineage entry.',\n    {\n      name: z.string().describe('Skill directory name (kebab-case, NO colon). The myco: prefix goes in the SKILL.md frontmatter name field, not here.'),\n      display_name: z.string().describe('Human-readable display name'),\n      description: z.string().describe('Short description of what the skill does'),\n      content: z.string().describe('Full SKILL.md content in markdown'),\n      source_ids: z.string().optional().describe('JSON array of source spore/entity IDs'),\n      candidate_id: z.string().optional().describe('Candidate ID that prompted this skill creation'),\n      rationale: z.string().optional().describe('Why this skill was created or updated'),\n    },\n    async (args) => {\n      // Validate skill content before writing — reject malformed skills\n      const validationErrors = validateSkillContent(args.content, args.name);\n      if (validationErrors.length > 0) {\n        recordTurn('vault_write_skill', args);\n        return textResult({\n          error: 'Skill validation failed. Fix these issues and try again.',\n          issues: validationErrors,\n        });\n      }\n\n      // Path traversal guard — reject names containing path separators or dot-dot sequences\n      if (!args.name || /[/\\\\]|\\.\\./.test(args.name)) {\n        recordTurn('vault_write_skill', args);\n        return textResult({\n          error: 'Invalid skill name: must be a simple directory name without path separators or \"..\"',\n        });\n      }\n\n      const root = projectRoot ?? process.cwd();\n      const skillDir = resolve(root, '.agents', 'skills', args.name);\n      const skillPath = resolve(skillDir, 'SKILL.md');\n\n      // Write file to disk — must succeed before any DB operations\n      try {\n        mkdirSync(skillDir, { recursive: true });\n        writeFileSync(skillPath, args.content, 'utf-8');\n      } catch (err) {\n        return textResult({ error: `Failed to write skill file: ${err instanceof Error ? err.message : String(err)}` });\n      }\n\n      // Create agent-specific symlinks so each symbiont discovers the skill.\n      // Uses the shared syncSkillSymlinks which reads manifest skillsTarget paths.\n      try {\n        const { syncSkillSymlinks } = await import('@myco/symbionts/installer.js');\n        syncSkillSymlinks(root, args.name);\n      } catch (err) {\n        // Best-effort — skill file is written, symlinks are convenience\n        console.warn('[vault_write_skill] syncSkillSymlinks failed:', err instanceof Error ? err.message : err);\n      }\n\n      const now = epochSeconds();\n      const relativePath = `.agents/skills/${args.name}/SKILL.md`;\n\n      // Check for existing record\n      const existing = getSkillRecordByName(args.name);\n\n      let recordId = '';\n      let generation = 0;\n\n      // All DB mutations wrapped in a transaction for atomicity.\n      // File write (above) is the source of truth; DB is derived.\n      const txDb = getDatabase();\n      txDb.transaction(() => {\n        if (existing) {\n          // Update existing record — bump generation\n          generation = existing.generation + 1;\n          recordId = existing.id;\n          updateSkillRecord(existing.id, {\n            display_name: args.display_name,\n            description: args.description,\n            generation,\n            ...(args.source_ids !== undefined ? { source_ids: args.source_ids } : {}),\n            path: relativePath,\n            updated_at: now,\n          });\n\n          // Record lineage\n          insertLineage({\n            id: crypto.randomUUID(),\n            skill_id: existing.id,\n            generation,\n            action: 'updated',\n            rationale: args.rationale ?? 'Skill content updated',\n            source_ids_added: args.source_ids,\n            content_snapshot: args.content,\n            created_at: now,\n          });\n        } else {\n          // Create new record\n          recordId = crypto.randomUUID();\n          generation = 1;\n          insertSkillRecord({\n            id: recordId,\n            agent_id: agentId,\n            machine_id: machineId,\n            name: args.name,\n            display_name: args.display_name,\n            description: args.description,\n            candidate_id: args.candidate_id ?? null,\n            source_ids: args.source_ids,\n            path: relativePath,\n            created_at: now,\n            updated_at: now,\n          });\n\n          // Record lineage\n          insertLineage({\n            id: crypto.randomUUID(),\n            skill_id: recordId,\n            generation,\n            action: 'created',\n            rationale: args.rationale ?? 'Initial skill creation',\n            source_ids_added: args.source_ids,\n            content_snapshot: args.content,\n            created_at: now,\n          });\n\n          // Auto-link candidate: find the approved candidate this skill was generated from.\n          // Strategy: exact candidate_id → prefix match.\n          // Does NOT depend on the agent passing the correct ID.\n          const approvedCandidates = listCandidates({ status: 'approved', limit: 10 });\n          let linkedCandidate = false;\n\n          // 1. Try exact candidate_id if provided\n          if (args.candidate_id && !linkedCandidate) {\n            const exact = updateCandidate(args.candidate_id, {\n              status: 'generated', skill_id: recordId, updated_at: now,\n            });\n            if (exact) linkedCandidate = true;\n          }\n\n          // 2. Try prefix match on candidate_id (agent truncates UUIDs)\n          if (args.candidate_id && !linkedCandidate) {\n            const prefixMatch = approvedCandidates.find((c) => c.id.startsWith(args.candidate_id!));\n            if (prefixMatch) {\n              updateCandidate(prefixMatch.id, {\n                status: 'generated', skill_id: recordId, updated_at: now,\n              });\n              linkedCandidate = true;\n            }\n          }\n\n          // No blind fallback — if neither exact nor prefix match found the candidate,\n          // skip linking. The candidate stays 'approved' for the next generate cycle.\n          // The daemon injection (Layer 2) ensures candidate_id is always provided in\n          // scheduled runs, making this fallback-skip path rare.\n        }\n      })();\n\n      const isNew = generation === 1;\n      notify(vaultDir, {\n        domain: 'skills',\n        type: isNew ? 'skill.created' : 'skill.evolved',\n        title: isNew ? `Skill created: ${args.display_name}` : `Skill evolved: ${args.display_name}`,\n        message: args.description.slice(0, 120),\n        link: `/skills?skill=${encodeURIComponent(args.name)}`,\n        metadata: { skillId: recordId, name: args.name, generation },\n      });\n\n      recordTurn('vault_write_skill', args);\n      return textResult({\n        id: recordId,\n        name: args.name,\n        path: relativePath,\n        generation,\n      });\n    },\n  );\n\n  // -------------------------------------------------------------------------\n  // Assemble and return\n  // -------------------------------------------------------------------------\n\n  return [\n    vaultUnprocessed,\n    vaultSpores,\n    vaultSessions,\n    vaultSearchFts,\n    vaultSearchSemantic,\n    vaultState,\n    vaultEntities,\n    vaultEdges,\n    vaultCreateSpore,\n    vaultCreateEntity,\n    vaultCreateEdge,\n    vaultResolveSpore,\n    vaultUpdateSession,\n    vaultSetState,\n    vaultReadDigest,\n    vaultWriteDigest,\n    vaultMarkProcessed,\n    vaultReport,\n    vaultSkillCandidates,\n    vaultSkillRecords,\n    vaultWriteSkill,\n  ];\n}\n\n// ---------------------------------------------------------------------------\n// MCP server factory\n// ---------------------------------------------------------------------------\n\n/**\n * Create a vault MCP tool server with 21 tools for the agent.\n *\n * Wraps `createVaultTools()` with `createSdkMcpServer()` from the\n * Claude Agent SDK.\n *\n * @param agentId — the agent identity, injected into all write operations.\n * @param runId — the current agent run ID, injected into reports and turns.\n * @returns an MCP server config with instance, suitable for the SDK.\n */\nexport function createVaultToolServer(agentId: string, runId: string, options?: Pick<VaultToolOptions, 'embeddingManager' | 'vaultDir'>) {\n  const tools = createVaultTools(agentId, runId, options);\n\n  return createSdkMcpServer({\n    name: 'myco-vault',\n    version: getPluginVersion(),\n    tools,\n  });\n}\n\n/**\n * Create a vault MCP tool server scoped to a subset of tools.\n *\n * Used by the phased executor to restrict each phase to only the tools\n * it needs. Tools not in `toolNames` are excluded from the server.\n *\n * @param agentId — the agent identity, injected into all write operations.\n * @param runId — the current agent run ID, injected into reports and turns.\n * @param toolNames — tool names to include (e.g., ['vault_unprocessed', 'vault_create_spore']).\n * @returns an MCP server config with only the specified tools.\n */\nexport function createScopedVaultToolServer(\n  agentId: string,\n  runId: string,\n  toolNames: string[],\n  options?: Pick<VaultToolOptions, 'turnOffset' | 'embeddingManager' | 'projectRoot' | 'vaultDir'>,\n) {\n  const allTools = createVaultTools(agentId, runId, options);\n  const nameSet = new Set(toolNames);\n  const scopedTools = allTools.filter((t) => nameSet.has(t.name));\n\n  return createSdkMcpServer({\n    name: 'myco-vault',\n    version: getPluginVersion(),\n    tools: scopedTools,\n  });\n}\n","/**\n * Agent state key-value query helpers.\n *\n * All functions obtain the SQLite instance internally via `getDatabase()`.\n * Queries use positional `?` placeholders throughout (better-sqlite3).\n */\n\nimport { getDatabase } from '@myco/db/client.js';\n\n// ---------------------------------------------------------------------------\n// Types\n// ---------------------------------------------------------------------------\n\n/** Row shape returned from agent_state queries. */\nexport interface AgentStateRow {\n  agent_id: string;\n  key: string;\n  value: string;\n  updated_at: number;\n}\n\n// ---------------------------------------------------------------------------\n// Column list\n// ---------------------------------------------------------------------------\n\nconst STATE_COLUMNS = [\n  'agent_id',\n  'key',\n  'value',\n  'updated_at',\n] as const;\n\nconst SELECT_COLUMNS = STATE_COLUMNS.join(', ');\n\n// ---------------------------------------------------------------------------\n// Helpers\n// ---------------------------------------------------------------------------\n\n/** Normalize a SQLite result row into a typed AgentStateRow. */\nfunction toAgentStateRow(row: Record<string, unknown>): AgentStateRow {\n  return {\n    agent_id: row.agent_id as string,\n    key: row.key as string,\n    value: row.value as string,\n    updated_at: row.updated_at as number,\n  };\n}\n\n// ---------------------------------------------------------------------------\n// Public API\n// ---------------------------------------------------------------------------\n\n/**\n * Get a single state value for an agent by key.\n *\n * @returns the state row, or null if not found.\n */\nexport function getState(\n  agentId: string,\n  key: string,\n): AgentStateRow | null {\n  const db = getDatabase();\n\n  const row = db.prepare(\n    `SELECT ${SELECT_COLUMNS} FROM agent_state WHERE agent_id = ? AND key = ?`,\n  ).get(agentId, key) as Record<string, unknown> | undefined;\n\n  if (!row) return null;\n  return toAgentStateRow(row);\n}\n\n/**\n * Set a state value for an agent. Inserts or updates on conflict.\n *\n * The composite primary key (agent_id, key) ensures each agent\n * has at most one value per key. On conflict, the value and updated_at\n * are overwritten.\n */\nexport function setState(\n  agentId: string,\n  key: string,\n  value: string,\n  updatedAt: number,\n): AgentStateRow {\n  const db = getDatabase();\n\n  db.prepare(\n    `INSERT INTO agent_state (agent_id, key, value, updated_at)\n     VALUES (?, ?, ?, ?)\n     ON CONFLICT (agent_id, key) DO UPDATE SET\n       value      = EXCLUDED.value,\n       updated_at = EXCLUDED.updated_at`,\n  ).run(agentId, key, value, updatedAt);\n\n  return toAgentStateRow(\n    db.prepare(`SELECT ${SELECT_COLUMNS} FROM agent_state WHERE agent_id = ? AND key = ?`).get(agentId, key) as Record<string, unknown>,\n  );\n}\n\n/**\n * Get all state key-value pairs for an agent, ordered by key ASC.\n */\nexport function getStatesForAgent(\n  agentId: string,\n): AgentStateRow[] {\n  const db = getDatabase();\n\n  const rows = db.prepare(\n    `SELECT ${SELECT_COLUMNS}\n     FROM agent_state\n     WHERE agent_id = ?\n     ORDER BY key ASC`,\n  ).all(agentId) as Record<string, unknown>[];\n\n  return rows.map(toAgentStateRow);\n}\n","/**\n * Vault context builder for agent task prompt injection.\n *\n * Queries SQLite for aggregate vault metrics and agent state,\n * then formats them as a markdown block suitable for inclusion\n * in the agent's task prompt.\n */\n\nimport { getDatabase } from '@myco/db/client.js';\nimport { getStatesForAgent } from '@myco/db/queries/agent-state.js';\n\n// ---------------------------------------------------------------------------\n// Constants\n// ---------------------------------------------------------------------------\n\n/** Default value for unset state entries. */\nconst STATE_UNSET = '(unset)';\n\n/** Key used by the agent to store its last processed batch ID. */\nconst STATE_KEY_LAST_PROCESSED_BATCH = 'last_processed_batch_id';\n\n/** Status value for active spores. */\nconst SPORE_STATUS_ACTIVE = 'active';\n\n// ---------------------------------------------------------------------------\n// Count helpers\n// ---------------------------------------------------------------------------\n\n/**\n * Count rows in a table with optional WHERE clause.\n *\n * The table name is validated by the caller (always a literal from this module).\n * Parameterized `conditions` protect against SQL injection for dynamic values.\n */\nfunction countRows(\n  table: string,\n  conditions: Array<{ clause: string; value: unknown }> = [],\n): number {\n  const db = getDatabase();\n\n  const whereParts: string[] = [];\n  const params: unknown[] = [];\n\n  for (const { clause, value } of conditions) {\n    whereParts.push(clause);\n    params.push(value);\n  }\n\n  const whereClause = whereParts.length > 0 ? `WHERE ${whereParts.join(' AND ')}` : '';\n\n  const row = db.prepare(\n    `SELECT count(*) AS count FROM ${table} ${whereClause}`,\n  ).get(...params) as { count: number };\n\n  return Number(row.count);\n}\n\n// ---------------------------------------------------------------------------\n// Public API\n// ---------------------------------------------------------------------------\n\n/**\n * Build a markdown context block describing the current vault state\n * for a specific agent.\n *\n * Includes:\n * - Agent state key-value pairs (cursor position, preferences)\n * - Aggregate counts (sessions, spores, entities, edges, unprocessed batches)\n * - Last digest timestamp (if any)\n *\n * @param agentId — the agent to build context for.\n * @returns a markdown-formatted string.\n */\nexport function buildVaultContext(agentId: string): string {\n  // All queries are synchronous\n  const states = getStatesForAgent(agentId);\n  const totalSessions = countRows('sessions');\n  const totalActiveSpores = countRows('spores', [{ clause: 'status = ?', value: SPORE_STATUS_ACTIVE }]);\n  const totalEntities = countRows('entities');\n  const totalEdges = countRows('graph_edges');\n  const unprocessedBatches = countRows('prompt_batches', [{ clause: 'processed = ?', value: 0 }]);\n  const lastDigestAt = getLastDigestTimestamp(agentId);\n\n  const stateMap = new Map(states.map((s) => [s.key, s.value]));\n\n  const lastProcessedBatchId = stateMap.get(STATE_KEY_LAST_PROCESSED_BATCH) ?? STATE_UNSET;\n\n  const lines = [\n    '## Current Vault State',\n    `agent_id: ${agentId}`,\n    `last_processed_batch_id: ${lastProcessedBatchId}`,\n    `unprocessed_batches: ${unprocessedBatches}`,\n    `total_sessions: ${totalSessions}`,\n    `total_active_spores: ${totalActiveSpores}`,\n    `total_entities: ${totalEntities}`,\n    `total_edges: ${totalEdges}`,\n    `last_digest_at: ${lastDigestAt}`,\n  ];\n\n  return lines.join('\\n');\n}\n\n/**\n * Get the most recent digest generation timestamp for an agent.\n *\n * @returns epoch seconds of the last digest, or 0 if no digests exist.\n */\nfunction getLastDigestTimestamp(agentId: string): number {\n  const db = getDatabase();\n\n  const row = db.prepare(\n    `SELECT MAX(generated_at) AS max_at\n     FROM digest_extracts\n     WHERE agent_id = ?`,\n  ).get(agentId) as { max_at: number | null } | undefined;\n\n  return row?.max_at ?? 0;\n}\n","/**\n * Orchestrator planning call.\n *\n * Composes the orchestrator prompt, parses the LLM response into a structured\n * plan, and applies phase directives to PhaseDefinition objects.\n *\n * This module is pure logic — no SDK calls. SDK invocation happens in the\n * executor integration (Task 5).\n */\n\nimport fs from 'node:fs';\nimport path from 'node:path';\nimport { fileURLToPath } from 'node:url';\nimport { findPackageRoot } from '@myco/utils/find-package-root.js';\nimport { extractJson } from '@myco/intelligence/response.js';\nimport type { PhaseDefinition, OrchestratorPlan, OrchestratorPhaseDirective } from './types.js';\nimport type { ContextQueryResult } from './context-queries.js';\n\n// ---------------------------------------------------------------------------\n// Constants\n// ---------------------------------------------------------------------------\n\n/** Default max turns for the orchestrator's own LLM call. */\nexport const DEFAULT_ORCHESTRATOR_MAX_TURNS = 3;\n\n/** Filename of the orchestrator prompt template. */\nconst ORCHESTRATOR_PROMPT_FILE = 'orchestrator.md';\n\n/** Number of characters to show from a phase's prompt as a preview. */\nconst PHASE_PROMPT_PREVIEW_CHARS = 100;\n\n/** Section header injected into a phase prompt when contextNotes are present. */\nconst ORCHESTRATOR_GUIDANCE_HEADER = '## Orchestrator Guidance';\n\n/** Placeholder substituted when no context query results are available. */\nconst NO_CONTEXT_QUERIES_TEXT = 'No context queries configured.';\n\n/** Fallback reasoning string used when JSON parsing fails. */\nconst FALLBACK_REASONING_PARSE_ERROR = 'Orchestrator response could not be parsed — running all phases with defaults.';\n\n/** Fallback reasoning string used when the parsed plan has no phases array. */\nconst FALLBACK_REASONING_MISSING_PHASES = 'Orchestrator plan missing phases array — running all phases with defaults.';\n\n// ---------------------------------------------------------------------------\n// Template placeholder names\n// ---------------------------------------------------------------------------\n\nconst PLACEHOLDER_VAULT_STATE = '{{vault_state}}';\nconst PLACEHOLDER_PHASE_DEFINITIONS = '{{phase_definitions}}';\nconst PLACEHOLDER_CONTEXT_RESULTS = '{{context_results}}';\n\n// ---------------------------------------------------------------------------\n// Prompt template loading\n// ---------------------------------------------------------------------------\n\n/**\n * Load the orchestrator prompt template from disk.\n *\n * Resolves the path relative to this file so it works in both dev and built\n * (tsup) environments. The `prompts/` directory is a sibling of this file.\n */\n/** Cached prompt template — loaded once, reused across calls. */\nlet cachedPromptTemplate: string | undefined;\n\nfunction loadPromptTemplate(): string {\n  if (!cachedPromptTemplate) {\n    const scriptDir = path.dirname(fileURLToPath(import.meta.url));\n\n    // Check sibling prompts/ directory first (tsc output or dev mode)\n    const adjacentPath = path.join(scriptDir, 'prompts', ORCHESTRATOR_PROMPT_FILE);\n    if (fs.existsSync(adjacentPath)) {\n      cachedPromptTemplate = fs.readFileSync(adjacentPath, 'utf-8');\n      return cachedPromptTemplate;\n    }\n\n    // tsup bundles into dist/chunk-XXXX.js — walk up to package root\n    const root = findPackageRoot(scriptDir);\n    if (root) {\n      const distPath = path.join(root, 'dist', 'src', 'agent', 'prompts', ORCHESTRATOR_PROMPT_FILE);\n      if (fs.existsSync(distPath)) {\n        cachedPromptTemplate = fs.readFileSync(distPath, 'utf-8');\n        return cachedPromptTemplate;\n      }\n      const srcPath = path.join(root, 'src', 'agent', 'prompts', ORCHESTRATOR_PROMPT_FILE);\n      cachedPromptTemplate = fs.readFileSync(srcPath, 'utf-8');\n      return cachedPromptTemplate;\n    }\n\n    // Final fallback\n    cachedPromptTemplate = fs.readFileSync(adjacentPath, 'utf-8');\n  }\n  return cachedPromptTemplate;\n}\n\n// ---------------------------------------------------------------------------\n// Public API\n// ---------------------------------------------------------------------------\n\n/**\n * Compose the orchestrator prompt by substituting runtime data into the\n * template.\n *\n * @param vaultState     - Free-form summary of current vault state.\n * @param phases         - Phase definitions available for this task.\n * @param contextResults - Results from pre-execution context queries.\n * @returns The fully composed prompt string.\n */\nexport function composeOrchestratorPrompt(\n  vaultState: string,\n  phases: PhaseDefinition[],\n  contextResults: ContextQueryResult[],\n): string {\n  const template = loadPromptTemplate();\n\n  const phaseList = formatPhaseList(phases);\n  const contextSection = formatContextResults(contextResults);\n\n  return template\n    .replace(PLACEHOLDER_VAULT_STATE, vaultState)\n    .replace(PLACEHOLDER_PHASE_DEFINITIONS, phaseList)\n    .replace(PLACEHOLDER_CONTEXT_RESULTS, contextSection);\n}\n\n/**\n * Parse the orchestrator's LLM response into a structured plan.\n *\n * Accepts JSON that is either raw or wrapped in a ```json code block.\n * Validates that the parsed value has a `phases` array.\n *\n * On any failure — malformed JSON, missing array, empty input — returns a\n * safe fallback plan that runs all phases with no modifications.\n *\n * Never throws.\n *\n * @param response - Raw LLM response text.\n * @param phases   - Phase definitions; used to construct the fallback plan.\n * @returns A valid OrchestratorPlan.\n */\nexport function parseOrchestratorPlan(\n  response: string,\n  phases: PhaseDefinition[],\n): OrchestratorPlan {\n  const trimmed = response.trim();\n\n  if (!trimmed) {\n    return buildRunAllPlan(phases, FALLBACK_REASONING_PARSE_ERROR);\n  }\n\n  try {\n    const parsed = extractJson(trimmed);\n\n    if (!isOrchestratorPlanShape(parsed)) {\n      return buildRunAllPlan(phases, FALLBACK_REASONING_MISSING_PHASES);\n    }\n\n    return parsed;\n  } catch {\n    return buildRunAllPlan(phases, FALLBACK_REASONING_PARSE_ERROR);\n  }\n}\n\n/**\n * Apply orchestrator directives to a set of phase definitions.\n *\n * For each phase:\n * - If the directive says `skip: true` and the phase is not required, it is\n *   excluded from the result.\n * - If the directive says `skip: true` but the phase IS required, it is kept\n *   and a warning is logged.\n * - If the directive provides `maxTurns`, the phase's turn limit is overridden.\n * - If the directive provides `contextNotes`, they are appended to the phase\n *   prompt under `## Orchestrator Guidance`.\n *\n * Phase order is preserved. Phases with no matching directive pass through\n * unchanged.\n *\n * @param phases     - Original phase definitions.\n * @param directives - Directives from the orchestrator's plan.\n * @returns Modified phase definitions.\n */\nexport function applyDirectives(\n  phases: PhaseDefinition[],\n  directives: OrchestratorPhaseDirective[],\n): PhaseDefinition[] {\n  const directiveMap = new Map<string, OrchestratorPhaseDirective>(\n    directives.map((d) => [d.name, d]),\n  );\n\n  const result: PhaseDefinition[] = [];\n\n  for (const phase of phases) {\n    const directive = directiveMap.get(phase.name);\n\n    if (!directive) {\n      result.push(phase);\n      continue;\n    }\n\n    if (directive.skip) {\n      if (phase.required) {\n        console.warn(\n          `[orchestrator] Cannot skip required phase \"${phase.name}\" — keeping it. Reason: ${directive.skipReason ?? 'none given'}`,\n        );\n        result.push(applyNonSkipDirective(phase, directive));\n      }\n      // Non-required phases with skip: true are simply excluded.\n      continue;\n    }\n\n    result.push(applyNonSkipDirective(phase, directive));\n  }\n\n  return result;\n}\n\n// ---------------------------------------------------------------------------\n// Private helpers\n// ---------------------------------------------------------------------------\n\n/**\n * Apply non-skip directive fields (maxTurns, contextNotes) to a phase.\n */\nfunction applyNonSkipDirective(\n  phase: PhaseDefinition,\n  directive: OrchestratorPhaseDirective,\n): PhaseDefinition {\n  let updated = { ...phase };\n\n  if (directive.maxTurns !== undefined) {\n    updated = { ...updated, maxTurns: directive.maxTurns };\n  }\n\n  if (directive.contextNotes) {\n    updated = {\n      ...updated,\n      prompt: `${updated.prompt}\\n\\n${ORCHESTRATOR_GUIDANCE_HEADER}\\n\\n${directive.contextNotes}`,\n    };\n  }\n\n  return updated;\n}\n\n/**\n * Format phases as a bulleted list for the prompt template.\n */\nfunction formatPhaseList(phases: PhaseDefinition[]): string {\n  if (phases.length === 0) {\n    return '(no phases defined)';\n  }\n\n  return phases\n    .map((p) => {\n      const preview = p.prompt.slice(0, PHASE_PROMPT_PREVIEW_CHARS);\n      const ellipsis = p.prompt.length > PHASE_PROMPT_PREVIEW_CHARS ? '...' : '';\n      return `- **${p.name}** (maxTurns: ${p.maxTurns}, required: ${p.required}): ${preview}${ellipsis}`;\n    })\n    .join('\\n');\n}\n\n/**\n * Format context query results as sections for the prompt template.\n */\nfunction formatContextResults(results: ContextQueryResult[]): string {\n  if (results.length === 0) {\n    return NO_CONTEXT_QUERIES_TEXT;\n  }\n\n  return results\n    .map((r) => {\n      const dataSection = r.error\n        ? `Error: ${r.error}`\n        : JSON.stringify(r.data, null, 2);\n      return `### ${r.tool}\\nPurpose: ${r.purpose}\\n\\n${dataSection}`;\n    })\n    .join('\\n\\n');\n}\n\n/**\n * Type guard: check that a parsed value has the OrchestratorPlan shape.\n */\nfunction isOrchestratorPlanShape(value: unknown): value is OrchestratorPlan {\n  if (typeof value !== 'object' || value === null) return false;\n  const obj = value as Record<string, unknown>;\n  return Array.isArray(obj['phases']);\n}\n\n/**\n * Build a fallback \"run everything\" plan from the available phases.\n */\nfunction buildRunAllPlan(phases: PhaseDefinition[], reasoning: string): OrchestratorPlan {\n  return {\n    phases: phases.map((p) => ({ name: p.name, skip: false })),\n    reasoning,\n  };\n}\n","/**\n * Clean LLM response text before parsing.\n *\n * Reasoning models (DeepSeek, Qwen, GLM, etc.) embed chain-of-thought\n * in the response using special tags. These must be stripped before\n * JSON parsing or value extraction.\n */\n\n// Patterns for reasoning model chain-of-thought tokens.\n// Order matters: most specific patterns first.\nconst REASONING_PATTERNS = [\n  // <think>...</think>answer  (DeepSeek, Qwen, GLM, many others)\n  /<think>[\\s\\S]*?<\\/think>\\s*/gi,\n  // Implicit opening: reasoning...</think>answer  (GLM-4.7 observed)\n  /^[\\s\\S]*?<\\/think>\\s*/i,\n  // <reasoning>...</reasoning>answer\n  /<reasoning>[\\s\\S]*?<\\/reasoning>\\s*/gi,\n  // <|thinking|>...<|/thinking|>answer\n  /<\\|thinking\\|>[\\s\\S]*?<\\|\\/thinking\\|>\\s*/gi,\n  // Plain-text \"Thinking Process:\" block followed by actual content\n  // (Qwen 3.5 via LM Studio without native thinking mode)\n  // Matches from \"Thinking Process:\" up to the last numbered step, then the synthesis follows\n  /^Thinking Process:[\\s\\S]*?(?=\\n(?:## |# |\\*\\*[A-Z]))/i,\n];\n\n/**\n * Strip reasoning/chain-of-thought tokens from LLM response text.\n * Returns the final answer without the thinking process.\n */\nexport function stripReasoningTokens(text: string): string {\n  if (!text) return text;\n\n  for (const pattern of REASONING_PATTERNS) {\n    const stripped = text.replace(pattern, '').trim();\n    if (stripped && stripped !== text.trim()) {\n      return stripped;\n    }\n  }\n\n  return text;\n}\n\n/**\n * Extract JSON from an LLM response that may contain markdown fences,\n * reasoning tokens, or other wrapper text.\n *\n * Tries in order:\n * 1. Strip reasoning tokens\n * 2. Extract from ```json ... ``` code fences\n * 3. Find bare {...} JSON object\n * 4. Parse the cleaned text directly\n */\nexport function extractJson(text: string): unknown {\n  const cleaned = stripReasoningTokens(text);\n\n  // Try code fence extraction\n  const fenceMatch = cleaned.match(/```(?:json)?\\s*\\n?([\\s\\S]*?)\\n?```/);\n  if (fenceMatch) {\n    return JSON.parse(fenceMatch[1].trim());\n  }\n\n  // Try bare JSON object\n  const objectMatch = cleaned.match(/\\{[\\s\\S]*\\}/);\n  if (objectMatch) {\n    return JSON.parse(objectMatch[0]);\n  }\n\n  // Try direct parse\n  return JSON.parse(cleaned);\n}\n\n/**\n * Extract a numeric value from an LLM response that may contain\n * reasoning tokens or extra text around the number.\n */\nexport function extractNumber(text: string): number {\n  const cleaned = stripReasoningTokens(text).trim();\n  const match = cleaned.match(/(\\d+\\.?\\d*)/);\n  if (match) return parseFloat(match[1]);\n  return parseFloat(cleaned);\n}\n","/**\n * Context query execution for pre-phase vault lookups.\n *\n * Executes lightweight vault queries before the orchestrator makes planning\n * decisions. Uses the same DB query functions as the vault tools but bypasses\n * the MCP layer entirely.\n */\n\nimport type { ContextQuery } from './types.js';\nimport { errorMessage as toErrorMessage } from '@myco/utils/error-message.js';\nimport { getUnprocessedBatches } from '@myco/db/queries/batches.js';\nimport { listSpores } from '@myco/db/queries/spores.js';\nimport { listSessions } from '@myco/db/queries/sessions.js';\nimport { getStatesForAgent } from '@myco/db/queries/agent-state.js';\n\n// ---------------------------------------------------------------------------\n// Constants\n// ---------------------------------------------------------------------------\n\n/** Default limit for context query results when none specified. */\nconst DEFAULT_CONTEXT_QUERY_LIMIT = 10;\n\n// ---------------------------------------------------------------------------\n// Types\n// ---------------------------------------------------------------------------\n\n/** Result of a single context query execution. */\nexport interface ContextQueryResult {\n  tool: string;\n  purpose: string;\n  data: unknown;\n  error?: string;\n}\n\n// ---------------------------------------------------------------------------\n// Public API\n// ---------------------------------------------------------------------------\n\n/**\n * Execute a list of context queries against the vault database.\n *\n * Each query is routed to the appropriate DB function based on `query.tool`.\n * On failure:\n * - Required queries throw — the caller should abort.\n * - Optional queries return a result with `error` set and `data: null`.\n *\n * Unknown tool names always throw, regardless of `required`.\n *\n * @param agentId - The agent ID to scope agent-specific queries.\n * @param queries - The list of context queries to execute.\n * @returns Resolved results in the same order as the input queries.\n */\nexport async function executeContextQueries(\n  agentId: string,\n  queries: ContextQuery[],\n): Promise<ContextQueryResult[]> {\n  // Validate all tool names upfront — unknown tools are a programming error.\n  for (const query of queries) {\n    validateTool(query.tool);\n  }\n\n  // Execute all queries in parallel — they hit independent DB tables.\n  const settled = await Promise.allSettled(\n    queries.map(async (query) => {\n      const limit = query.limit ?? 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Only creates a new object when overrides are required,\n * avoiding unnecessary copies of the full process.env.\n */\nexport function buildPhaseEnv(provider?: ProviderConfig): Record<string, string | undefined> | undefined {\n  if (!provider || provider.type === 'cloud') return undefined;\n  return { ...process.env, ...getProviderEnvVars(provider) };\n}\n\n/**\n * Get env vars for a provider config.\n */\nexport function getProviderEnvVars(provider: ProviderConfig): Record<string, string> {\n  switch (provider.type) {\n    case 'cloud':\n      return {};\n    case 'ollama':\n      return {\n        [ENV_ANTHROPIC_BASE_URL]: provider.baseUrl ?? DEFAULT_OLLAMA_URL,\n        [ENV_ANTHROPIC_AUTH_TOKEN]: OLLAMA_AUTH_TOKEN,\n        [ENV_ANTHROPIC_API_KEY]: '',\n        ...(provider.contextLength ? { [ENV_OLLAMA_NUM_CTX]: String(provider.contextLength) } : {}),\n      };\n    case 'lmstudio':\n      return {\n        [ENV_ANTHROPIC_BASE_URL]: provider.baseUrl ?? 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package/dist/{init-7PCZOANM.js → init-KWCGGLP3.js}

@@ -5,7 +5,7 @@ import {
 import {
   VAULT_GITIGNORE,
   registerSymbionts
-} from "./chunk-EASRP2I3.js";
+} from "./chunk-HSMD2COQ.js";
 import {
   parseStringFlag
 } from "./chunk-SAKJMNSR.js";
@@ -24,8 +24,8 @@ import {
   initDatabase,
   vaultDbPath
 } from "./chunk-MYX5NCRH.js";
-import "./chunk-IUJLMJKN.js";
-import "./chunk-5JZWS63K.js";
+import "./chunk-QMGQSA5A.js";
+import "./chunk-PGYJSXSK.js";
 import {
   detectSymbionts,
   loadManifests,
@@ -52,7 +52,7 @@ async function run(args) {
   const nonInteractive = args.includes("--non-interactive");
   const isInteractive = !nonInteractive && !!process.stdin.isTTY;
   if (isInteractive) {
-    const { printBanner } = await import("./init-wizard-EQZ7YTRT.js");
+    const { printBanner } = await import("./init-wizard-YUT7MIYZ.js");
     printBanner();
   }
   const vaultDir = vaultPath ? vaultPath.startsWith("~/") ? path.join(os.homedir(), vaultPath.slice(2)) : path.resolve(vaultPath) : path.join(resolveVaultDir());
@@ -82,7 +82,7 @@ async function run(args) {
     }
   }
   if (shouldRunWizard) {
-    const { runWizard, buildEmbeddingConfig, buildAgentConfig } = await import("./init-wizard-EQZ7YTRT.js");
+    const { runWizard, buildEmbeddingConfig, buildAgentConfig } = await import("./init-wizard-YUT7MIYZ.js");
     const answers = await runWizard();
     wizardAnswers = answers;
     if (answers.embeddingProvider !== "skip") {
@@ -163,7 +163,7 @@ async function run(args) {
       registerSymbionts(selectedManifests, projectRoot, pkgRoot, "Registered");
     }
   }
-  const { DaemonClient } = await import("./client-CA4TAT5Q.js");
+  const { DaemonClient } = await import("./client-ZXC6IY63.js");
   const client = new DaemonClient(vaultDir);
   const daemonHealthy = await client.ensureRunning();
   let daemonUrl = "";
@@ -193,4 +193,4 @@ async function run(args) {
 export {
   run
 };
-//# sourceMappingURL=init-7PCZOANM.js.map
+//# sourceMappingURL=init-KWCGGLP3.js.map

package/dist/{init-wizard-EQZ7YTRT.js → init-wizard-YUT7MIYZ.js}

@@ -12,7 +12,7 @@ import {
 import "./chunk-5YQ6VOFZ.js";
 import {
   getPluginVersion
-} from "./chunk-5JZWS63K.js";
+} from "./chunk-PGYJSXSK.js";
 import "./chunk-LPUQPDC2.js";
 import {
   DEFAULT_OLLAMA_EMBEDDING_MODEL,
@@ -291,4 +291,4 @@ export {
   printBanner,
   runWizard
 };
-//# sourceMappingURL=init-wizard-EQZ7YTRT.js.map
+//# sourceMappingURL=init-wizard-YUT7MIYZ.js.map

package/dist/{main-RDRKAEEB.js → main-WHGJ6UV7.js}

@@ -65,7 +65,7 @@ import {
   getEmbeddingQueueDepth,
   getUnembedded,
   markEmbedded
-} from "./chunk-CD5SYW45.js";
+} from "./chunk-XRVLSSJY.js";
 import {
   getMachineId
 } from "./chunk-ENWBFX7F.js";
@@ -93,7 +93,7 @@ import {
   readSecrets,
   writeSecret
 } from "./chunk-RJMXDUMA.js";
-import "./chunk-EASRP2I3.js";
+import "./chunk-HSMD2COQ.js";
 import "./chunk-SAKJMNSR.js";
 import {
   checkLocalProvider
@@ -164,10 +164,10 @@ import {
 } from "./chunk-MYX5NCRH.js";
 import {
   resolveCliEntryPath
-} from "./chunk-IUJLMJKN.js";
+} from "./chunk-QMGQSA5A.js";
 import {
   getPluginVersion
-} from "./chunk-5JZWS63K.js";
+} from "./chunk-PGYJSXSK.js";
 import {
   loadManifests
 } from "./chunk-QFMBZ72S.js";
@@ -5241,7 +5241,7 @@ async function main() {
   async function triggerTitleSummary(sessionId) {
     if (config.agent.summary_batch_interval <= 0) return;
     try {
-      const { runAgent } = await import("./executor-SK3XFJQ7.js");
+      const { runAgent } = await import("./executor-YX2MA4T3.js");
       runAgent(vaultDir, {
         task: "title-summary",
         instruction: `Process session ${sessionId} only`,
@@ -6001,7 +6001,7 @@ async function main() {
     if (task === "skill-generate" && !instruction) {
       instruction = buildSkillGenerateInstruction();
     }
-    const { runAgent } = await import("./executor-SK3XFJQ7.js");
+    const { runAgent } = await import("./executor-YX2MA4T3.js");
     const resultPromise = runAgent(vaultDir, { task, instruction, agentId, embeddingManager });
     const effectiveAgentId = agentId ?? "myco-agent";
     const runId = getLatestRunId(effectiveAgentId, task);
@@ -6412,7 +6412,7 @@ async function main() {
           else runningTasks.delete(name);
         },
         runTask: async (taskName) => {
-          const { runAgent } = await import("./executor-SK3XFJQ7.js");
+          const { runAgent } = await import("./executor-YX2MA4T3.js");
           const instruction = taskName === "skill-generate" ? buildSkillGenerateInstruction() : void 0;
           const result = await runAgent(vaultDir, { task: taskName, instruction, embeddingManager });
           logger.info(LOG_KINDS.AGENT_RUN, `Scheduled task ${taskName} completed`, {
@@ -6522,4 +6522,4 @@ export {
   handleUserPrompt,
   main
 };
-//# sourceMappingURL=main-RDRKAEEB.js.map
+//# sourceMappingURL=main-WHGJ6UV7.js.map

package/dist/{open-GE6DB5GH.js → open-CBNGDM32.js}

@@ -1,13 +1,13 @@
 import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
 import {
   connectToDaemon
-} from "./chunk-EASRP2I3.js";
+} from "./chunk-HSMD2COQ.js";
 import "./chunk-SAKJMNSR.js";
 import "./chunk-TNCBMGWB.js";
 import "./chunk-HHZ3RTEI.js";
 import "./chunk-MYX5NCRH.js";
-import "./chunk-IUJLMJKN.js";
-import "./chunk-5JZWS63K.js";
+import "./chunk-QMGQSA5A.js";
+import "./chunk-PGYJSXSK.js";
 import "./chunk-LPUQPDC2.js";
 import "./chunk-TRA3R4EC.js";
 import "./chunk-S6I62FAH.js";
@@ -36,4 +36,4 @@ async function run(_args, vaultDir) {
 export {
   run
 };
-//# sourceMappingURL=open-GE6DB5GH.js.map
+//# sourceMappingURL=open-CBNGDM32.js.map

package/dist/{post-compact-YIOMON3E.js → post-compact-AANLN7TR.js}

@@ -1,11 +1,11 @@
 import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
 import {
   sendEvent
-} from "./chunk-PLMMWIJC.js";
+} from "./chunk-NBPZI5UD.js";
 import "./chunk-V7XG6V6C.js";
 import "./chunk-OQVKLTQY.js";
-import "./chunk-IUJLMJKN.js";
-import "./chunk-5JZWS63K.js";
+import "./chunk-QMGQSA5A.js";
+import "./chunk-PGYJSXSK.js";
 import "./chunk-QFMBZ72S.js";
 import "./chunk-LPUQPDC2.js";
 import "./chunk-TRA3R4EC.js";
@@ -27,4 +27,4 @@ async function main() {
 export {
   main
 };
-//# sourceMappingURL=post-compact-YIOMON3E.js.map
+//# sourceMappingURL=post-compact-AANLN7TR.js.map

package/dist/{post-tool-use-YRSXGMEC.js → post-tool-use-X3IFZEMV.js}

@@ -8,8 +8,8 @@ import {
 } from "./chunk-OQVKLTQY.js";
 import {
   DaemonClient
-} from "./chunk-IUJLMJKN.js";
-import "./chunk-5JZWS63K.js";
+} from "./chunk-QMGQSA5A.js";
+import "./chunk-PGYJSXSK.js";
 import "./chunk-QFMBZ72S.js";
 import "./chunk-LPUQPDC2.js";
 import {
@@ -60,4 +60,4 @@ async function main() {
 export {
   main
 };
-//# sourceMappingURL=post-tool-use-YRSXGMEC.js.map
+//# sourceMappingURL=post-tool-use-X3IFZEMV.js.map

package/dist/{post-tool-use-failure-XNNJ6INZ.js → post-tool-use-failure-T6KAFDFF.js}

@@ -1,11 +1,11 @@
 import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
 import {
   sendEvent
-} from "./chunk-PLMMWIJC.js";
+} from "./chunk-NBPZI5UD.js";
 import "./chunk-V7XG6V6C.js";
 import "./chunk-OQVKLTQY.js";
-import "./chunk-IUJLMJKN.js";
-import "./chunk-5JZWS63K.js";
+import "./chunk-QMGQSA5A.js";
+import "./chunk-PGYJSXSK.js";
 import "./chunk-QFMBZ72S.js";
 import "./chunk-LPUQPDC2.js";
 import "./chunk-TRA3R4EC.js";
@@ -29,4 +29,4 @@ async function main() {
 export {
   main
 };
-//# sourceMappingURL=post-tool-use-failure-XNNJ6INZ.js.map
+//# sourceMappingURL=post-tool-use-failure-T6KAFDFF.js.map

package/dist/{pre-compact-X7BNZVUO.js → pre-compact-FY7BPS4J.js}

@@ -1,11 +1,11 @@
 import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
 import {
   sendEvent
-} from "./chunk-PLMMWIJC.js";
+} from "./chunk-NBPZI5UD.js";
 import "./chunk-V7XG6V6C.js";
 import "./chunk-OQVKLTQY.js";
-import "./chunk-IUJLMJKN.js";
-import "./chunk-5JZWS63K.js";
+import "./chunk-QMGQSA5A.js";
+import "./chunk-PGYJSXSK.js";
 import "./chunk-QFMBZ72S.js";
 import "./chunk-LPUQPDC2.js";
 import "./chunk-TRA3R4EC.js";
@@ -26,4 +26,4 @@ async function main() {
 export {
   main
 };
-//# sourceMappingURL=pre-compact-X7BNZVUO.js.map
+//# sourceMappingURL=pre-compact-FY7BPS4J.js.map