@goondocks/myco 0.17.1 → 0.17.2

package/dist/executor-NXKJU5KW.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/agent/executor.ts","../src/agent/tools.ts","../src/agent/tools/read-tools.ts","../src/db/queries/agent-state.ts","../src/agent/tools/types.ts","../src/agent/tools/write-tools.ts","../src/agent/tools/observability-tools.ts","../src/agent/tools/skill-tools.ts","../src/agent/tools/skill-validator.ts","../src/agent/context.ts","../src/agent/orchestrator.ts","../src/intelligence/response.ts","../src/agent/context-queries.ts","../src/agent/provider.ts","../src/agent/ollama-context.ts","../src/agent/wave-computation.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 { 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 { loadSystemPrompt } from './loader.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 { resolveRunConfig } from './config-resolver.js';\nimport { resolveOllamaContextVariants } from './ollama-context.js';\nimport { computeWaves, phaseSessionId } from './wave-computation.js';\nimport { SKILL_GENERATE_TASK } from './instruction-builders.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// Re-export computeWaves for backward compatibility (tests import from executor)\nexport { computeWaves } from './wave-computation.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// Per-turn tool-call debug logging\n// ---------------------------------------------------------------------------\n//\n// When MYCO_AGENT_DEBUG=1, every tool_use and tool_result inside a phase is\n// logged to stdout with a short input/output preview. This is intended for\n// diagnosing turn-budget exhaustion: it surfaces rejection loops, malformed\n// tool-call retries, and unexpected exploration that the per-phase\n// `num_turns` summary alone cannot explain.\n//\n// The daemon sets this env var automatically when log_level is \"debug\"\n// (see src/daemon/main.ts). It can also be set manually for ad-hoc runs.\n\nconst DEBUG_TOOL_CALLS = process.env.MYCO_AGENT_DEBUG === '1';\n\n/** Max chars to print from tool input/output payloads. */\nconst TOOL_DEBUG_PREVIEW_CHARS = 240;\n\ninterface SdkContentBlock {\n  type: string;\n  name?: string;\n  input?: unknown;\n  tool_use_id?: string;\n  content?: unknown;\n  is_error?: boolean;\n}\n\ninterface SdkMessageWithContent {\n  message?: { content?: SdkContentBlock[] };\n}\n\nfunction previewPayload(value: unknown): string {\n  const str = typeof value === 'string' ? value : JSON.stringify(value);\n  if (str === undefined) return '';\n  return str.length > TOOL_DEBUG_PREVIEW_CHARS\n    ? `${str.slice(0, TOOL_DEBUG_PREVIEW_CHARS)}…(${str.length - TOOL_DEBUG_PREVIEW_CHARS} more chars)`\n    : str;\n}\n\nfunction logToolUseBlocks(phaseName: string, message: unknown): void {\n  if (!DEBUG_TOOL_CALLS) return;\n  const blocks = (message as SdkMessageWithContent).message?.content;\n  if (!Array.isArray(blocks)) return;\n  for (const block of blocks) {\n    if (block.type === 'tool_use') {\n      console.log(\n        `[agent:debug] ${phaseName} tool_use: ${block.name ?? 'unknown'} input=${previewPayload(block.input)}`,\n      );\n    }\n  }\n}\n\nfunction logToolResultBlocks(phaseName: string, message: unknown): void {\n  if (!DEBUG_TOOL_CALLS) return;\n  const blocks = (message as SdkMessageWithContent).message?.content;\n  if (!Array.isArray(blocks)) return;\n  for (const block of blocks) {\n    if (block.type === 'tool_result') {\n      const flag = block.is_error ? ' [ERROR]' : '';\n      console.log(\n        `[agent:debug] ${phaseName} tool_result${flag}: ${previewPayload(block.content)}`,\n      );\n    }\n  }\n}\n\n// ---------------------------------------------------------------------------\n// Prompt composition\n// ---------------------------------------------------------------------------\n\n/**\n * Build the full task prompt from vault context, task definition, and\n * optional user instruction.\n *\n * Task prompts support template variables:\n * - `{{session_id}}` — replaced with the session ID from instruction (if present)\n * - `{{instruction}}` — the raw user instruction text\n */\nexport function composeTaskPrompt(\n  vaultContext: string,\n  taskDisplayName: string,\n  taskPrompt: string,\n  instruction?: string,\n): string {\n  // Extract session_id from instruction if it contains one (UUID pattern)\n  const sessionIdMatch = instruction?.match(/\\b([0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12})\\b/i);\n  const sessionId = sessionIdMatch?.[1] ?? '';\n\n  // Template variable substitution in task prompt\n  let resolvedPrompt = taskPrompt;\n  resolvedPrompt = resolvedPrompt.replace(/\\{\\{session_id\\}\\}/g, sessionId);\n  resolvedPrompt = resolvedPrompt.replace(/\\{\\{instruction\\}\\}/g, instruction ?? '');\n\n  const parts = [\n    vaultContext,\n    `${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// 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 agenticTurns = 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 === 'assistant') {\n        agenticTurns++;\n        logToolUseBlocks(phase.name, message);\n      }\n      if (message.type === 'user') {\n        logToolResultBlocks(phase.name, message);\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.maxTurns) {\n      console.log(\n        `[agent] Phase \"${phase.name}\": num_turns=${phaseTurns}, assistant_msgs=${agenticTurns}, budget=${phase.maxTurns}`,\n      );\n    }\n\n    if (phase.required && phaseTurns === 0) {\n      console.warn(`[agent] Required phase \"${phase.name}\" produced 0 turns`);\n    }\n\n    // Use SDK's num_turns — it's what the SDK enforces against.\n    // agenticTurns (assistant message count) is logged for diagnostics\n    // but not reliable as the primary metric.\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    const orchestratorEnv = { ...(buildPhaseEnv(taskProviderOverride) ?? process.env), MYCO_AGENT_SESSION: '1' };\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        strictMcpConfig: true,\n        env: orchestratorEnv,\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          readOnly: phase.readOnly,\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 from all sources\n  const {\n    config,\n    definitionsDir,\n    taskProviderOverride: resolvedTaskProvider,\n    phaseProviderOverrides: resolvedPhaseOverrides,\n  } = resolveRunConfig(agentId, requestedTask, vaultDir);\n\n  // Both are mutated by the Ollama variant resolver below — it rewrites\n  // provider.model to the variant name and may reconcile context conflicts.\n  let taskProviderOverride = resolvedTaskProvider;\n  let phaseProviderOverrides = resolvedPhaseOverrides;\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 ?? 'anthropic',\n    ...(effectiveProvider?.baseUrl ? { baseUrl: effectiveProvider.baseUrl } : {}),\n  };\n\n  // 7. Resolve Ollama context variants across task + phase scopes.\n  //    Applies DEFAULT_OLLAMA_CONTEXT_LENGTH when no value is set, and\n  //    reconciles same-model-different-context conflicts to one variant\n  //    per model (max wins) so Ollama loads each model at most once.\n  //    Non-ollama providers are passed through unchanged.\n  {\n    const resolved = await resolveOllamaContextVariants(\n      taskProviderOverride,\n      phaseProviderOverrides,\n    );\n    taskProviderOverride = resolved.taskProvider;\n    phaseProviderOverrides = resolved.phaseOverrides;\n    for (const conflict of resolved.conflicts) {\n      console.warn(\n        `[agent] Ollama model \"${conflict.model}\" referenced with conflicting ` +\n        `context_length values [${conflict.values.join(', ')}] — reconciled to ` +\n        `${conflict.resolved} to avoid loading multiple variants. Configure one ` +\n        `value per model to silence this warning.`,\n      );\n    }\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\n      // A required-phase failure stops the pipeline (executePhasedQuery breaks\n      // the wave loop) but returns normally. Surface it as a run-level failure\n      // by throwing — the catch block writes STATUS_FAILED while preserving\n      // the accumulated phase results in the DB row.\n      const requiredPhaseNames = new Set(\n        config.phases!.filter((p) => p.required).map((p) => p.name),\n      );\n      const failedRequired = phaseResults.find(\n        (p) => p.status === 'failed' && requiredPhaseNames.has(p.name),\n      );\n      if (failedRequired) {\n        throw new Error(\n          `Required phase \"${failedRequired.name}\" failed: ${failedRequired.summary}`,\n        );\n      }\n    } else {\n      // Single-query execution (backward compatible)\n      const taskPrompt = composeTaskPrompt(\n        vaultContext,\n        config.taskDisplayName,\n        config.taskPrompt,\n        options?.instruction,\n      );\n\n      // Provider priority for single-query: myco.yaml task override → task execution config → default\n      const singleProvider = taskProviderOverride ?? config.execution?.provider;\n\n      const result = await executeSingleQuery(\n        config,\n        systemPrompt,\n        taskPrompt,\n        agentId,\n        runId,\n        singleProvider,\n        options?.embeddingManager,\n        taskAbortController,\n        vaultDir,\n      );\n      tokensUsed = result.tokensUsed;\n      costUsd = result.costUsd;\n    }\n\n    clearTimeout(timeoutId);\n    const completedAt = epochSeconds();\n    updateRunStatus(runId, STATUS_COMPLETED, {\n      completed_at: completedAt,\n      tokens_used: tokensUsed,\n      cost_usd: costUsd,\n      actions_taken: JSON.stringify({ ...runMeta, ...(phaseResults ? { phases: phaseResults } : {}) }),\n    });\n\n    return {\n      runId,\n      status: STATUS_COMPLETED,\n      tokensUsed,\n      costUsd,\n      ...(phaseResults ? { phases: phaseResults } : {}),\n    };\n  } catch (err) {\n    clearTimeout(timeoutId);\n    // 7. Error handling — mark run as failed, preserve phase results\n    // Aggressively extract error info — the SDK may throw non-Error objects\n    let errorMessage: string;\n    if (err instanceof Error) {\n      errorMessage = err.message || err.constructor.name || 'Error (no message)';\n      if (err.stack) errorMessage += `\\n${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    await cleanupOnTaskFailure({\n      taskName: config.taskName,\n      vaultDir,\n      runContext: options?.runContext,\n    });\n\n    return {\n      runId,\n      status: STATUS_FAILED,\n      error: errorMessage,\n      ...(phaseResults ? { phases: phaseResults } : {}),\n    };\n  }\n}\n\n/**\n * Task-specific cleanup fired when a run ends in failure. Exported\n * for direct unit testing — the real executor call site lives in\n * runAgent's catch block.\n *\n * skill-generate: the draft phase stages SKILL.md + manifest to\n * .myco/staging/skills/<candidate_id>/ via vault_stage_skill. If the\n * validate phase (or any later required phase) fails, the staged\n * content must be removed so the next generate cycle doesn't find an\n * orphan draft. The daemon periodic sweep is the belt-and-suspenders\n * backup for anything this hook misses.\n */\nexport async function cleanupOnTaskFailure(args: {\n  taskName: string | undefined;\n  vaultDir: string | undefined;\n  runContext: RunOptions['runContext'];\n}): Promise<void> {\n  if (args.taskName !== SKILL_GENERATE_TASK) return;\n  if (!args.vaultDir) return;\n  const candidateId = args.runContext?.candidate_id;\n  if (!candidateId) return;\n\n  try {\n    const { cleanupStagedSkill } = await import('./tools/skill-staging.js');\n    cleanupStagedSkill(args.vaultDir, candidateId);\n    console.warn(\n      `[agent] skill-generate failed — cleaned up staging for candidate ${candidateId}`,\n    );\n  } catch (cleanupErr) {\n    console.warn(\n      `[agent] Failed to clean staging for candidate ${candidateId}:`,\n      cleanupErr instanceof Error ? cleanupErr.message : cleanupErr,\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 (8): vault_unprocessed, vault_spores, vault_sessions, vault_search_fts,\n *                    vault_search_semantic, vault_state, vault_entities, vault_edges\n * - Write tools (9): vault_create_spore, vault_create_entity, vault_create_edge,\n *                     vault_resolve_spore, vault_update_session, vault_set_state,\n *                     vault_read_digest, vault_write_digest, vault_mark_processed\n * - Observability (1): vault_report\n * - Skill tools (3): vault_skill_candidates, vault_skill_records, vault_write_skill\n *\n * `agentId` and `runId` are captured in closures — tools inject them\n * automatically so the agent cannot impersonate another agent.\n */\n\nimport { createSdkMcpServer } from '@anthropic-ai/claude-agent-sdk';\nimport { epochSeconds } from '@myco/constants.js';\nimport { getPluginVersion } from '@myco/version.js';\nimport { insertTurn } from '@myco/db/queries/turns.js';\nimport { createReadTools } from './tools/read-tools.js';\nimport { createWriteTools } from './tools/write-tools.js';\nimport { createObservabilityTools } from './tools/observability-tools.js';\nimport { createSkillTools } from './tools/skill-tools.js';\nimport type { VaultToolDeps } from './tools/types.js';\nimport type { EmbeddingManager } from '@myco/daemon/embedding/index.js';\nimport type { TeamSyncClient } from '@myco/daemon/team-sync.js';\n\n// Re-exports for backward compatibility\nexport { validateSkillContent, MAX_SKILL_LINES, REQUIRED_FRONTMATTER_FIELDS } from './tools/skill-validator.js';\n\n// ---------------------------------------------------------------------------\n// Constants\n// ---------------------------------------------------------------------------\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// Tool definitions factory\n// ---------------------------------------------------------------------------\n\n// ---------------------------------------------------------------------------\n// Tool group membership — used to skip factory calls for unneeded groups\n// ---------------------------------------------------------------------------\n\nconst READ_TOOL_NAMES = new Set([\n  'vault_unprocessed', 'vault_spores', 'vault_sessions', 'vault_search_fts',\n  'vault_search_semantic', 'vault_state', 'vault_entities', 'vault_edges',\n]);\n\nconst WRITE_TOOL_NAMES = new Set([\n  'vault_create_spore', 'vault_create_entity', 'vault_create_edge',\n  'vault_resolve_spore', 'vault_update_session', 'vault_set_state',\n  'vault_read_digest', 'vault_write_digest', 'vault_mark_processed',\n]);\n\nconst OBSERVABILITY_TOOL_NAMES = new Set(['vault_report']);\n\nconst SKILL_TOOL_NAMES = new Set([\n  'vault_skill_candidates', 'vault_skill_records', 'vault_write_skill',\n  'vault_stage_skill', 'vault_finalize_skill',\n]);\n\n/**\n * Total number of vault tools defined. Derived from the union of the\n * four tool-group sets above so this constant can never drift from the\n * actual factory output — adding a tool to a group bumps the count\n * automatically. Each set is disjoint so the straight sum is correct.\n */\nexport const VAULT_TOOL_COUNT =\n  READ_TOOL_NAMES.size +\n  WRITE_TOOL_NAMES.size +\n  OBSERVABILITY_TOOL_NAMES.size +\n  SKILL_TOOL_NAMES.size;\n\nfunction setsOverlap(a: Set<string>, b: Set<string>): boolean {\n  for (const item of a) { if (b.has(item)) return true; }\n  return false;\n}\n\n/**\n * Create vault tool definitions for the agent.\n *\n * When `onlyNames` is provided, only tool groups that contain at least one\n * requested name are instantiated — avoids building all 21 closures when\n * a phase only needs 2-3 tools.\n *\n * Exposed for testing (call handler directly) and for the MCP server factory.\n */\nexport function createVaultTools(agentId: string, runId: string, options?: VaultToolOptions & { onlyNames?: Set<string> }) {\n  const { turnOffset = 0, embeddingManager, teamClient, machineId, projectRoot, vaultDir, onlyNames } = options ?? {};\n\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  const deps: VaultToolDeps = {\n    agentId,\n    runId,\n    embeddingManager,\n    teamClient,\n    machineId,\n    projectRoot,\n    vaultDir,\n    recordTurn,\n  };\n\n  // When onlyNames is provided, skip factory calls for groups with no overlap\n  const needsAll = !onlyNames;\n  return [\n    ...(needsAll || setsOverlap(onlyNames!, READ_TOOL_NAMES) ? createReadTools(deps) : []),\n    ...(needsAll || setsOverlap(onlyNames!, WRITE_TOOL_NAMES) ? createWriteTools(deps) : []),\n    ...(needsAll || setsOverlap(onlyNames!, OBSERVABILITY_TOOL_NAMES) ? createObservabilityTools(deps) : []),\n    ...(needsAll || setsOverlap(onlyNames!, SKILL_TOOL_NAMES) ? createSkillTools(deps) : []),\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'> & { readOnly?: boolean },\n) {\n  const nameSet = new Set(toolNames);\n  const allTools = createVaultTools(agentId, runId, { ...options, onlyNames: nameSet });\n  // readOnly gate first — structural enforcement before name scoping,\n  // so a write tool in the name list can never pass the readOnly filter.\n  const eligible = options?.readOnly\n    ? allTools.filter((t) => t.annotations?.readOnlyHint === true)\n    : allTools;\n  const scopedTools = eligible.filter((t) => nameSet.has(t.name));\n\n  return createSdkMcpServer({\n    name: 'myco-vault',\n    version: getPluginVersion(),\n    tools: scopedTools,\n  });\n}\n","/**\n * Read-only vault tools.\n *\n * 8 tools: vault_unprocessed, vault_spores, vault_sessions, vault_search_fts,\n * vault_search_semantic, vault_state, vault_entities, vault_edges\n */\n\nimport { z } from 'zod/v4';\nimport { tool } from '@anthropic-ai/claude-agent-sdk';\nimport { SEARCH_SIMILARITY_THRESHOLD, TEAM_SOURCE_PREFIX } from '@myco/constants.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';\nimport { fullTextSearch } from '@myco/db/queries/search.js';\nimport { listEntities } from '@myco/db/queries/entities.js';\nimport { listGraphEdges } from '@myco/db/queries/graph-edges.js';\nimport { textResult, type VaultToolDeps } from './types.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 limit for entity listing. */\nconst DEFAULT_ENTITIES_LIMIT = 50;\n\n/** Default limit for edge listing. */\nconst DEFAULT_EDGES_LIMIT = 50;\n\n// ---------------------------------------------------------------------------\n// Factory\n// ---------------------------------------------------------------------------\n\nexport function createReadTools(deps: VaultToolDeps) {\n  const { agentId, embeddingManager, teamClient, machineId, recordTurn } = deps;\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, openWorldHint: 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  return [\n    vaultUnprocessed,\n    vaultSpores,\n    vaultSessions,\n    vaultSearchFts,\n    vaultSearchSemantic,\n    vaultState,\n    vaultEntities,\n    vaultEdges,\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 * Shared types and helpers for vault tool modules.\n */\n\nimport type { SdkMcpToolDefinition } from '@anthropic-ai/claude-agent-sdk';\nimport type { EmbeddingManager } from '@myco/daemon/embedding/index.js';\nimport type { TeamSyncClient } from '@myco/daemon/team-sync.js';\n\n// Re-export for convenience\nexport type { SdkMcpToolDefinition };\n\n/** MCP tool response helper -- wraps data as text content for the agent. */\nexport function textResult(data: unknown): { content: Array<{ type: 'text'; text: string }> } {\n  return { content: [{ type: 'text' as const, text: JSON.stringify(data) }] };\n}\n\n/** Dependencies shared by all vault tool factories. */\nexport interface VaultToolDeps {\n  agentId: string;\n  runId: string;\n  embeddingManager?: EmbeddingManager;\n  teamClient?: TeamSyncClient | null;\n  machineId?: string;\n  projectRoot?: string;\n  vaultDir?: string;\n  /** Record a turn in the audit trail. Fire-and-forget. */\n  recordTurn: (toolName: string, toolInput: unknown) => void;\n}\n","/**\n * Write vault tools.\n *\n * 9 tools: vault_create_spore, vault_create_entity, vault_create_edge,\n * vault_resolve_spore, vault_update_session, vault_set_state,\n * vault_read_digest, vault_write_digest, vault_mark_processed\n */\n\nimport crypto from 'node:crypto';\nimport { z } from 'zod/v4';\nimport { tool } from '@anthropic-ai/claude-agent-sdk';\nimport { epochSeconds } from '@myco/constants.js';\nimport { insertSpore, updateSporeStatus, DEFAULT_IMPORTANCE } from '@myco/db/queries/spores.js';\nimport { updateSession } from '@myco/db/queries/sessions.js';\nimport { setState } from '@myco/db/queries/agent-state.js';\nimport { markBatchProcessed } from '@myco/db/queries/batches.js';\nimport { insertEntity } from '@myco/db/queries/entities.js';\nimport { insertGraphEdge } 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 { textResult, type VaultToolDeps } from './types.js';\n\n// ---------------------------------------------------------------------------\n// Factory\n// ---------------------------------------------------------------------------\n\nexport function createWriteTools(deps: VaultToolDeps) {\n  const { agentId, embeddingManager, machineId, recordTurn } = deps;\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    { annotations: { openWorldHint: true } },\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    { annotations: { idempotentHint: true } },\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    { annotations: { idempotentHint: true } },\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    { annotations: { destructiveHint: true } },\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    { annotations: { idempotentHint: true } },\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    { annotations: { idempotentHint: true } },\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    { annotations: { idempotentHint: true } },\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    { annotations: { destructiveHint: true } },\n  );\n\n  return [\n    vaultCreateSpore,\n    vaultCreateEntity,\n    vaultCreateEdge,\n    vaultResolveSpore,\n    vaultUpdateSession,\n    vaultSetState,\n    vaultReadDigest,\n    vaultWriteDigest,\n    vaultMarkProcessed,\n  ];\n}\n","/**\n * Observability vault tools.\n *\n * 1 tool: vault_report\n */\n\nimport { z } from 'zod/v4';\nimport { tool } from '@anthropic-ai/claude-agent-sdk';\nimport { epochSeconds } from '@myco/constants.js';\nimport { insertReport } from '@myco/db/queries/reports.js';\nimport { textResult, type VaultToolDeps } from './types.js';\n\n// ---------------------------------------------------------------------------\n// Factory\n// ---------------------------------------------------------------------------\n\nexport function createObservabilityTools(deps: VaultToolDeps) {\n  const { runId, agentId, recordTurn } = deps;\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    { annotations: {} },\n  );\n\n  return [vaultReport];\n}\n","/**\n * Skill lifecycle vault tools.\n *\n * 5 tools:\n *   - vault_skill_candidates: CRUD over skill candidate rows. The agent\n *     can only set 'identified' or 'dismissed' on updates; human-only\n *     'approved' transitions go through the UI / MCP approve action, and\n *     'generated' is set internally by vault_finalize_skill.\n *   - vault_skill_records: read/update/delete live skill records.\n *   - vault_write_skill: one-shot create-or-evolve write path used by\n *     skill-evolve and any non-staged skill authoring.\n *   - vault_stage_skill: provisional write used by skill-generate's draft\n *     phase. Stages SKILL.md + manifest.json under .myco/staging/skills/\n *     without touching the live DB or .agents/skills/ directory.\n *   - vault_finalize_skill: promotes a staged skill. Only commit point;\n *     re-runs dedup + validation as defense in depth, then atomically\n *     inserts the skill_records row, lineage, candidate transition to\n *     'generated', disk file, and symlinks. Cleans up staging on success.\n */\n\nimport crypto from 'node:crypto';\nimport { readFileSync, writeFileSync, mkdirSync, rmSync, existsSync } from 'node:fs';\nimport { resolve } from 'node:path';\nimport { z } from 'zod/v4';\nimport { tool } from '@anthropic-ai/claude-agent-sdk';\nimport { epochSeconds, DEFAULT_LIST_LIMIT } from '@myco/constants.js';\nimport { getDatabase } from '@myco/db/client.js';\nimport {\n  insertCandidate, getCandidate, listCandidates, updateCandidate, deleteCandidate,\n} from '@myco/db/queries/skill-candidates.js';\nimport {\n  insertSkillRecord, getSkillRecord, getSkillRecordByName,\n  listSkillRecords, updateSkillRecord, deleteSkillRecordCascade,\n} from '@myco/db/queries/skill-records.js';\nimport { insertLineage } from '@myco/db/queries/skill-lineage.js';\nimport { notify } from '@myco/notifications/notify.js';\nimport {\n  CANDIDATE_STATUS,\n  AGENT_SETTABLE_STATUSES,\n} from '@myco/constants/skill-candidate-status.js';\nimport {\n  validateSkillContent,\n  checkFrontmatterPreservation,\n  descriptionSimilarity,\n  topicOverlapSimilarity,\n  DESCRIPTION_DUPLICATE_THRESHOLD,\n  TOPIC_OVERLAP_THRESHOLD,\n} from './skill-validator.js';\nimport {\n  writeStagedSkill,\n  readStagedSkill,\n  writeStagedManifest,\n  readStagedManifest,\n  cleanupStagedSkill,\n  type StagedManifest,\n} from './skill-staging.js';\nimport { textResult, type VaultToolDeps } from './types.js';\n\n// ---------------------------------------------------------------------------\n// Factory\n// ---------------------------------------------------------------------------\n\nexport function createSkillTools(deps: VaultToolDeps) {\n  const { agentId, machineId, projectRoot, vaultDir, recordTurn } = deps;\n\n  /**\n   * Find the best-matching existing candidate (if any) whose topic\n   * overlaps the proposed new topic. Uses a two-path check:\n   *\n   * 1. Jaccard (`descriptionSimilarity` >= DESCRIPTION_DUPLICATE_THRESHOLD)\n   *    — catches classic near-duplicates with similar token counts.\n   * 2. Overlap coefficient (`topicOverlapSimilarity` >= TOPIC_OVERLAP_THRESHOLD)\n   *    — catches asymmetric kebab-case vs. natural-language duplicates\n   *    where a short topic's significant tokens are mostly a subset of\n   *    the longer one. Jaccard misses these because the inflated union\n   *    pushes the score below 0.4 even when the overlap is strong.\n   *\n   * Returns the candidate with the highest matching score under either\n   * metric. Reported `score` is the max of the two so the rejection\n   * message surfaces the stronger signal.\n   */\n  function findOverlappingCandidate(\n    newTopic: string,\n    existing: ReturnType<typeof listCandidates>,\n  ): { candidate: typeof existing[number]; score: number } | null {\n    let best: { candidate: typeof existing[number]; score: number } | null = null;\n    for (const candidate of existing) {\n      const jaccard = descriptionSimilarity(newTopic, candidate.topic);\n      const overlap = topicOverlapSimilarity(newTopic, candidate.topic);\n      const hitsJaccard = jaccard >= DESCRIPTION_DUPLICATE_THRESHOLD;\n      const hitsOverlap = overlap >= TOPIC_OVERLAP_THRESHOLD;\n      if (!hitsJaccard && !hitsOverlap) continue;\n      const score = Math.max(jaccard, overlap);\n      if (!best || score > best.score) {\n        best = { candidate, score };\n      }\n    }\n    return best;\n  }\n\n  /**\n   * Build a status-aware rejection message. Each status gets guidance\n   * that matches the lifecycle: dismissed → stay away; generated →\n   * already fulfilled; approved → already queued; identified → update\n   * the existing entry instead of duplicating.\n   */\n  function candidateOverlapError(match: { status: string; topic: string }): string {\n    const common = `already has an existing candidate with a similar topic: \"${match.topic}\"`;\n    switch (match.status) {\n      case CANDIDATE_STATUS.DISMISSED:\n        return `Candidate rejected: the vault ${common} that was previously dismissed. Do not re-identify dismissed topics.`;\n      case CANDIDATE_STATUS.GENERATED:\n        return `Candidate rejected: the vault ${common} that was already fulfilled by a generated skill. Do not re-identify.`;\n      case CANDIDATE_STATUS.APPROVED:\n        return `Candidate rejected: the vault ${common} that is already queued in approved state. Wait for the generate task to process it.`;\n      case CANDIDATE_STATUS.IDENTIFIED:\n        return `Candidate rejected: the vault ${common} already in the review queue. Update the existing candidate with new evidence (action: update) instead of creating a duplicate.`;\n      default:\n        return `Candidate rejected: the vault ${common} in status '${match.status}'.`;\n    }\n  }\n\n  /**\n   * Structural gate enforcing the skill lifecycle invariant: ONLY\n   * candidates in 'approved' state can be materialized into skills.\n   * Used by vault_stage_skill, vault_finalize_skill, and\n   * vault_write_skill's create path.\n   */\n  function requireApprovedCandidate(\n    candidateId: string,\n  ): Record<string, unknown> | null {\n    const candidate = getCandidate(candidateId);\n    if (!candidate) {\n      return {\n        error:\n          `Candidate ${candidateId} not found. Skill writes require a ` +\n          'candidate in the approved state.',\n      };\n    }\n    if (candidate.status !== CANDIDATE_STATUS.APPROVED) {\n      return {\n        error:\n          `Candidate ${candidateId} is in '${candidate.status}' state. ` +\n          \"Skills can only be generated from candidates in 'approved' \" +\n          'state — the human review step. If a candidate in an earlier ' +\n          'state needs to become a skill, route it through the normal ' +\n          'approval flow first.',\n        candidate_status: candidate.status,\n      };\n    }\n    return null;\n  }\n\n  /**\n   * Self-contained dedup gate for skill create paths. Returns `null`\n   * when the write is allowed, or an error payload object ready for\n   * textResult() when it should be rejected.\n   *\n   * The gate is a no-op on the evolve path (same name as an existing\n   * active skill) — the caller does not need to guard the call.\n   *\n   * Three checks, in order:\n   *   (1) Same-name exists: delegate to the evolve path. Return null\n   *       so vault_write_skill's existing-record branch can handle it;\n   *       callers that only want create (vault_stage_skill,\n   *       vault_finalize_skill) opt in via `rejectSameName: true`.\n   *   (2) Candidate-already-fulfilled: if the candidate is already\n   *       linked to a different-named active skill.\n   *   (3) Description similarity: Jaccard on significant-word tokens\n   *       against all active skills for this agent.\n   */\n  function checkDedupGates(args: {\n    candidate_id?: string;\n    name: string;\n    description: string;\n    /**\n     * When true, treat an existing skill with the same name as a\n     * rejection (create-only callers). When false, same-name passes\n     * through silently so the caller can dispatch the evolve path.\n     */\n    rejectSameName?: boolean;\n  }): Record<string, unknown> | null {\n    // (1) Same-name check\n    const existingSameName = getSkillRecordByName(args.name);\n    if (existingSameName) {\n      if (args.rejectSameName) {\n        return {\n          error:\n            `Skill \"${args.name}\" already exists. This path is create-only. ` +\n            'Use vault_write_skill to evolve the existing skill (it bumps the generation), ' +\n            'or mark the current record stale via vault_skill_records first.',\n          existing_skill: {\n            id: existingSameName.id,\n            name: existingSameName.name,\n            path: existingSameName.path,\n          },\n        };\n      }\n      return null;\n    }\n\n    // (2) Candidate-already-fulfilled check\n    if (args.candidate_id) {\n      const candidate = getCandidate(args.candidate_id);\n      if (candidate?.skill_id) {\n        const linkedSkill = getSkillRecord(candidate.skill_id);\n        if (linkedSkill && linkedSkill.name !== args.name) {\n          return {\n            error:\n              `Candidate ${args.candidate_id} is already fulfilled by skill \"${linkedSkill.name}\". ` +\n              'Do not create a sibling skill. If the existing skill needs changes, ' +\n              'write to the same name to evolve it (this bumps its generation), or ' +\n              'mark it stale via vault_skill_records before replacing.',\n            existing_skill: {\n              id: linkedSkill.id,\n              name: linkedSkill.name,\n              description: linkedSkill.description,\n              path: linkedSkill.path,\n            },\n          };\n        }\n      }\n    }\n\n    // (3) Description similarity check\n    const activeSkills = listSkillRecords({ agent_id: agentId, status: 'active', limit: 200 });\n    let bestMatch: { skill: typeof activeSkills[number]; score: number } | null = null;\n    for (const skill of activeSkills) {\n      const score = descriptionSimilarity(args.description, skill.description);\n      if (score >= DESCRIPTION_DUPLICATE_THRESHOLD && (!bestMatch || score > bestMatch.score)) {\n        bestMatch = { skill, score };\n      }\n    }\n    if (bestMatch) {\n      return {\n        error:\n          `Description overlaps with existing active skill \"${bestMatch.skill.name}\" ` +\n          `(Jaccard ${bestMatch.score.toFixed(2)}, threshold ${DESCRIPTION_DUPLICATE_THRESHOLD}). ` +\n          'Do not create a duplicate. Either evolve the existing skill by writing to ' +\n          `its name (\"${bestMatch.skill.name}\"), or reframe this skill so its description ` +\n          'describes a distinct procedure.',\n        overlapping_skill: {\n          id: bestMatch.skill.id,\n          name: bestMatch.skill.name,\n          description: bestMatch.skill.description,\n          path: bestMatch.skill.path,\n        },\n        similarity: bestMatch.score,\n      };\n    }\n\n    return null;\n  }\n\n  /**\n   * Shared create-path promotion: write SKILL.md to the live\n   * .agents/skills/<name>/ directory, create symbiont symlinks, then\n   * insert the skill_records row + lineage entry in one DB transaction.\n   * If the transaction throws, the disk write is reversed so no orphan\n   * file survives.\n   *\n   * Used by both vault_write_skill's create branch and\n   * vault_finalize_skill. Evolve (generation > 1) stays inline in\n   * vault_write_skill because its rollback semantics differ — it\n   * restores prior content rather than deleting the whole directory.\n   *\n   * `linkCandidate` runs inside the same transaction after the record\n   * is inserted. Callers use it for their own candidate-linking policy:\n   * vault_write_skill does an exact/prefix search over approved\n   * candidates; vault_finalize_skill sets the candidate directly from\n   * the staged manifest.\n   */\n  async function promoteNewSkill(params: {\n    name: string;\n    display_name: string;\n    description: string;\n    content: string;\n    source_ids?: string;\n    candidate_id?: string | null;\n    rationale?: string;\n    linkCandidate?: (recordId: string, now: number) => void;\n    label: string;\n  }): Promise<\n    | { id: string; name: string; path: string; generation: number }\n    | { error: string }\n  > {\n    const root = projectRoot ?? process.cwd();\n    const skillDir = resolve(root, '.agents', 'skills', params.name);\n    const skillPath = resolve(skillDir, 'SKILL.md');\n    // If the directory already exists for a create, it's an orphan\n    // from a prior failed run — we overwrite the file and only remove\n    // the file itself on rollback (not the whole directory) to avoid\n    // clobbering anything else that may share the dir.\n    const skillDirPreexisted = existsSync(skillDir);\n\n    async function cleanupCreatedSkillArtifactsOnRollback(): Promise<void> {\n      try {\n        if (!skillDirPreexisted) {\n          rmSync(skillDir, { recursive: true, force: true });\n        } else {\n          rmSync(skillPath, { force: true });\n        }\n      } catch (rollbackErr) {\n        console.warn(\n          `[${params.label}] file rollback after DB failure also failed:`,\n          rollbackErr instanceof Error ? rollbackErr.message : rollbackErr,\n        );\n      }\n\n      try {\n        const { syncSkillSymlinks } = await import('@myco/symbionts/installer.js');\n        syncSkillSymlinks(root, params.name, { remove: true });\n      } catch (rollbackErr) {\n        console.warn(\n          `[${params.label}] symlink rollback after DB failure also failed:`,\n          rollbackErr instanceof Error ? rollbackErr.message : rollbackErr,\n        );\n      }\n    }\n\n    try {\n      mkdirSync(skillDir, { recursive: true });\n      writeFileSync(skillPath, params.content, 'utf-8');\n    } catch (err) {\n      return {\n        error: `Failed to write skill file: ${err instanceof Error ? err.message : String(err)}`,\n      };\n    }\n\n    try {\n      const { syncSkillSymlinks } = await import('@myco/symbionts/installer.js');\n      syncSkillSymlinks(root, params.name);\n    } catch (err) {\n      console.warn(\n        `[${params.label}] syncSkillSymlinks failed:`,\n        err instanceof Error ? err.message : err,\n      );\n    }\n\n    const now = epochSeconds();\n    const relativePath = `.agents/skills/${params.name}/SKILL.md`;\n    const recordId = crypto.randomUUID();\n    const generation = 1;\n\n    const txDb = getDatabase();\n    try {\n      txDb.transaction(() => {\n        insertSkillRecord({\n          id: recordId,\n          agent_id: agentId,\n          machine_id: machineId,\n          name: params.name,\n          display_name: params.display_name,\n          description: params.description,\n          candidate_id: params.candidate_id ?? null,\n          source_ids: params.source_ids,\n          path: relativePath,\n          created_at: now,\n          updated_at: now,\n        });\n\n        insertLineage({\n          id: crypto.randomUUID(),\n          skill_id: recordId,\n          generation,\n          action: 'created',\n          rationale: params.rationale ?? 'Initial skill creation',\n          source_ids_added: params.source_ids,\n          content_snapshot: params.content,\n          created_at: now,\n        });\n\n        params.linkCandidate?.(recordId, now);\n      })();\n    } catch (err) {\n      await cleanupCreatedSkillArtifactsOnRollback();\n      return {\n        error: `Skill write aborted: database transaction failed and on-disk state was rolled back. ${err instanceof Error ? err.message : String(err)}`,\n      };\n    }\n\n    return {\n      id: recordId,\n      name: params.name,\n      path: relativePath,\n      generation,\n    };\n  }\n\n  /** Emit the standard notification after a successful create or evolve. */\n  function emitSkillNotification(\n    kind: 'created' | 'evolved',\n    opts: { name: string; display_name: string; description: string; recordId: string; generation: number },\n  ) {\n    notify(vaultDir, {\n      domain: 'skills',\n      type: kind === 'created' ? 'skill.created' : 'skill.evolved',\n      title: `Skill ${kind}: ${opts.display_name}`,\n      message: opts.description.slice(0, 120),\n      link: `/skills?skill=${encodeURIComponent(opts.name)}`,\n      metadata: { skillId: opts.recordId, name: opts.name, generation: opts.generation },\n    });\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(AGENT_SETTABLE_STATUSES as readonly [string, ...string[]]).optional().describe(\n        \"Candidate status — agent-settable values only. 'identified' is \" +\n        \"the initial state; 'dismissed' retires a candidate. 'approved' \" +\n        \"and 'generated' are lifecycle transitions owned by the human UI \" +\n        'and vault_finalize_skill respectively.',\n      ),\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\n          // Guard 1: reject if an active skill already covers this topic.\n          // Checks whether all significant words from a skill name appear in the topic.\n          const activeSkills = listSkillRecords({ agent_id: agentId, status: 'active', limit: 100 });\n          const topicLower = args.topic.toLowerCase();\n          const overlapping = activeSkills.filter((s) => {\n            const nameWords = s.name.split('-').filter((w: string) => w.length > 2);\n            if (nameWords.length < 2) return false;\n            return nameWords.every((w: string) => topicLower.includes(w));\n          });\n          if (overlapping.length > 0) {\n            return textResult({\n              error: 'Candidate rejected: active skill(s) already cover this topic. Update the existing skill via vault_skill_records instead.',\n              overlapping_skills: overlapping.map((s) => ({ name: s.name, display_name: s.display_name, description: s.description })),\n            });\n          }\n\n          // Guard 2: reject if an existing candidate (any status) has an\n          // overlapping topic. The skill-survey prompt tells the agent to\n          // check dismissed/generated candidates before re-identifying,\n          // but self-grading is unreliable so the check is enforced here.\n          const allExisting = listCandidates({ agent_id: agentId, limit: 500 });\n          const match = findOverlappingCandidate(args.topic, allExisting);\n          if (match) {\n            return textResult({\n              error: candidateOverlapError(match.candidate),\n              existing_candidate: {\n                id: match.candidate.id,\n                status: match.candidate.status,\n                topic: match.candidate.topic,\n              },\n              similarity: match.score,\n            });\n          }\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    { annotations: {} },\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('@myco/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    { annotations: {} },\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      // Dedup gate is self-gating: returns null when same-name exists\n      // (the evolve path) so the caller falls through.\n      const dedupError = checkDedupGates({\n        candidate_id: args.candidate_id,\n        name: args.name,\n        description: args.description,\n      });\n      if (dedupError) {\n        recordTurn('vault_write_skill', args);\n        return textResult(dedupError);\n      }\n      const existing = getSkillRecordByName(args.name);\n\n      const root = projectRoot ?? process.cwd();\n      const skillPath = resolve(root, '.agents', 'skills', args.name, 'SKILL.md');\n\n      // Frontmatter preservation guard — when updating an existing skill,\n      // reject writes that change protected fields (user-invocable, allowed-tools).\n      if (existsSync(skillPath)) {\n        const existingContent = readFileSync(skillPath, 'utf-8');\n        const violations = checkFrontmatterPreservation(existingContent, args.content);\n        if (violations.length > 0) {\n          recordTurn('vault_write_skill', args);\n          return textResult({\n            error: 'Skill update rejected: protected frontmatter fields were changed. Read the existing skill and preserve these values exactly.',\n            violations,\n          });\n        }\n      }\n\n      // Create path: delegate to the shared promoteNewSkill helper.\n      // Candidate linking uses exact-then-prefix matching since the\n      // agent may pass a truncated UUID in the instruction.\n      if (!existing) {\n        // Structural gate: if the caller passed a candidate_id, the\n        // candidate must be in 'approved' state. Evolve path (above)\n        // skips this because the caller is updating an existing skill,\n        // not materializing a fresh candidate.\n        if (args.candidate_id) {\n          const candidateError = requireApprovedCandidate(args.candidate_id);\n          if (candidateError) {\n            recordTurn('vault_write_skill', args);\n            return textResult(candidateError);\n          }\n        }\n\n        const linkCandidate = (recordId: string, now: number) => {\n          if (!args.candidate_id) return;\n          const exact = updateCandidate(args.candidate_id, {\n            status: CANDIDATE_STATUS.GENERATED, skill_id: recordId, updated_at: now,\n          });\n          if (exact) return;\n          const approvedCandidates = listCandidates({ status: CANDIDATE_STATUS.APPROVED, limit: 10 });\n          const prefixMatch = approvedCandidates.find((c) => c.id.startsWith(args.candidate_id!));\n          if (prefixMatch) {\n            updateCandidate(prefixMatch.id, {\n              status: CANDIDATE_STATUS.GENERATED, skill_id: recordId, updated_at: now,\n            });\n          }\n        };\n\n        const result = await promoteNewSkill({\n          name: args.name,\n          display_name: args.display_name,\n          description: args.description,\n          content: args.content,\n          source_ids: args.source_ids,\n          candidate_id: args.candidate_id,\n          rationale: args.rationale,\n          linkCandidate,\n          label: 'vault_write_skill',\n        });\n        recordTurn('vault_write_skill', args);\n        if ('error' in result) return textResult(result);\n        emitSkillNotification('created', {\n          name: result.name,\n          display_name: args.display_name,\n          description: args.description,\n          recordId: result.id,\n          generation: result.generation,\n        });\n        return textResult(result);\n      }\n\n      // Evolve path: update existing record, bump generation, preserve\n      // prior SKILL.md content on rollback. This branch stays inline\n      // because its rollback semantics (restore prior content) differ\n      // from the create helper.\n      const priorSkillContent = readFileSync(skillPath, 'utf-8');\n\n      try {\n        writeFileSync(skillPath, args.content, 'utf-8');\n      } catch (err) {\n        return textResult({ error: `Failed to write skill file: ${err instanceof Error ? err.message : String(err)}` });\n      }\n\n      try {\n        const { syncSkillSymlinks } = await import('@myco/symbionts/installer.js');\n        syncSkillSymlinks(root, args.name);\n      } catch (err) {\n        console.warn('[vault_write_skill] syncSkillSymlinks failed:', err instanceof Error ? err.message : err);\n      }\n\n      const now = epochSeconds();\n      const relativePath = `.agents/skills/${args.name}/SKILL.md`;\n      const generation = existing.generation + 1;\n      const recordId = existing.id;\n\n      const txDb = getDatabase();\n      try {\n        txDb.transaction(() => {\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          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        })();\n      } catch (err) {\n        try {\n          writeFileSync(skillPath, priorSkillContent, 'utf-8');\n        } catch (rollbackErr) {\n          console.warn(\n            '[vault_write_skill] file rollback after DB failure also failed:',\n            rollbackErr instanceof Error ? rollbackErr.message : rollbackErr,\n          );\n        }\n        recordTurn('vault_write_skill', args);\n        return textResult({\n          error: `Skill write aborted: database transaction failed and on-disk state was rolled back. ${err instanceof Error ? err.message : String(err)}`,\n        });\n      }\n\n      emitSkillNotification('evolved', {\n        name: args.name,\n        display_name: args.display_name,\n        description: args.description,\n        recordId,\n        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    { annotations: { openWorldHint: true } },\n  );\n\n  const vaultStageSkill = tool(\n    'vault_stage_skill',\n    \"Stage a provisional SKILL.md under .myco/staging/skills/<candidate_id>/ for later promotion by vault_finalize_skill. Use this from the skill-generate draft phase. The write is NOT live — the skill does not appear under .agents/skills/ and no DB rows are created until vault_finalize_skill is called with the same candidate_id.\",\n    {\n      candidate_id: z.string().describe(\n        'Candidate ID from the instruction. Required — staging is keyed by candidate so the validate phase (and on-failure cleanup) can find the staged content.',\n      ),\n      name: z.string().describe('Final skill directory name (kebab-case, no colon). Stored in the manifest for finalize.'),\n      display_name: z.string().describe('Human-readable display name'),\n      description: z.string().describe('Short description — used for the dedup gate and the final skill record'),\n      content: z.string().describe('Full SKILL.md content in markdown including frontmatter'),\n      source_ids: z.string().optional().describe('JSON array of source spore/entity IDs'),\n      rationale: z.string().optional().describe('Why this skill is being created — stored in lineage after finalize'),\n    },\n    async (args) => {\n      recordTurn('vault_stage_skill', args);\n\n      if (!vaultDir) {\n        return textResult({\n          error: 'vault_stage_skill requires vaultDir on the tool deps — staging has no location otherwise',\n        });\n      }\n\n      // Static validation — same rules as vault_write_skill\n      const validationErrors = validateSkillContent(args.content, args.name);\n      if (validationErrors.length > 0) {\n        return textResult({\n          error: 'Skill validation failed. Fix these issues and re-stage.',\n          issues: validationErrors,\n        });\n      }\n\n      // Path traversal guard for the skill name (which becomes a directory)\n      if (!args.name || /[/\\\\]|\\.\\./.test(args.name)) {\n        return textResult({\n          error: 'Invalid skill name: must be a simple directory name without path separators or \"..\"',\n        });\n      }\n\n      // Structural gate: candidate must exist and be in 'approved' state.\n      const candidateError = requireApprovedCandidate(args.candidate_id);\n      if (candidateError) return textResult(candidateError);\n\n      // Dedup gate — create-only, so rejectSameName surfaces the\n      // evolve path as an explicit error. Finalize re-runs the same\n      // gate as defense in depth.\n      const dedupError = checkDedupGates({\n        candidate_id: args.candidate_id,\n        name: args.name,\n        description: args.description,\n        rejectSameName: true,\n      });\n      if (dedupError) return textResult(dedupError);\n\n      // Write staging content + manifest\n      let stagingFilePath: string;\n      try {\n        stagingFilePath = writeStagedSkill(vaultDir, args.candidate_id, args.content);\n        const manifest: StagedManifest = {\n          candidate_id: args.candidate_id,\n          name: args.name,\n          display_name: args.display_name,\n          description: args.description,\n          source_ids: args.source_ids ?? '[]',\n          rationale: args.rationale ?? 'Initial draft',\n        };\n        writeStagedManifest(vaultDir, args.candidate_id, manifest);\n      } catch (err) {\n        return textResult({\n          error: `Failed to write staged skill: ${err instanceof Error ? err.message : String(err)}`,\n        });\n      }\n\n      return textResult({\n        candidate_id: args.candidate_id,\n        staging_path: stagingFilePath,\n        status: 'staged',\n      });\n    },\n    { annotations: { openWorldHint: true } },\n  );\n\n  const vaultFinalizeSkill = tool(\n    'vault_finalize_skill',\n    'Promote a staged skill to live at .agents/skills/<name>/ and insert the skill_records / lineage rows. Call this from skill-generate validate phase after your quality checks pass. Requires vault_stage_skill to have been called earlier with the same candidate_id; reads the staged SKILL.md + manifest rather than taking duplicate metadata.',\n    {\n      candidate_id: z.string().describe('Candidate ID whose staged skill should be promoted. Must match a previous vault_stage_skill call.'),\n    },\n    async (args) => {\n      recordTurn('vault_finalize_skill', args);\n\n      if (!vaultDir) {\n        return textResult({\n          error: 'vault_finalize_skill requires vaultDir on the tool deps',\n        });\n      }\n\n      // Read staged content + manifest\n      const stagedContent = readStagedSkill(vaultDir, args.candidate_id);\n      const manifest = readStagedManifest(vaultDir, args.candidate_id);\n      if (!stagedContent || !manifest) {\n        return textResult({\n          error:\n            `No staged skill found for candidate ${args.candidate_id}. ` +\n            'Call vault_stage_skill first.',\n        });\n      }\n\n      // Defense-in-depth: candidate must still be 'approved' at\n      // finalize time. If a human (or another tool) dismissed the\n      // candidate between stage and finalize, the finalize should\n      // refuse rather than promote the now-rescinded skill.\n      const candidateError = requireApprovedCandidate(args.candidate_id);\n      if (candidateError) return textResult(candidateError);\n\n      // Defense-in-depth: re-run validation against the staged content.\n      // The staging write already validated once, but the file on disk\n      // could have been mutated (tests do this explicitly to check the\n      // guard; a crash between stage and finalize could too).\n      const validationErrors = validateSkillContent(stagedContent, manifest.name);\n      if (validationErrors.length > 0) {\n        return textResult({\n          error: 'Staged skill failed validation on finalize. Re-stage with valid content.',\n          issues: validationErrors,\n        });\n      }\n\n      // Defense-in-depth: re-run dedup against the manifest-declared\n      // description. Catches the \"agent staged a fresh description,\n      // then tampered the manifest to collide with a live skill\" case,\n      // and also trips if a concurrent evolve landed a same-named skill\n      // between stage and finalize.\n      const dedupError = checkDedupGates({\n        candidate_id: args.candidate_id,\n        name: manifest.name,\n        description: manifest.description,\n        rejectSameName: true,\n      });\n      if (dedupError) return textResult(dedupError);\n\n      // Promote via the shared helper. Candidate link is direct — the\n      // staged manifest guarantees candidate_id exists, so no search.\n      // updateCandidate moves the candidate OUT of 'approved' so its\n      // approved_at audit timestamp is preserved by construction.\n      const result = await promoteNewSkill({\n        name: manifest.name,\n        display_name: manifest.display_name,\n        description: manifest.description,\n        content: stagedContent,\n        source_ids: manifest.source_ids,\n        candidate_id: manifest.candidate_id,\n        rationale: manifest.rationale,\n        linkCandidate: (recordId, now) => {\n          updateCandidate(manifest.candidate_id, {\n            status: CANDIDATE_STATUS.GENERATED,\n            skill_id: recordId,\n            updated_at: now,\n          });\n        },\n        label: 'vault_finalize_skill',\n      });\n      if ('error' in result) return textResult(result);\n\n      // Success — clean up staging and notify.\n      cleanupStagedSkill(vaultDir, args.candidate_id);\n      emitSkillNotification('created', {\n        name: manifest.name,\n        display_name: manifest.display_name,\n        description: manifest.description,\n        recordId: result.id,\n        generation: result.generation,\n      });\n\n      return textResult(result);\n    },\n    { annotations: { openWorldHint: true } },\n  );\n\n  return [\n    vaultSkillCandidates,\n    vaultSkillRecords,\n    vaultWriteSkill,\n    vaultStageSkill,\n    vaultFinalizeSkill,\n  ];\n}\n","/**\n * Skill content validation.\n *\n * Deterministic quality gate -- the agent must fix all issues before\n * a skill is accepted.\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/** Frontmatter fields that must not change when updating an existing skill. */\nexport const PROTECTED_FRONTMATTER_FIELDS = ['user-invocable', 'allowed-tools'] as const;\n\n/**\n * Whitelist of Claude Code tool names that may appear in `allowed-tools`.\n * Myco-managed skills run in developer Claude Code sessions — anything not\n * on this list is almost certainly a model confabulation (e.g. \"[None]\",\n * \"ReadFile\", \"search\", or a vault_* tool copied from the agent's own context).\n *\n * Kept intentionally narrow: add entries when a legitimate tool is rejected.\n */\nexport const ALLOWED_CLAUDE_CODE_TOOLS: ReadonlySet<string> = new Set([\n  'Read', 'Edit', 'Write', 'MultiEdit', 'Bash', 'Grep', 'Glob',\n  'NotebookRead', 'NotebookEdit', 'WebFetch', 'WebSearch',\n  'Task', 'TodoWrite',\n]);\n\n/**\n * Extract a frontmatter field value from SKILL.md content.\n * Returns the raw value string, or undefined if not found.\n */\nexport function extractFrontmatterField(content: string, field: string): string | undefined {\n  const fmMatch = content.match(/^---\\n([\\s\\S]*?)\\n---/);\n  if (!fmMatch) return undefined;\n  const match = fmMatch[1].match(new RegExp(`^${field}:\\\\s*(.+)$`, 'm'));\n  return match?.[1].trim();\n}\n\n/**\n * Parse the `allowed-tools` frontmatter value into a list of tool names.\n *\n * Accepts either of these YAML shapes:\n *   allowed-tools: Read, Edit, Write\n *   allowed-tools: [Read, Edit, Write]\n *\n * Returns null if the value is absent, empty, or clearly malformed\n * (e.g. a bare word like `None`, or a list containing `None` / `null`).\n * Caller treats null as a validation failure.\n */\nexport function parseAllowedTools(rawValue: string | undefined): string[] | null {\n  if (!rawValue) return null;\n  let stripped = rawValue.trim();\n  if (stripped.length === 0) return null;\n\n  // Strip YAML inline-list brackets if present: [Read, Edit] -> Read, Edit\n  if (stripped.startsWith('[') && stripped.endsWith(']')) {\n    stripped = stripped.slice(1, -1).trim();\n  }\n  if (stripped.length === 0) return null;\n\n  const parts = stripped\n    .split(',')\n    .map((s) => s.trim().replace(/^['\"]|['\"]$/g, '')) // strip quotes\n    .filter((s) => s.length > 0);\n\n  if (parts.length === 0) return null;\n\n  // Reject literal \"None\" / \"null\" / \"~\" — common model confabulations\n  // when the model means \"no tools needed.\"\n  const sentinels = new Set(['None', 'none', 'null', 'Null', '~']);\n  if (parts.some((p) => sentinels.has(p))) return null;\n\n  return parts;\n}\n\n/**\n * Light English stemmer applied to every significant token before set\n * comparison. Collapses common suffix variants so that `task`/`tasks`,\n * `gate`/`gates`, `model`/`models`, `configure`/`configuring`, and\n * `implement`/`implemented` all share a stem.\n *\n * The order matters: strip -ing / -ed before trailing -s so \"parking\"\n * doesn't become \"parkin\" then \"parki\"; strip trailing -e last so\n * \"validate\" and \"validating\" both land on \"validat\".\n *\n * Length guards prevent degenerate stems on short words (e.g. \"ring\"\n * must not become empty, \"cod\" must not become \"c\").\n */\nfunction stemToken(word: string): string {\n  let w = word;\n  if (w.length > 5 && w.endsWith('ing')) w = w.slice(0, -3);\n  else if (w.length > 5 && w.endsWith('ed')) w = w.slice(0, -2);\n  if (w.length > 4 && w.endsWith('s')) w = w.slice(0, -1);\n  if (w.length > 4 && w.endsWith('e')) w = w.slice(0, -1);\n  return w;\n}\n\n/**\n * Lowercase-word token set from a string, excluding stopwords and\n * short/noise tokens, with light stemming applied. Used for all\n * similarity metrics in this file.\n */\nfunction tokenSet(text: string): Set<string> {\n  const stopwords = new Set([\n    'the', 'a', 'an', 'and', 'or', 'but', 'is', 'are', 'was', 'were',\n    'be', 'been', 'being', 'have', 'has', 'had', 'do', 'does', 'did',\n    'will', 'would', 'should', 'could', 'may', 'might', 'must', 'can',\n    'this', 'that', 'these', 'those', 'with', 'from', 'into', 'onto',\n    'for', 'when', 'where', 'which', 'what', 'who', 'how', 'why',\n    'use', 'uses', 'used', 'using', 'not', 'also', 'than', 'then',\n    'ensure', 'ensures', 'make', 'makes',\n  ]);\n  return new Set(\n    text\n      .toLowerCase()\n      .replace(/[^a-z0-9_\\s]/g, ' ')\n      .split(/\\s+/)\n      .filter((w) => w.length >= 4 && !stopwords.has(w))\n      .map(stemToken),\n  );\n}\n\n/** Internal helper: count shared stems between two token sets. */\nfunction intersectionSize(a: Set<string>, b: Set<string>): number {\n  let count = 0;\n  for (const token of a) {\n    if (b.has(token)) count++;\n  }\n  return count;\n}\n\n/**\n * Jaccard similarity between two text strings on their significant-word\n * token sets. Returns a value in [0, 1].\n *\n * Purpose: detect near-duplicate skill descriptions so `vault_write_skill`\n * can refuse to create sibling skills covering the same topic. This is a\n * deterministic gate — unlike asking the model to self-check for conflicts,\n * which is known to hallucinate \"no overlap\" on visibly overlapping pairs.\n */\nexport function descriptionSimilarity(a: string, b: string): number {\n  const aTokens = tokenSet(a);\n  const bTokens = tokenSet(b);\n  if (aTokens.size === 0 || bTokens.size === 0) return 0;\n\n  const intersection = intersectionSize(aTokens, bTokens);\n  const union = aTokens.size + bTokens.size - intersection;\n  return union === 0 ? 0 : intersection / union;\n}\n\n/**\n * Overlap coefficient (Szymkiewicz–Simpson) between two topic strings:\n * `|A ∩ B| / min(|A|, |B|)`. Returns 0 when either side has fewer than\n * `minTokens` significant tokens — 1-2 token topics are dominated by\n * single-token collisions under this metric and must fall back to\n * Jaccard for duplicate detection.\n *\n * Why this exists alongside `descriptionSimilarity`: candidate topics are\n * often short kebab-case labels like `add-idle-skip-watermark-to-agent-task`\n * (5 tokens) paired against longer natural-language topics like\n * `Implementing DB Watermark Prefilters for Incremental Agent Tasks`\n * (6 tokens). The asymmetric token-count inflates Jaccard's union and\n * pushes real duplicates below the 0.4 threshold. Overlap coefficient is\n * robust to that asymmetry because the denominator is the smaller set.\n *\n * The 3-token minimum is calibrated to catch cases like\n * `publish-npm-package-with-oidc-in-ci` (3 significant tokens) against\n * `npm OIDC Trusted Publishing in GitHub Actions` (5 tokens) while\n * leaving 2-token topic pairs to the Jaccard path. Two-token topics\n * with a single shared word would score 0.5 under naive overlap —\n * noisy — so they are deliberately excluded.\n */\nexport function topicOverlapSimilarity(\n  a: string,\n  b: string,\n  minTokens: number = 3,\n): number {\n  const aTokens = tokenSet(a);\n  const bTokens = tokenSet(b);\n  if (aTokens.size < minTokens || bTokens.size < minTokens) return 0;\n\n  const intersection = intersectionSize(aTokens, bTokens);\n  const smaller = Math.min(aTokens.size, bTokens.size);\n  return smaller === 0 ? 0 : intersection / smaller;\n}\n\n/**\n * Similarity threshold above which two descriptions are treated as\n * covering the same topic. Chosen empirically from the unifi-mcp incident\n * that motivated this gate: the real duplicate pair\n * (`unifi-validator-coercion-pattern` vs `unifi-validator-registry-coercion`)\n * scored ~0.42 on this metric — lower than intuition suggests because each\n * description reframes roughly half its content with different wording.\n * Clearly-distinct skill pairs score under 0.2 on the same metric, so 0.4\n * is a comfortable middle that catches real duplicates without flagging\n * incidentally-adjacent topics.\n *\n * Tuning note: the cost of a false positive here is \"agent must reframe\n * its description and try again\" (low); the cost of a false negative is\n * \"sibling skill on disk for the same topic\" (high). Lean aggressive.\n */\nexport const DESCRIPTION_DUPLICATE_THRESHOLD = 0.4;\n\n/**\n * Threshold for the overlap-coefficient topic dedup path. At 0.6 and\n * with a 4-token minimum, this catches recent false negatives where\n * short kebab-case topics were re-identifying dismissed natural-language\n * candidates (watermark/agent/task overlap, structural/enforcement/gate\n * overlap, configure/local/model overlap) while leaving genuinely-new\n * candidates like `implement-spa-sub-navigation-with-browser-history`\n * unaffected.\n */\nexport const TOPIC_OVERLAP_THRESHOLD = 0.6;\n\n/**\n * Compare protected frontmatter fields between existing and new content.\n * Returns an array of violation descriptions (empty = all preserved).\n *\n * Also guards against description shortening — the description is the\n * primary triggering mechanism for skills, so losing content degrades\n * skill activation quality.\n */\nexport function checkFrontmatterPreservation(existing: string, incoming: string): string[] {\n  const violations: string[] = [];\n  for (const field of PROTECTED_FRONTMATTER_FIELDS) {\n    const oldValue = extractFrontmatterField(existing, field);\n    const newValue = extractFrontmatterField(incoming, field);\n    if (oldValue !== undefined && newValue !== undefined && oldValue !== newValue) {\n      violations.push(`${field}: was \"${oldValue}\", changed to \"${newValue}\"`);\n    }\n  }\n\n  // Guard against description shortening — descriptions drive skill triggering.\n  // Lengthening is allowed (adding context), shortening is not (losing trigger keywords).\n  const oldDesc = extractFrontmatterField(existing, 'description');\n  const newDesc = extractFrontmatterField(incoming, 'description');\n  if (oldDesc && newDesc && newDesc.length < oldDesc.length * 0.9) {\n    violations.push(\n      `description shortened from ${oldDesc.length} to ${newDesc.length} chars (${Math.round((1 - newDesc.length / oldDesc.length) * 100)}% reduction). ` +\n      'Descriptions are the primary triggering mechanism — do not shorten them.',\n    );\n  }\n\n  return violations;\n}\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 rawValue = allowedToolsMatch[1].trim();\n    // Reject vault_* tool names first — most informative message for the\n    // common LLM mistake of copying its own agent tool context into the skill.\n    if (rawValue.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    } else {\n      // Positive whitelist check — catches \"[None]\", \"None\", invented tool\n      // names, and other confabulations that the vault_* reject misses.\n      const parsed = parseAllowedTools(rawValue);\n      if (parsed === null) {\n        issues.push(\n          `allowed-tools value is malformed or empty: \"${rawValue}\". ` +\n          'Provide a comma-separated list of Claude Code tools, e.g. ' +\n          '\"Read, Edit, Write, Bash, Grep, Glob\". Use the narrowest set ' +\n          'the skill actually needs.',\n        );\n      } else {\n        const unknown = parsed.filter((t) => !ALLOWED_CLAUDE_CODE_TOOLS.has(t));\n        if (unknown.length > 0) {\n          issues.push(\n            `allowed-tools contains unknown tool name(s): ${unknown.join(', ')}. ` +\n            `Valid Claude Code tools: ${[...ALLOWED_CLAUDE_CODE_TOOLS].join(', ')}.`,\n          );\n        }\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 * 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 ?? DEFAULT_CONTEXT_QUERY_LIMIT;\n      const data = await executeQuery(agentId, query.tool, limit);\n      return { tool: query.tool, purpose: query.purpose, data } satisfies ContextQueryResult;\n    }),\n  );\n\n  // Map settled results, throwing for required failures.\n  const results: ContextQueryResult[] = [];\n  for (let i = 0; i < settled.length; i++) {\n    const outcome = settled[i];\n    const query = queries[i];\n\n    if (outcome.status === 'fulfilled') {\n      results.push(outcome.value);\n    } else {\n      const message = toErrorMessage(outcome.reason);\n\n      if (query.required) {\n        throw new Error(\n          `Required context query \"${query.tool}\" failed: ${message}`,\n        );\n      }\n\n      results.push({\n        tool: query.tool,\n        purpose: query.purpose,\n        data: null,\n        error: message,\n      });\n    }\n  }\n\n  return results;\n}\n\n// ---------------------------------------------------------------------------\n// Private helpers\n// ---------------------------------------------------------------------------\n\n/** Set of recognized context query tool names. */\nconst KNOWN_CONTEXT_QUERY_TOOLS = new Set([\n  'vault_unprocessed',\n  'vault_spores',\n  'vault_sessions',\n  'vault_state',\n]);\n\n/**\n * Guard against unknown tool names.\n *\n * Unknown tools are a programming error (misconfigured task YAML), so they\n * always throw — even if the query is not marked required.\n */\nfunction validateTool(tool: string): void {\n  if (!KNOWN_CONTEXT_QUERY_TOOLS.has(tool)) {\n    throw new Error(`Unknown context query tool: \"${tool}\"`);\n  }\n}\n\n/**\n * Route a single query to the appropriate DB function.\n */\nasync function executeQuery(\n  agentId: string,\n  tool: string,\n  limit: number,\n): Promise<unknown> {\n  switch (tool) {\n    case 'vault_unprocessed':\n      return getUnprocessedBatches({ limit });\n\n    case 'vault_spores':\n      return listSpores({ agent_id: agentId, limit });\n\n    case 'vault_sessions':\n      return listSessions({ limit });\n\n    case 'vault_state':\n      return getStatesForAgent(agentId);\n\n    default:\n      throw new Error(`Unknown context query tool: \"${tool}\"`);\n  }\n}\n","import type { ProviderConfig } from './types.js';\n\n// ---------------------------------------------------------------------------\n// Named constants — env var names and default values\n// ---------------------------------------------------------------------------\n\nconst ENV_ANTHROPIC_BASE_URL = 'ANTHROPIC_BASE_URL';\nconst ENV_ANTHROPIC_AUTH_TOKEN = 'ANTHROPIC_AUTH_TOKEN';\nconst ENV_ANTHROPIC_API_KEY = 'ANTHROPIC_API_KEY';\nconst ENV_OLLAMA_NUM_CTX = 'OLLAMA_NUM_CTX';\nconst DEFAULT_OLLAMA_URL = 'http://localhost:11434';\nconst DEFAULT_LMSTUDIO_URL = 'http://localhost:1234';\nconst OLLAMA_AUTH_TOKEN = 'ollama';\nconst LMSTUDIO_AUTH_TOKEN = 'lmstudio';\n\n// ---------------------------------------------------------------------------\n// Public API\n// ---------------------------------------------------------------------------\n\n/**\n * Build an env object for a phase's query() call.\n *\n * Returns `undefined` when no provider override is needed (SDK defaults to\n * `process.env`). 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 === 'anthropic') 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 'anthropic':\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 ?? DEFAULT_LMSTUDIO_URL,\n        [ENV_ANTHROPIC_AUTH_TOKEN]: provider.apiKey ?? LMSTUDIO_AUTH_TOKEN,\n        [ENV_ANTHROPIC_API_KEY]: '',\n      };\n    default:\n      return {};\n  }\n}\n","/**\n * Ollama model context window management.\n */\n\nimport { execFileSync } from 'node:child_process';\nimport { writeFileSync, unlinkSync } from 'node:fs';\nimport { tmpdir } from 'node:os';\nimport { join } from 'node:path';\nimport type { ProviderConfig } from './types.js';\n\n/** Timeout for Ollama model pre-load request (ms). */\nconst OLLAMA_PRELOAD_TIMEOUT_MS = 30_000;\n\n/**\n * Default context window for Ollama models when no `context_length` is\n * configured. 32K is comfortably larger than any current agent task prompt\n * (skill-generate's source-material payload is the worst case and stays\n * well under 16K) and dramatically smaller than the 128K–256K native\n * defaults modern Ollama models ship with — which would otherwise allocate\n * tens of GB of KV cache for context that is never filled.\n *\n * Override by setting `context_length` on the provider config, either\n * globally, per-task, or per-phase (all scopes are reconciled to a single\n * variant per model — see `resolveOllamaContextVariants`).\n */\nexport const DEFAULT_OLLAMA_CONTEXT_LENGTH = 32768;\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 */\nexport async function ensureOllamaContextVariant(\n  model: string,\n  contextLength: number,\n): Promise<string> {\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// Unified variant resolution for task + phase scopes\n// ---------------------------------------------------------------------------\n\n/**\n * Per-phase provider override shape. Mirrors the record passed through\n * `runAgent` → `executePhasedQuery`; kept here so the ollama-context module\n * doesn't have to import executor-internal types.\n */\nexport interface PhaseProviderOverride {\n  provider?: ProviderConfig;\n  maxTurns?: number;\n}\n\n/**\n * Resolve every Ollama model referenced by a task run into a single variant\n * per (model) pair and return rewritten providers that point at those\n * variants.\n *\n * Why this exists at all:\n *   - The runtime default for gemma4:26b and similar modern Ollama models\n *     is 128K–256K tokens, which allocates tens of GB of KV cache for\n *     context we never come close to filling. Applying a sensible default\n *     (32K) on behalf of users who haven't set `context_length` recovers\n *     that VRAM without changing anything else.\n *   - Historically the variant-creation call only ran at the task scope,\n *     so a phase override that pointed at a different Ollama model bypassed\n *     the variant logic entirely and loaded at native default.\n *   - If the same model is referenced at multiple scopes with different\n *     `context_length` values, creating a variant per scope would load the\n *     same base model multiple times. That's the failure mode this function\n *     prevents — one (model) → one variant → one Ollama load per run.\n *\n * Reconciliation rule: when the same model appears with different\n * `context_length` values across scopes, the MAX is used. This guarantees\n * every call site has at least as much context as it asked for, at the cost\n * of slightly more VRAM than the smallest-asking scope requested. Users who\n * want scope-specific contexts should use different *models*, not different\n * context values on the same model.\n *\n * Providers that aren't Ollama (cloud, lmstudio) and providers without a\n * resolved model name pass through unchanged.\n */\nexport async function resolveOllamaContextVariants(\n  taskProvider: ProviderConfig | undefined,\n  phaseOverrides: Record<string, PhaseProviderOverride>,\n  // Injected variant creator for testability. Defaults to the real\n  // `ensureOllamaContextVariant` which shells out to `ollama`; tests pass\n  // a pure stub so the logic can be exercised without the CLI.\n  createVariant: (model: string, contextLength: number) => Promise<string> = ensureOllamaContextVariant,\n): Promise<{\n  taskProvider: ProviderConfig | undefined;\n  phaseOverrides: Record<string, PhaseProviderOverride>;\n  conflicts: Array<{ model: string; values: number[]; resolved: number }>;\n}> {\n  // --- Pass 1: collect ---------------------------------------------------\n  // For each Ollama model we find, track every distinct context value we\n  // saw for it. We need the full set (not just a running max) so we can\n  // report conflicts afterwards.\n  const seen = new Map<string, Set<number>>();\n\n  const recordOllama = (p: ProviderConfig | undefined): void => {\n    if (p?.type !== 'ollama' || !p.model) return;\n    const ctx = p.contextLength ?? DEFAULT_OLLAMA_CONTEXT_LENGTH;\n    const set = seen.get(p.model) ?? new Set<number>();\n    set.add(ctx);\n    seen.set(p.model, set);\n  };\n\n  recordOllama(taskProvider);\n  for (const override of Object.values(phaseOverrides)) {\n    recordOllama(override.provider);\n  }\n\n  // No Ollama providers at all — pass through unchanged.\n  if (seen.size === 0) {\n    return { taskProvider, phaseOverrides, conflicts: [] };\n  }\n\n  // --- Pass 2: reconcile -------------------------------------------------\n  const resolvedContext = new Map<string, number>();\n  const conflicts: Array<{ model: string; values: number[]; resolved: number }> = [];\n  for (const [model, values] of seen) {\n    const sorted = [...values].sort((a, b) => a - b);\n    const max = sorted[sorted.length - 1];\n    resolvedContext.set(model, max);\n    if (sorted.length > 1) {\n      conflicts.push({ model, values: sorted, resolved: max });\n    }\n  }\n\n  // --- Pass 3: create variants in parallel -------------------------------\n  const variantEntries = await Promise.all(\n    [...resolvedContext.entries()].map(async ([model, ctx]) => {\n      const variant = await createVariant(model, ctx);\n      return [model, variant] as const;\n    }),\n  );\n  const variantByModel = new Map(variantEntries);\n\n  // --- Pass 4: rewrite providers -----------------------------------------\n  const rewriteProvider = (p: ProviderConfig | undefined): ProviderConfig | undefined => {\n    if (!p) return p;\n    if (p.type !== 'ollama' || !p.model) return p;\n    const variant = variantByModel.get(p.model);\n    const resolvedCtx = resolvedContext.get(p.model);\n    if (!variant) return p;\n    // Preserve the resolved context_length on the rewritten provider so\n    // downstream code (env var builders, diagnostics) sees the effective\n    // value rather than undefined. 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