nodebench-mcp 2.11.0 → 2.13.0

package/NODEBENCH_AGENTS.md

@@ -1,809 +1,809 @@
-# NodeBench Agents Protocol
-
-This file provides the standard operating procedure for AI agents using the NodeBench MCP. Drop this into any repository and agents will auto-configure their workflow.
-
-Reference: [agents.md](https://agents.md/) standard.
-
----
-
-## Quick Setup
-
-Add to `~/.claude/settings.json`:
-
-```json
-{
-  "mcpServers": {
-    "nodebench": {
-      "command": "npx",
-      "args": ["-y", "nodebench-mcp"]
-    }
-  }
-}
-```
-
-Restart Claude Code. 89+ tools available immediately.
-
-### Preset Selection
-
-By default all toolsets are enabled. Use `--preset` to start with a scoped subset:
-
-```json
-{
-  "mcpServers": {
-    "nodebench": {
-      "command": "npx",
-      "args": ["-y", "nodebench-mcp", "--preset", "meta"]
-    }
-  }
-}
-```
-
-The **meta** preset is the recommended front door for new agents: start with just 5 discovery tools, use `discover_tools` to find what you need, then self-escalate to a larger preset. See [Toolset Gating & Presets](#toolset-gating--presets) for the full breakdown.
-
-**→ Quick Refs:** After setup, run `getMethodology("overview")` | First task? See [Verification Cycle](#verification-cycle-workflow) | New to codebase? See [Environment Setup](#environment-setup) | Preset options: See [Toolset Gating & Presets](#toolset-gating--presets)
-
----
-
-## The AI Flywheel (Mandatory)
-
-Every non-trivial change MUST go through this 6-step verification process before shipping.
-
-### Step 1: Static Analysis
-```
-tsc --noEmit
-```
-Zero errors. Zero warnings. No exceptions.
-
-### Step 2: Happy-Path Test
-Run the changed functionality with valid inputs. Confirm expected output.
-
-### Step 3: Failure-Path Test
-Test each failure mode the code handles. Invalid inputs, edge cases, error states.
-
-### Step 4: Gap Analysis
-Review the code for:
-- Dead code, unused variables
-- Missing integrations (new functions not wired to existing systems)
-- Logic that doesn't match stated intent
-- Hardcoded values that should be configurable
-
-### Step 5: Fix and Re-Verify
-If any gap found: fix it, then restart from Step 1.
-
-### Step 6: Live E2E Test (MANDATORY)
-**Before declaring done or publishing:**
-```bash
-echo '{"jsonrpc":"2.0","id":1,"method":"tools/call","params":{"name":"YOUR_TOOL","arguments":{...}}}' | node dist/index.js
-```
-Every new/modified tool MUST pass stdio E2E test. No exceptions.
-
-For workflow-level changes (verification, eval, recon, quality gates, flywheel, or knowledge tools), also run the long-running open-source benchmark:
-```bash
-npm --prefix packages/mcp-local run dataset:bfcl:refresh
-NODEBENCH_OPEN_DATASET_TASK_LIMIT=12 NODEBENCH_OPEN_DATASET_CONCURRENCY=6 npm --prefix packages/mcp-local run test:open-dataset
-npm --prefix packages/mcp-local run dataset:toolbench:refresh
-NODEBENCH_TOOLBENCH_TASK_LIMIT=6 NODEBENCH_TOOLBENCH_CONCURRENCY=3 npm --prefix packages/mcp-local run test:open-dataset:toolbench
-npm --prefix packages/mcp-local run dataset:swebench:refresh
-NODEBENCH_SWEBENCH_TASK_LIMIT=8 NODEBENCH_SWEBENCH_CONCURRENCY=4 npm --prefix packages/mcp-local run test:open-dataset:swebench
-```
-
-### Step 7: Document Learnings
-Record edge cases discovered. Update this file if needed.
-
-**Rule: No change ships without passing all 7 steps.**
-
-**→ Quick Refs:** Track progress with `start_verification_cycle` | Record findings with `record_learning` | Run gate with `run_quality_gate` | See [Post-Implementation Checklist](#post-implementation-checklist)
-
----
-
-## Open-Source Long-Running MCP Benchmark
-
-Use open-source long-context tasks to validate real orchestration behavior under parallel load.
-
-- Dataset: `gorilla-llm/Berkeley-Function-Calling-Leaderboard`
-- Split: `BFCL_v3_multi_turn_long_context`
-- Source: `https://huggingface.co/datasets/gorilla-llm/Berkeley-Function-Calling-Leaderboard`
-
-Refresh local fixture:
-```bash
-npm run mcp:dataset:refresh
-```
-
-Run parallel subagent benchmark:
-```bash
-NODEBENCH_OPEN_DATASET_TASK_LIMIT=12 NODEBENCH_OPEN_DATASET_CONCURRENCY=6 npm run mcp:dataset:test
-```
-
-Run refresh + benchmark in one shot:
-```bash
-npm run mcp:dataset:bench
-```
-
-Second lane (ToolBench multi-tool instructions):
-- Dataset: `OpenBMB/ToolBench`
-- Split: `data_example/instruction (G1,G2,G3)`
-- Source: `https://github.com/OpenBMB/ToolBench`
-
-Refresh ToolBench fixture:
-```bash
-npm run mcp:dataset:toolbench:refresh
-```
-
-Run ToolBench parallel subagent benchmark:
-```bash
-NODEBENCH_TOOLBENCH_TASK_LIMIT=6 NODEBENCH_TOOLBENCH_CONCURRENCY=3 npm run mcp:dataset:toolbench:test
-```
-
-Run all public lanes:
-```bash
-npm run mcp:dataset:bench:all
-```
-
-Third lane (SWE-bench Verified long-horizon software tasks):
-- Dataset: `princeton-nlp/SWE-bench_Verified`
-- Split: `test`
-- Source: `https://huggingface.co/datasets/princeton-nlp/SWE-bench_Verified`
-
-Refresh SWE-bench fixture:
-```bash
-npm run mcp:dataset:swebench:refresh
-```
-
-Run SWE-bench parallel subagent benchmark:
-```bash
-NODEBENCH_SWEBENCH_TASK_LIMIT=8 NODEBENCH_SWEBENCH_CONCURRENCY=4 npm run mcp:dataset:swebench:test
-```
-
-Fourth lane (GAIA gated long-horizon tool-augmented tasks):
-- Dataset: `gaia-benchmark/GAIA` (gated)
-- Default config: `2023_level3`
-- Default split: `validation`
-- Source: `https://huggingface.co/datasets/gaia-benchmark/GAIA`
-
-Notes:
-- Fixture is written to `.cache/gaia` (gitignored). Do not commit GAIA question/answer content.
-- Refresh requires `HF_TOKEN` or `HUGGINGFACE_HUB_TOKEN` in your shell.
-- Python deps: `pandas`, `huggingface_hub`, `pyarrow` (or equivalent parquet engine).
-
-Refresh GAIA fixture:
-```bash
-npm run mcp:dataset:gaia:refresh
-```
-
-Run GAIA parallel subagent benchmark:
-```bash
-NODEBENCH_GAIA_TASK_LIMIT=8 NODEBENCH_GAIA_CONCURRENCY=4 npm run mcp:dataset:gaia:test
-```
-
-GAIA capability benchmark (accuracy: LLM-only vs LLM+tools):
-- This runs real model calls and web search. It is disabled by default and only intended for regression checks.
-- Uses Gemini by default. Ensure `GEMINI_API_KEY` is available (repo `.env.local` is loaded by the test).
-- Scoring fixture includes ground-truth answers and MUST remain under `.cache/gaia` (gitignored).
-
-Generate scoring fixture (local only, gated):
-```bash
-npm run mcp:dataset:gaia:capability:refresh
-```
-
-Run capability benchmark:
-```bash
-NODEBENCH_GAIA_CAPABILITY_TASK_LIMIT=6 NODEBENCH_GAIA_CAPABILITY_CONCURRENCY=1 npm run mcp:dataset:gaia:capability:test
-```
-
-GAIA capability benchmark (file-backed lane: PDF / XLSX / CSV):
-- This lane measures the impact of deterministic local parsing tools on GAIA tasks with attachments.
-- Fixture includes ground-truth answers and MUST remain under `.cache/gaia` (gitignored).
-- Attachments are copied into `.cache/gaia/data/<file_path>` for offline deterministic runs after the first download.
-
-Generate file-backed scoring fixture + download attachments (local only, gated):
-```bash
-npm run mcp:dataset:gaia:capability:files:refresh
-```
-
-Run file-backed capability benchmark:
-```bash
-NODEBENCH_GAIA_CAPABILITY_TASK_LIMIT=6 NODEBENCH_GAIA_CAPABILITY_CONCURRENCY=1 npm run mcp:dataset:gaia:capability:files:test
-```
-
-Modes:
-- Recommended (more stable): `NODEBENCH_GAIA_CAPABILITY_TOOLS_MODE=rag` (single deterministic extract + answer)
-- More realistic (higher variance): `NODEBENCH_GAIA_CAPABILITY_TOOLS_MODE=agent` (small tool loop)
-Web lane only: `NODEBENCH_GAIA_CAPABILITY_FORCE_WEB_SEARCH=1` and/or `NODEBENCH_GAIA_CAPABILITY_FORCE_FETCH_URL=1`
-
-Run all public lanes:
-```bash
-npm run mcp:dataset:bench:all
-```
-
-Run full lane suite (includes GAIA):
-```bash
-npm run mcp:dataset:bench:full
-```
-
-Implementation files:
-- `packages/mcp-local/src/__tests__/fixtures/generateBfclLongContextFixture.ts`
-- `packages/mcp-local/src/__tests__/fixtures/bfcl_v3_long_context.sample.json`
-- `packages/mcp-local/src/__tests__/openDatasetParallelEval.test.ts`
-- `packages/mcp-local/src/__tests__/fixtures/generateToolbenchInstructionFixture.ts`
-- `packages/mcp-local/src/__tests__/fixtures/toolbench_instruction.sample.json`
-- `packages/mcp-local/src/__tests__/openDatasetParallelEvalToolbench.test.ts`
-- `packages/mcp-local/src/__tests__/fixtures/generateSwebenchVerifiedFixture.ts`
-- `packages/mcp-local/src/__tests__/fixtures/swebench_verified.sample.json`
-- `packages/mcp-local/src/__tests__/openDatasetParallelEvalSwebench.test.ts`
-- `packages/mcp-local/src/__tests__/fixtures/generateGaiaLevel3Fixture.py`
-- `.cache/gaia/gaia_2023_level3_validation.sample.json`
-- `packages/mcp-local/src/__tests__/openDatasetParallelEvalGaia.test.ts`
-- `packages/mcp-local/src/__tests__/fixtures/generateGaiaCapabilityFixture.py`
-- `.cache/gaia/gaia_capability_2023_all_validation.sample.json`
-- `packages/mcp-local/src/__tests__/gaiaCapabilityEval.test.ts`
-- `packages/mcp-local/src/__tests__/fixtures/generateGaiaCapabilityFilesFixture.py`
-- `.cache/gaia/gaia_capability_files_2023_all_validation.sample.json`
-- `.cache/gaia/data/...` (local GAIA attachments; do not commit)
-- `packages/mcp-local/src/__tests__/gaiaCapabilityFilesEval.test.ts`
-
-Required tool chain per dataset task:
-- `run_recon`
-- `log_recon_finding`
-- `findTools`
-- `getMethodology`
-- `start_eval_run`
-- `record_eval_result`
-- `complete_eval_run`
-- `run_closed_loop`
-- `run_mandatory_flywheel`
-- `search_all_knowledge`
-
-**→ Quick Refs:** Core process in [AI Flywheel](#the-ai-flywheel-mandatory) | Verification flow in [Verification Cycle](#verification-cycle-workflow) | Loop discipline in [Closed Loop Principle](#closed-loop-principle)
-
----
-
-## MCP Tool Categories
-
-Use `getMethodology("overview")` to see all available workflows.
-
-| Category | Tools | When to Use |
-|----------|-------|-------------|
-| **Web** | `web_search`, `fetch_url` | Research, reading docs, market validation |
-| **Local Files** | `read_pdf_text`, `pdf_search_text`, `read_xlsx_file`, `xlsx_select_rows`, `xlsx_aggregate`, `read_csv_file`, `csv_select_rows`, `csv_aggregate`, `read_text_file`, `read_json_file`, `json_select`, `read_jsonl_file`, `zip_list_files`, `zip_read_text_file`, `zip_extract_file`, `read_docx_text`, `read_pptx_text` | Deterministic parsing and aggregation of local attachments (GAIA file-backed lane) |
-| **GitHub** | `search_github`, `analyze_repo` | Finding libraries, studying implementations |
-| **Verification** | `start_cycle`, `log_phase`, `complete_cycle` | Tracking the flywheel process |
-| **Eval** | `start_eval_run`, `log_test_result` | Test case management |
-| **Quality Gates** | `run_quality_gate`, `get_gate_history` | Pass/fail checkpoints |
-| **Learning** | `record_learning`, `search_all_knowledge` | Persistent knowledge base |
-| **Vision** | `analyze_screenshot`, `capture_ui_screenshot` | UI/UX verification |
-| **Bootstrap** | `discover_infrastructure`, `triple_verify`, `self_implement` | Self-setup, triple verification |
-| **Autonomous** | `assess_risk`, `decide_re_update`, `run_self_maintenance` | Risk-aware execution, self-maintenance |
-| **Parallel Agents** | `claim_agent_task`, `release_agent_task`, `list_agent_tasks`, `assign_agent_role`, `get_agent_role`, `log_context_budget`, `run_oracle_comparison`, `get_parallel_status` | Multi-agent coordination, task locking, role specialization, oracle testing |
-| **LLM** | `call_llm`, `extract_structured_data`, `benchmark_models` | LLM calling, structured extraction, model comparison |
-| **Security** | `scan_dependencies`, `run_code_analysis` | Dependency auditing, static code analysis |
-| **Platform** | `query_daily_brief`, `query_funding_entities`, `query_research_queue`, `publish_to_queue` | Convex platform bridge: intelligence, funding, research, publishing |
-| **Meta** | `findTools`, `getMethodology` | Discover tools, get workflow guides |
-| **Discovery** | `discover_tools`, `get_tool_quick_ref`, `get_workflow_chain` | Hybrid search, quick refs, workflow chains |
-
-Meta + Discovery tools (5 total) are **always included** regardless of preset. See [Toolset Gating & Presets](#toolset-gating--presets).
-
-**→ Quick Refs:** Find tools by keyword: `findTools({ query: "verification" })` | Hybrid search: `discover_tools({ query: "security" })` | Get workflow guide: `getMethodology({ topic: "..." })` | See [Methodology Topics](#methodology-topics) for all topics
-
----
-
-## Toolset Gating & Presets
-
-NodeBench MCP supports 4 presets that control which domain toolsets are loaded at startup. Meta + Discovery tools (5 total) are **always included** on top of any preset.
-
-### Preset Table
-
-| Preset | Domain Toolsets | Domain Tools | Total (with meta+discovery) | Use Case |
-|--------|----------------|-------------|----------------------------|----------|
-| **meta** | 0 | 0 | 5 | Discovery-only front door. Agents start here and self-escalate. |
-| **lite** | 7 | ~35 | ~40 | Lightweight verification-focused workflows. CI bots, quick checks. |
-| **core** | 16 | ~75 | ~80 | Full development workflow. Most agent sessions. |
-| **full** | all | 89+ | 94+ | Everything enabled. Benchmarking, exploration, advanced use. |
-
-### Usage
-
-```bash
-npx nodebench-mcp --preset meta       # Discovery-only (5 tools)
-npx nodebench-mcp --preset lite       # Verification + eval + recon + security
-npx nodebench-mcp --preset core       # Full dev workflow without vision/parallel
-npx nodebench-mcp --preset full       # All toolsets (default)
-npx nodebench-mcp --toolsets verification,eval,recon   # Custom selection
-npx nodebench-mcp --exclude vision,ui_capture          # Exclude specific toolsets
-```
-
-### The Meta Preset — Discovery-Only Front Door
-
-The **meta** preset loads zero domain tools. Agents start with only 5 tools:
-
-| Tool | Purpose |
-|------|---------|
-| `findTools` | Keyword search across all registered tools |
-| `getMethodology` | Get workflow guides by topic |
-| `discover_tools` | Hybrid search with relevance scoring (richer than findTools) |
-| `get_tool_quick_ref` | Quick reference card for any specific tool |
-| `get_workflow_chain` | Recommended tool sequence for common workflows |
-
-This is the recommended starting point for autonomous agents. The self-escalation pattern:
-
-```
-1. Start with --preset meta (5 tools)
-2. discover_tools({ query: "what I need to do" })    // Find relevant tools
-3. get_workflow_chain({ workflow: "verification" })    // Get the tool sequence
-4. If needed tools are not loaded:
-   → Restart with --preset core or --preset full
-   → Or use --toolsets to add specific domains
-5. Proceed with full workflow
-```
-
-### Preset Domain Breakdown
-
-**meta** (0 domains): No domain tools. Meta + Discovery only.
-
-**lite** (7 domains): `verification`, `eval`, `quality_gate`, `learning`, `recon`, `security`, `boilerplate`
-
-**core** (16 domains): Everything in lite plus `flywheel`, `bootstrap`, `self_eval`, `llm`, `platform`, `research_writing`, `flicker_detection`, `figma_flow`, `benchmark`
-
-**full** (all domains): All toolsets in TOOLSET_MAP including `ui_capture`, `vision`, `local_file`, `web`, `github`, `docs`, `parallel`, and everything in core.
-
-**→ Quick Refs:** Check current toolset: `findTools({ query: "*" })` | Self-escalate: restart with `--preset core` | See [MCP Tool Categories](#mcp-tool-categories) | CLI help: `npx nodebench-mcp --help`
-
----
-
-## Verification Cycle Workflow
-
-Start every significant task with a verification cycle:
-
-```
-1. start_cycle({ goal: "Implement feature X" })
-2. log_phase({ phase: "context", notes: "Researched existing patterns..." })
-3. log_phase({ phase: "implementation", notes: "Added new function..." })
-4. log_phase({ phase: "testing", notes: "All tests pass..." })
-5. complete_cycle({ status: "success", summary: "Feature X shipped" })
-```
-
-If blocked or failed:
-```
-abandon_cycle({ reason: "Blocked by external dependency" })
-```
-
-**→ Quick Refs:** Before starting: `search_all_knowledge({ query: "your task" })` | After completing: `record_learning({ ... })` | Run flywheel: See [AI Flywheel](#the-ai-flywheel-mandatory) | Track quality: See [Quality Gates](#quality-gates)
-
----
-
-## Recording Learnings
-
-After discovering something useful, record it:
-
-```
-record_learning({
-  title: "Convex index predicates must use withIndex chaining",
-  content: "Using .filter() after .withIndex() bypasses the index...",
-  category: "convex",
-  tags: ["database", "performance", "gotcha"]
-})
-```
-
-Search later with:
-```
-search_all_knowledge({ query: "convex index" })
-```
-
-**→ Quick Refs:** Search before implementing: `search_all_knowledge` | `search_learnings` and `list_learnings` are DEPRECATED | Part of flywheel Step 7 | See [Verification Cycle](#verification-cycle-workflow)
-
----
-
-## Quality Gates
-
-Before shipping, run quality gates:
-
-```
-run_quality_gate({
-  gateName: "deploy_readiness",
-  results: [
-    { rule: "tests_pass", passed: true },
-    { rule: "no_type_errors", passed: true },
-    { rule: "code_reviewed", passed: true }
-  ]
-})
-```
-
-Gate history tracks pass/fail over time.
-
-**→ Quick Refs:** Get preset rules: `get_gate_preset({ preset: "ui_ux_qa" })` | View history: `get_gate_history({ gateName: "..." })` | UI/UX gates: See [Vision](#vision-analysis) | Part of flywheel Step 5 re-verify
-
----
-
-## Web Research Workflow
-
-For market research or tech evaluation:
-
-```
-1. web_search({ query: "MCP servers 2026", maxResults: 10 })
-2. search_github({ query: "mcp typescript", minStars: 100 })
-3. analyze_repo({ repoUrl: "owner/repo" })  // study top results
-4. fetch_url({ url: "https://docs.example.com" })  // read their docs
-5. record_learning({ ... })  // save key findings
-```
-
-**→ Quick Refs:** Analyze repo structure: `analyze_repo` | Save findings: `record_learning` | Part of: `getMethodology({ topic: "project_ideation" })` | See [Recording Learnings](#recording-learnings)
-
----
-
-## Project Ideation Workflow
-
-Before building anything new:
-
-```
-getMethodology({ topic: "project_ideation" })
-```
-
-This returns a 6-step process:
-1. Define Concept
-2. Research Market
-3. Analyze Competition
-4. Define Requirements
-5. Plan Metrics
-6. Gate Approval
-
-**→ Quick Refs:** Research tools: `web_search`, `search_github`, `analyze_repo` | Record requirements: `log_recon_finding` | Create baseline: `start_eval_run` | See [Web Research](#web-research-workflow)
-
----
-
-## Closed Loop Principle
-
-**Never present changes without full local verification.**
-
-The loop:
-1. Compile. Build clean.
-2. Lint. Style clean. No warnings.
-3. Test. Run automated suites.
-4. Self-debug. If 1-3 fail: read logs, hypothesize, fix, restart loop.
-
-Only when all green: present to user.
-
-**→ Quick Refs:** Track loop: `run_closed_loop({ ... })` | Part of flywheel Steps 1-5 | See [AI Flywheel](#the-ai-flywheel-mandatory) | After loop: See [Post-Implementation Checklist](#post-implementation-checklist)
-
----
-
-## Environment Setup
-
-Check your environment:
-```
-setup_local_env({ checkSdks: true })
-```
-
-Returns:
-- Node/npm versions
-- Missing API keys
-- Recommended SDK installations
-- Actionable next steps
-
-**→ Quick Refs:** After setup: `getMethodology("overview")` | Check vision: `discover_vision_env()` | See [API Keys](#api-keys-optional) | Then: See [Verification Cycle](#verification-cycle-workflow)
-
----
-
-## API Keys (Optional)
-
-Set these for enhanced functionality:
-
-| Key | Purpose |
-|-----|---------|
-| `GEMINI_API_KEY` | Web search (Google grounding), vision analysis |
-| `OPENAI_API_KEY` | Alternative search/vision provider |
-| `GITHUB_TOKEN` | Higher rate limits (5000/hr vs 60/hr) |
-| `ANTHROPIC_API_KEY` | Alternative vision provider |
-
-**→ Quick Refs:** Check what's available: `setup_local_env({ checkSdks: true })` | Vision capabilities: `discover_vision_env()` | See [Environment Setup](#environment-setup)
-
----
-
-## Vision Analysis
-
-For UI/UX verification:
-
-```
-1. capture_ui_screenshot({ url: "http://localhost:3000", viewport: "desktop" })
-2. analyze_screenshot({ imageBase64: "...", prompt: "Check accessibility" })
-3. capture_responsive_suite({ url: "...", label: "homepage" })
-```
-
-**→ Quick Refs:** Check capabilities: `discover_vision_env()` | UI QA methodology: `getMethodology({ topic: "ui_ux_qa" })` | Agentic vision: `getMethodology({ topic: "agentic_vision" })` | See [Quality Gates](#quality-gates)
-
----
-
-## Post-Implementation Checklist
-
-After every implementation, answer these 3 questions:
-
-1. **MCP gaps?** — Were all relevant tools called? Any unexpected results?
-2. **Implementation gaps?** — Dead code? Missing integrations? Hardcoded values?
-3. **Flywheel complete?** — All 7 steps passed including E2E test?
-
-If any answer reveals a gap: fix it before proceeding.
-
-**→ Quick Refs:** Run self-check: `run_self_maintenance({ scope: "quick" })` | Record learnings: `record_learning` | Update docs: `update_agents_md` | See [AI Flywheel](#the-ai-flywheel-mandatory)
-
----
-
-## Agent Self-Bootstrap System
-
-For agents to self-configure and validate against authoritative sources.
-
-### 1. Discover Existing Infrastructure
-```
-discover_infrastructure({
-  categories: ["agent_loop", "telemetry", "evaluation", "verification"],
-  depth: "thorough"
-})
-```
-
-Returns: discovered patterns, missing components, bootstrap plan.
-
-### 2. Triple Verification (with Source Citations)
-
-Run 3-layer verification with authoritative sources:
-
-```
-triple_verify({
-  target: "my-feature",
-  scope: "full",
-  includeWebSearch: true,
-  generateInstructions: true
-})
-```
-
-**V1: Internal Analysis** — Checks codebase patterns
-**V2: External Validation** — Cross-references Anthropic, OpenAI, LangChain, MCP spec
-**V3: Synthesis** — Generates recommendations with source citations
-
-### 3. Self-Implement Missing Components
-```
-self_implement({
-  component: "telemetry",  // or: agent_loop, evaluation, verification, multi_channel
-  dryRun: true
-})
-```
-
-Generates production-ready templates based on industry patterns.
-
-### 4. Generate Self-Instructions
-```
-generate_self_instructions({
-  format: "skills_md",  // or: rules_md, guidelines, claude_md
-  includeExternalSources: true
-})
-```
-
-Creates persistent instructions with authoritative source citations.
-
-### 5. Multi-Channel Information Gathering
-```
-connect_channels({
-  channels: ["web", "github", "slack", "docs"],
-  query: "agent verification patterns",
-  aggressive: true
-})
-```
-
-Aggregates findings from multiple sources.
-
-### Authoritative Sources (Tier 1)
-- https://www.anthropic.com/research/building-effective-agents
-- https://openai.github.io/openai-agents-python/
-- https://www.langchain.com/langgraph
-- https://modelcontextprotocol.io/specification/2025-11-25
-
-**→ Quick Refs:** Full methodology: `getMethodology({ topic: "agent_bootstrap" })` | After bootstrap: See [Autonomous Maintenance](#autonomous-self-maintenance-system) | Before implementing: `assess_risk` | See [Triple Verification](#2-triple-verification-with-source-citations)
-
----
-
-## Autonomous Self-Maintenance System
-
-Aggressive autonomous self-management with risk-aware execution. Based on OpenClaw patterns and Ralph Wiggum stop-hooks.
-
-### 1. Risk-Tiered Execution
-
-Before any action, assess its risk tier:
-
-```
-assess_risk({ action: "push to remote" })
-```
-
-Risk tiers:
-- **Low**: Reading, analyzing, searching — auto-approve
-- **Medium**: Writing local files, running tests — log and proceed
-- **High**: Pushing to remote, posting externally — require confirmation
-
-### 2. Re-Update Before Create
-
-**CRITICAL:** Before creating new files, check if updating existing is better:
-
-```
-decide_re_update({
-  targetContent: "New agent instructions",
-  contentType: "instructions",
-  existingFiles: ["AGENTS.md", "README.md"]
-})
-```
-
-This prevents file sprawl and maintains single source of truth.
-
-### 3. Self-Maintenance Cycles
-
-Run periodic self-checks:
-
-```
-run_self_maintenance({
-  scope: "standard",  // quick | standard | thorough
-  autoFix: false,
-  dryRun: true
-})
-```
-
-Checks: TypeScript compilation, documentation sync, tool counts, test coverage.
-
-### 4. Directory Scaffolding (OpenClaw Style)
-
-When adding infrastructure, use standardized scaffolding:
-
-```
-scaffold_directory({
-  component: "agent_loop",  // or: telemetry, evaluation, multi_channel, etc.
-  includeTests: true,
-  dryRun: true
-})
-```
-
-Creates organized subdirectories with proper test structure.
-
-### 5. Autonomous Loops with Guardrails
-
-For multi-step autonomous tasks, use controlled loops:
-
-```
-run_autonomous_loop({
-  goal: "Verify all tools pass static analysis",
-  maxIterations: 5,
-  maxDurationMs: 60000,
-  stopOnFirstFailure: true
-})
-```
-
-Implements Ralph Wiggum pattern with checkpoints and stop conditions.
-
-**→ Quick Refs:** Full methodology: `getMethodology({ topic: "autonomous_maintenance" })` | Before actions: `assess_risk` | Before new files: `decide_re_update` | Scaffold structure: `scaffold_directory` | See [Self-Bootstrap](#agent-self-bootstrap-system)
-
----
-
-## Methodology Topics
-
-Available via `getMethodology({ topic: "..." })`:
-
-| Topic | Description | Quick Ref |
-|-------|-------------|-----------|
-| `overview` | See all methodologies | Start here |
-| `verification` | 6-phase development cycle | [AI Flywheel](#the-ai-flywheel-mandatory) |
-| `eval` | Test case management | [Quality Gates](#quality-gates) |
-| `flywheel` | Continuous improvement loop | [AI Flywheel](#the-ai-flywheel-mandatory) |
-| `mandatory_flywheel` | Required verification for changes | [AI Flywheel](#the-ai-flywheel-mandatory) |
-| `reconnaissance` | Codebase discovery | [Self-Bootstrap](#agent-self-bootstrap-system) |
-| `quality_gates` | Pass/fail checkpoints | [Quality Gates](#quality-gates) |
-| `ui_ux_qa` | Frontend verification | [Vision Analysis](#vision-analysis) |
-| `agentic_vision` | AI-powered visual QA | [Vision Analysis](#vision-analysis) |
-| `closed_loop` | Build/test before presenting | [Closed Loop](#closed-loop-principle) |
-| `learnings` | Knowledge persistence | [Recording Learnings](#recording-learnings) |
-| `project_ideation` | Validate ideas before building | [Project Ideation](#project-ideation-workflow) |
-| `tech_stack_2026` | Dependency management | [Environment Setup](#environment-setup) |
-| `agents_md_maintenance` | Keep docs in sync | [Auto-Update](#auto-update-this-file) |
-| `agent_bootstrap` | Self-discover, triple verify | [Self-Bootstrap](#agent-self-bootstrap-system) |
-| `autonomous_maintenance` | Risk-tiered execution | [Autonomous Maintenance](#autonomous-self-maintenance-system) |
-| `parallel_agent_teams` | Multi-agent coordination, task locking, oracle testing | [Parallel Agent Teams](#parallel-agent-teams) |
-| `self_reinforced_learning` | Trajectory analysis, self-eval, improvement recs | [Self-Reinforced Learning](#self-reinforced-learning-loop) |
-| `toolset_gating` | 4 presets (meta, lite, core, full) and self-escalation | [Toolset Gating & Presets](#toolset-gating--presets) |
-
-**→ Quick Refs:** Find tools: `findTools({ query: "..." })` | Get any methodology: `getMethodology({ topic: "..." })` | See [MCP Tool Categories](#mcp-tool-categories)
-
----
-
-## Parallel Agent Teams
-
-Based on Anthropic's ["Building a C Compiler with Parallel Claudes"](https://www.anthropic.com/engineering/building-c-compiler) (Feb 2026).
-
-Run multiple AI agents in parallel on a shared codebase with coordination via task locking, role specialization, context budget management, and oracle-based testing.
-
-### Quick Start — Parallel Agents
-
-```
-1. get_parallel_status({ includeHistory: true })     // Orient: what's happening?
-2. assign_agent_role({ role: "implementer" })         // Specialize
-3. claim_agent_task({ taskKey: "fix_auth" })           // Lock task
-4. ... do work ...
-5. log_context_budget({ eventType: "test_output", tokensUsed: 5000 })  // Track budget
-6. run_oracle_comparison({ testLabel: "auth_output", actualOutput: "...", expectedOutput: "...", oracleSource: "prod_v2" })
-7. release_agent_task({ taskKey: "fix_auth", status: "completed", progressNote: "Fixed JWT, added tests" })
-```
-
-### Predefined Agent Roles
-
-| Role | Focus |
-|------|-------|
-| `implementer` | Primary feature work. Picks failing tests, implements fixes. |
-| `dedup_reviewer` | Finds and coalesces duplicate implementations. |
-| `performance_optimizer` | Profiles bottlenecks, optimizes hot paths. |
-| `documentation_maintainer` | Keeps READMEs and progress files in sync. |
-| `code_quality_critic` | Structural improvements, pattern enforcement. |
-| `test_writer` | Writes targeted tests for edge cases and failure modes. |
-| `security_auditor` | Audits for vulnerabilities, logs CRITICAL gaps. |
-
-### Key Patterns (from Anthropic blog)
-
-- **Task Locking**: Claim before working. If two agents try the same task, the second picks a different one.
-- **Context Window Budget**: Do NOT print thousands of useless bytes. Pre-compute summaries. Use `--fast` mode (1-10% random sample) for large test suites. Log errors with ERROR prefix on same line for grep.
-- **Oracle Testing**: Compare output against known-good reference. Each failing comparison is an independent work item for a parallel agent.
-- **Time Blindness**: Agents can't tell time. Print progress infrequently. Use deterministic random sampling per-agent but randomized across VMs.
-- **Progress Files**: Maintain running docs of status, failed approaches, and remaining tasks. Fresh agent sessions read these to orient.
-- **Delta Debugging**: When tests pass individually but fail together, split the set in half to narrow down the minimal failing combination.
-
-### Bootstrap for External Repos
-
-When nodebench-mcp is connected to a project that lacks parallel agent infrastructure, it can auto-detect gaps and scaffold everything needed:
-
-```
-1. bootstrap_parallel_agents({ projectRoot: "/path/to/their/repo", dryRun: true })
-   // Scans 7 categories: task coordination, roles, oracle, context budget,
-   // progress files, AGENTS.md parallel section, git worktrees
-
-2. bootstrap_parallel_agents({ projectRoot: "...", dryRun: false, techStack: "TypeScript/React" })
-   // Creates .parallel-agents/ dir, progress.md, roles.json, lock dirs, oracle dirs
-
-3. generate_parallel_agents_md({ techStack: "TypeScript/React", projectName: "their-project", maxAgents: 4 })
-   // Generates portable AGENTS.md section — paste into their repo
-
-4. Run the 6-step flywheel plan returned by the bootstrap tool to verify
-5. Fix any issues, re-verify
-6. record_learning({ key: "bootstrap_their_project", content: "...", category: "pattern" })
-```
-
-The generated AGENTS.md section is framework-agnostic and works with any AI agent (Claude, GPT, etc.). It includes:
-- Task locking protocol (file-based, no dependencies)
-- Role definitions and assignment guide
-- Oracle testing workflow with idiomatic examples
-- Context budget rules
-- Progress file protocol
-- Anti-patterns to avoid
-- Optional nodebench-mcp tool mapping table
-
-### MCP Prompts for Parallel Agent Teams
-
-- `parallel-agent-team` — Full team setup with role assignment and task breakdown
-- `oracle-test-harness` — Oracle-based testing setup for a component
-- `bootstrap-parallel-agents` — Detect and scaffold parallel agent infra for any external repo
-
-**→ Quick Refs:** Full methodology: `getMethodology({ topic: "parallel_agent_teams" })` | Find parallel tools: `findTools({ category: "parallel_agents" })` | Bootstrap external repo: `bootstrap_parallel_agents({ projectRoot: "..." })` | See [AI Flywheel](#the-ai-flywheel-mandatory)
-
----
-
-## Auto-Update This File
-
-Agents can self-update this file:
-
-```
-update_agents_md({
-  operation: "update_section",
-  section: "Custom Section",
-  content: "New content here...",
-  projectRoot: "/path/to/project"
-})
-```
-
-Or read current structure:
-```
-update_agents_md({ operation: "read", projectRoot: "/path/to/project" })
-```
-
-**→ Quick Refs:** Before updating: `decide_re_update({ contentType: "instructions", ... })` | After updating: Run flywheel Steps 1-7 | See [Re-Update Before Create](#2-re-update-before-create)
-
----
-
-## License
-
-MIT — Use freely in any project.
+# NodeBench Agents Protocol
+
+This file provides the standard operating procedure for AI agents using the NodeBench MCP. Drop this into any repository and agents will auto-configure their workflow.
+
+Reference: [agents.md](https://agents.md/) standard.
+
+---
+
+## Quick Setup
+
+Add to `~/.claude/settings.json`:
+
+```json
+{
+  "mcpServers": {
+    "nodebench": {
+      "command": "npx",
+      "args": ["-y", "nodebench-mcp"]
+    }
+  }
+}
+```
+
+Restart Claude Code. 89+ tools available immediately.
+
+### Preset Selection
+
+By default all toolsets are enabled. Use `--preset` to start with a scoped subset:
+
+```json
+{
+  "mcpServers": {
+    "nodebench": {
+      "command": "npx",
+      "args": ["-y", "nodebench-mcp", "--preset", "meta"]
+    }
+  }
+}
+```
+
+The **meta** preset is the recommended front door for new agents: start with just 5 discovery tools, use `discover_tools` to find what you need, then self-escalate to a larger preset. See [Toolset Gating & Presets](#toolset-gating--presets) for the full breakdown.
+
+**→ Quick Refs:** After setup, run `getMethodology("overview")` | First task? See [Verification Cycle](#verification-cycle-workflow) | New to codebase? See [Environment Setup](#environment-setup) | Preset options: See [Toolset Gating & Presets](#toolset-gating--presets)
+
+---
+
+## The AI Flywheel (Mandatory)
+
+Every non-trivial change MUST go through this 6-step verification process before shipping.
+
+### Step 1: Static Analysis
+```
+tsc --noEmit
+```
+Zero errors. Zero warnings. No exceptions.
+
+### Step 2: Happy-Path Test
+Run the changed functionality with valid inputs. Confirm expected output.
+
+### Step 3: Failure-Path Test
+Test each failure mode the code handles. Invalid inputs, edge cases, error states.
+
+### Step 4: Gap Analysis
+Review the code for:
+- Dead code, unused variables
+- Missing integrations (new functions not wired to existing systems)
+- Logic that doesn't match stated intent
+- Hardcoded values that should be configurable
+
+### Step 5: Fix and Re-Verify
+If any gap found: fix it, then restart from Step 1.
+
+### Step 6: Live E2E Test (MANDATORY)
+**Before declaring done or publishing:**
+```bash
+echo '{"jsonrpc":"2.0","id":1,"method":"tools/call","params":{"name":"YOUR_TOOL","arguments":{...}}}' | node dist/index.js
+```
+Every new/modified tool MUST pass stdio E2E test. No exceptions.
+
+For workflow-level changes (verification, eval, recon, quality gates, flywheel, or knowledge tools), also run the long-running open-source benchmark:
+```bash
+npm --prefix packages/mcp-local run dataset:bfcl:refresh
+NODEBENCH_OPEN_DATASET_TASK_LIMIT=12 NODEBENCH_OPEN_DATASET_CONCURRENCY=6 npm --prefix packages/mcp-local run test:open-dataset
+npm --prefix packages/mcp-local run dataset:toolbench:refresh
+NODEBENCH_TOOLBENCH_TASK_LIMIT=6 NODEBENCH_TOOLBENCH_CONCURRENCY=3 npm --prefix packages/mcp-local run test:open-dataset:toolbench
+npm --prefix packages/mcp-local run dataset:swebench:refresh
+NODEBENCH_SWEBENCH_TASK_LIMIT=8 NODEBENCH_SWEBENCH_CONCURRENCY=4 npm --prefix packages/mcp-local run test:open-dataset:swebench
+```
+
+### Step 7: Document Learnings
+Record edge cases discovered. Update this file if needed.
+
+**Rule: No change ships without passing all 7 steps.**
+
+**→ Quick Refs:** Track progress with `start_verification_cycle` | Record findings with `record_learning` | Run gate with `run_quality_gate` | See [Post-Implementation Checklist](#post-implementation-checklist)
+
+---
+
+## Open-Source Long-Running MCP Benchmark
+
+Use open-source long-context tasks to validate real orchestration behavior under parallel load.
+
+- Dataset: `gorilla-llm/Berkeley-Function-Calling-Leaderboard`
+- Split: `BFCL_v3_multi_turn_long_context`
+- Source: `https://huggingface.co/datasets/gorilla-llm/Berkeley-Function-Calling-Leaderboard`
+
+Refresh local fixture:
+```bash
+npm run mcp:dataset:refresh
+```
+
+Run parallel subagent benchmark:
+```bash
+NODEBENCH_OPEN_DATASET_TASK_LIMIT=12 NODEBENCH_OPEN_DATASET_CONCURRENCY=6 npm run mcp:dataset:test
+```
+
+Run refresh + benchmark in one shot:
+```bash
+npm run mcp:dataset:bench
+```
+
+Second lane (ToolBench multi-tool instructions):
+- Dataset: `OpenBMB/ToolBench`
+- Split: `data_example/instruction (G1,G2,G3)`
+- Source: `https://github.com/OpenBMB/ToolBench`
+
+Refresh ToolBench fixture:
+```bash
+npm run mcp:dataset:toolbench:refresh
+```
+
+Run ToolBench parallel subagent benchmark:
+```bash
+NODEBENCH_TOOLBENCH_TASK_LIMIT=6 NODEBENCH_TOOLBENCH_CONCURRENCY=3 npm run mcp:dataset:toolbench:test
+```
+
+Run all public lanes:
+```bash
+npm run mcp:dataset:bench:all
+```
+
+Third lane (SWE-bench Verified long-horizon software tasks):
+- Dataset: `princeton-nlp/SWE-bench_Verified`
+- Split: `test`
+- Source: `https://huggingface.co/datasets/princeton-nlp/SWE-bench_Verified`
+
+Refresh SWE-bench fixture:
+```bash
+npm run mcp:dataset:swebench:refresh
+```
+
+Run SWE-bench parallel subagent benchmark:
+```bash
+NODEBENCH_SWEBENCH_TASK_LIMIT=8 NODEBENCH_SWEBENCH_CONCURRENCY=4 npm run mcp:dataset:swebench:test
+```
+
+Fourth lane (GAIA gated long-horizon tool-augmented tasks):
+- Dataset: `gaia-benchmark/GAIA` (gated)
+- Default config: `2023_level3`
+- Default split: `validation`
+- Source: `https://huggingface.co/datasets/gaia-benchmark/GAIA`
+
+Notes:
+- Fixture is written to `.cache/gaia` (gitignored). Do not commit GAIA question/answer content.
+- Refresh requires `HF_TOKEN` or `HUGGINGFACE_HUB_TOKEN` in your shell.
+- Python deps: `pandas`, `huggingface_hub`, `pyarrow` (or equivalent parquet engine).
+
+Refresh GAIA fixture:
+```bash
+npm run mcp:dataset:gaia:refresh
+```
+
+Run GAIA parallel subagent benchmark:
+```bash
+NODEBENCH_GAIA_TASK_LIMIT=8 NODEBENCH_GAIA_CONCURRENCY=4 npm run mcp:dataset:gaia:test
+```
+
+GAIA capability benchmark (accuracy: LLM-only vs LLM+tools):
+- This runs real model calls and web search. It is disabled by default and only intended for regression checks.
+- Uses Gemini by default. Ensure `GEMINI_API_KEY` is available (repo `.env.local` is loaded by the test).
+- Scoring fixture includes ground-truth answers and MUST remain under `.cache/gaia` (gitignored).
+
+Generate scoring fixture (local only, gated):
+```bash
+npm run mcp:dataset:gaia:capability:refresh
+```
+
+Run capability benchmark:
+```bash
+NODEBENCH_GAIA_CAPABILITY_TASK_LIMIT=6 NODEBENCH_GAIA_CAPABILITY_CONCURRENCY=1 npm run mcp:dataset:gaia:capability:test
+```
+
+GAIA capability benchmark (file-backed lane: PDF / XLSX / CSV):
+- This lane measures the impact of deterministic local parsing tools on GAIA tasks with attachments.
+- Fixture includes ground-truth answers and MUST remain under `.cache/gaia` (gitignored).
+- Attachments are copied into `.cache/gaia/data/<file_path>` for offline deterministic runs after the first download.
+
+Generate file-backed scoring fixture + download attachments (local only, gated):
+```bash
+npm run mcp:dataset:gaia:capability:files:refresh
+```
+
+Run file-backed capability benchmark:
+```bash
+NODEBENCH_GAIA_CAPABILITY_TASK_LIMIT=6 NODEBENCH_GAIA_CAPABILITY_CONCURRENCY=1 npm run mcp:dataset:gaia:capability:files:test
+```
+
+Modes:
+- Recommended (more stable): `NODEBENCH_GAIA_CAPABILITY_TOOLS_MODE=rag` (single deterministic extract + answer)
+- More realistic (higher variance): `NODEBENCH_GAIA_CAPABILITY_TOOLS_MODE=agent` (small tool loop)
+Web lane only: `NODEBENCH_GAIA_CAPABILITY_FORCE_WEB_SEARCH=1` and/or `NODEBENCH_GAIA_CAPABILITY_FORCE_FETCH_URL=1`
+
+Run all public lanes:
+```bash
+npm run mcp:dataset:bench:all
+```
+
+Run full lane suite (includes GAIA):
+```bash
+npm run mcp:dataset:bench:full
+```
+
+Implementation files:
+- `packages/mcp-local/src/__tests__/fixtures/generateBfclLongContextFixture.ts`
+- `packages/mcp-local/src/__tests__/fixtures/bfcl_v3_long_context.sample.json`
+- `packages/mcp-local/src/__tests__/openDatasetParallelEval.test.ts`
+- `packages/mcp-local/src/__tests__/fixtures/generateToolbenchInstructionFixture.ts`
+- `packages/mcp-local/src/__tests__/fixtures/toolbench_instruction.sample.json`
+- `packages/mcp-local/src/__tests__/openDatasetParallelEvalToolbench.test.ts`
+- `packages/mcp-local/src/__tests__/fixtures/generateSwebenchVerifiedFixture.ts`
+- `packages/mcp-local/src/__tests__/fixtures/swebench_verified.sample.json`
+- `packages/mcp-local/src/__tests__/openDatasetParallelEvalSwebench.test.ts`
+- `packages/mcp-local/src/__tests__/fixtures/generateGaiaLevel3Fixture.py`
+- `.cache/gaia/gaia_2023_level3_validation.sample.json`
+- `packages/mcp-local/src/__tests__/openDatasetParallelEvalGaia.test.ts`
+- `packages/mcp-local/src/__tests__/fixtures/generateGaiaCapabilityFixture.py`
+- `.cache/gaia/gaia_capability_2023_all_validation.sample.json`
+- `packages/mcp-local/src/__tests__/gaiaCapabilityEval.test.ts`
+- `packages/mcp-local/src/__tests__/fixtures/generateGaiaCapabilityFilesFixture.py`
+- `.cache/gaia/gaia_capability_files_2023_all_validation.sample.json`
+- `.cache/gaia/data/...` (local GAIA attachments; do not commit)
+- `packages/mcp-local/src/__tests__/gaiaCapabilityFilesEval.test.ts`
+
+Required tool chain per dataset task:
+- `run_recon`
+- `log_recon_finding`
+- `findTools`
+- `getMethodology`
+- `start_eval_run`
+- `record_eval_result`
+- `complete_eval_run`
+- `run_closed_loop`
+- `run_mandatory_flywheel`
+- `search_all_knowledge`
+
+**→ Quick Refs:** Core process in [AI Flywheel](#the-ai-flywheel-mandatory) | Verification flow in [Verification Cycle](#verification-cycle-workflow) | Loop discipline in [Closed Loop Principle](#closed-loop-principle)
+
+---
+
+## MCP Tool Categories
+
+Use `getMethodology("overview")` to see all available workflows.
+
+| Category | Tools | When to Use |
+|----------|-------|-------------|
+| **Web** | `web_search`, `fetch_url` | Research, reading docs, market validation |
+| **Local Files** | `read_pdf_text`, `pdf_search_text`, `read_xlsx_file`, `xlsx_select_rows`, `xlsx_aggregate`, `read_csv_file`, `csv_select_rows`, `csv_aggregate`, `read_text_file`, `read_json_file`, `json_select`, `read_jsonl_file`, `zip_list_files`, `zip_read_text_file`, `zip_extract_file`, `read_docx_text`, `read_pptx_text` | Deterministic parsing and aggregation of local attachments (GAIA file-backed lane) |
+| **GitHub** | `search_github`, `analyze_repo` | Finding libraries, studying implementations |
+| **Verification** | `start_cycle`, `log_phase`, `complete_cycle` | Tracking the flywheel process |
+| **Eval** | `start_eval_run`, `log_test_result` | Test case management |
+| **Quality Gates** | `run_quality_gate`, `get_gate_history` | Pass/fail checkpoints |
+| **Learning** | `record_learning`, `search_all_knowledge` | Persistent knowledge base |
+| **Vision** | `analyze_screenshot`, `capture_ui_screenshot` | UI/UX verification |
+| **Bootstrap** | `discover_infrastructure`, `triple_verify`, `self_implement` | Self-setup, triple verification |
+| **Autonomous** | `assess_risk`, `decide_re_update`, `run_self_maintenance` | Risk-aware execution, self-maintenance |
+| **Parallel Agents** | `claim_agent_task`, `release_agent_task`, `list_agent_tasks`, `assign_agent_role`, `get_agent_role`, `log_context_budget`, `run_oracle_comparison`, `get_parallel_status` | Multi-agent coordination, task locking, role specialization, oracle testing |
+| **LLM** | `call_llm`, `extract_structured_data`, `benchmark_models` | LLM calling, structured extraction, model comparison |
+| **Security** | `scan_dependencies`, `run_code_analysis` | Dependency auditing, static code analysis |
+| **Platform** | `query_daily_brief`, `query_funding_entities`, `query_research_queue`, `publish_to_queue` | Convex platform bridge: intelligence, funding, research, publishing |
+| **Meta** | `findTools`, `getMethodology` | Discover tools, get workflow guides |
+| **Discovery** | `discover_tools`, `get_tool_quick_ref`, `get_workflow_chain` | Hybrid search, quick refs, workflow chains |
+
+Meta + Discovery tools (5 total) are **always included** regardless of preset. See [Toolset Gating & Presets](#toolset-gating--presets).
+
+**→ Quick Refs:** Find tools by keyword: `findTools({ query: "verification" })` | Hybrid search: `discover_tools({ query: "security" })` | Get workflow guide: `getMethodology({ topic: "..." })` | See [Methodology Topics](#methodology-topics) for all topics
+
+---
+
+## Toolset Gating & Presets
+
+NodeBench MCP supports 4 presets that control which domain toolsets are loaded at startup. Meta + Discovery tools (5 total) are **always included** on top of any preset.
+
+### Preset Table
+
+| Preset | Domain Toolsets | Domain Tools | Total (with meta+discovery) | Use Case |
+|--------|----------------|-------------|----------------------------|----------|
+| **meta** | 0 | 0 | 5 | Discovery-only front door. Agents start here and self-escalate. |
+| **lite** | 7 | ~35 | ~40 | Lightweight verification-focused workflows. CI bots, quick checks. |
+| **core** | 16 | ~75 | ~80 | Full development workflow. Most agent sessions. |
+| **full** | all | 89+ | 94+ | Everything enabled. Benchmarking, exploration, advanced use. |
+
+### Usage
+
+```bash
+npx nodebench-mcp --preset meta       # Discovery-only (5 tools)
+npx nodebench-mcp --preset lite       # Verification + eval + recon + security
+npx nodebench-mcp --preset core       # Full dev workflow without vision/parallel
+npx nodebench-mcp --preset full       # All toolsets (default)
+npx nodebench-mcp --toolsets verification,eval,recon   # Custom selection
+npx nodebench-mcp --exclude vision,ui_capture          # Exclude specific toolsets
+```
+
+### The Meta Preset — Discovery-Only Front Door
+
+The **meta** preset loads zero domain tools. Agents start with only 5 tools:
+
+| Tool | Purpose |
+|------|---------|
+| `findTools` | Keyword search across all registered tools |
+| `getMethodology` | Get workflow guides by topic |
+| `discover_tools` | Hybrid search with relevance scoring (richer than findTools) |
+| `get_tool_quick_ref` | Quick reference card for any specific tool |
+| `get_workflow_chain` | Recommended tool sequence for common workflows |
+
+This is the recommended starting point for autonomous agents. The self-escalation pattern:
+
+```
+1. Start with --preset meta (5 tools)
+2. discover_tools({ query: "what I need to do" })    // Find relevant tools
+3. get_workflow_chain({ workflow: "verification" })    // Get the tool sequence
+4. If needed tools are not loaded:
+   → Restart with --preset core or --preset full
+   → Or use --toolsets to add specific domains
+5. Proceed with full workflow
+```
+
+### Preset Domain Breakdown
+
+**meta** (0 domains): No domain tools. Meta + Discovery only.
+
+**lite** (7 domains): `verification`, `eval`, `quality_gate`, `learning`, `recon`, `security`, `boilerplate`
+
+**core** (16 domains): Everything in lite plus `flywheel`, `bootstrap`, `self_eval`, `llm`, `platform`, `research_writing`, `flicker_detection`, `figma_flow`, `benchmark`
+
+**full** (all domains): All toolsets in TOOLSET_MAP including `ui_capture`, `vision`, `local_file`, `web`, `github`, `docs`, `parallel`, and everything in core.
+
+**→ Quick Refs:** Check current toolset: `findTools({ query: "*" })` | Self-escalate: restart with `--preset core` | See [MCP Tool Categories](#mcp-tool-categories) | CLI help: `npx nodebench-mcp --help`
+
+---
+
+## Verification Cycle Workflow
+
+Start every significant task with a verification cycle:
+
+```
+1. start_cycle({ goal: "Implement feature X" })
+2. log_phase({ phase: "context", notes: "Researched existing patterns..." })
+3. log_phase({ phase: "implementation", notes: "Added new function..." })
+4. log_phase({ phase: "testing", notes: "All tests pass..." })
+5. complete_cycle({ status: "success", summary: "Feature X shipped" })
+```
+
+If blocked or failed:
+```
+abandon_cycle({ reason: "Blocked by external dependency" })
+```
+
+**→ Quick Refs:** Before starting: `search_all_knowledge({ query: "your task" })` | After completing: `record_learning({ ... })` | Run flywheel: See [AI Flywheel](#the-ai-flywheel-mandatory) | Track quality: See [Quality Gates](#quality-gates)
+
+---
+
+## Recording Learnings
+
+After discovering something useful, record it:
+
+```
+record_learning({
+  title: "Convex index predicates must use withIndex chaining",
+  content: "Using .filter() after .withIndex() bypasses the index...",
+  category: "convex",
+  tags: ["database", "performance", "gotcha"]
+})
+```
+
+Search later with:
+```
+search_all_knowledge({ query: "convex index" })
+```
+
+**→ Quick Refs:** Search before implementing: `search_all_knowledge` | `search_learnings` and `list_learnings` are DEPRECATED | Part of flywheel Step 7 | See [Verification Cycle](#verification-cycle-workflow)
+
+---
+
+## Quality Gates
+
+Before shipping, run quality gates:
+
+```
+run_quality_gate({
+  gateName: "deploy_readiness",
+  results: [
+    { rule: "tests_pass", passed: true },
+    { rule: "no_type_errors", passed: true },
+    { rule: "code_reviewed", passed: true }
+  ]
+})
+```
+
+Gate history tracks pass/fail over time.
+
+**→ Quick Refs:** Get preset rules: `get_gate_preset({ preset: "ui_ux_qa" })` | View history: `get_gate_history({ gateName: "..." })` | UI/UX gates: See [Vision](#vision-analysis) | Part of flywheel Step 5 re-verify
+
+---
+
+## Web Research Workflow
+
+For market research or tech evaluation:
+
+```
+1. web_search({ query: "MCP servers 2026", maxResults: 10 })
+2. search_github({ query: "mcp typescript", minStars: 100 })
+3. analyze_repo({ repoUrl: "owner/repo" })  // study top results
+4. fetch_url({ url: "https://docs.example.com" })  // read their docs
+5. record_learning({ ... })  // save key findings
+```
+
+**→ Quick Refs:** Analyze repo structure: `analyze_repo` | Save findings: `record_learning` | Part of: `getMethodology({ topic: "project_ideation" })` | See [Recording Learnings](#recording-learnings)
+
+---
+
+## Project Ideation Workflow
+
+Before building anything new:
+
+```
+getMethodology({ topic: "project_ideation" })
+```
+
+This returns a 6-step process:
+1. Define Concept
+2. Research Market
+3. Analyze Competition
+4. Define Requirements
+5. Plan Metrics
+6. Gate Approval
+
+**→ Quick Refs:** Research tools: `web_search`, `search_github`, `analyze_repo` | Record requirements: `log_recon_finding` | Create baseline: `start_eval_run` | See [Web Research](#web-research-workflow)
+
+---
+
+## Closed Loop Principle
+
+**Never present changes without full local verification.**
+
+The loop:
+1. Compile. Build clean.
+2. Lint. Style clean. No warnings.
+3. Test. Run automated suites.
+4. Self-debug. If 1-3 fail: read logs, hypothesize, fix, restart loop.
+
+Only when all green: present to user.
+
+**→ Quick Refs:** Track loop: `run_closed_loop({ ... })` | Part of flywheel Steps 1-5 | See [AI Flywheel](#the-ai-flywheel-mandatory) | After loop: See [Post-Implementation Checklist](#post-implementation-checklist)
+
+---
+
+## Environment Setup
+
+Check your environment:
+```
+setup_local_env({ checkSdks: true })
+```
+
+Returns:
+- Node/npm versions
+- Missing API keys
+- Recommended SDK installations
+- Actionable next steps
+
+**→ Quick Refs:** After setup: `getMethodology("overview")` | Check vision: `discover_vision_env()` | See [API Keys](#api-keys-optional) | Then: See [Verification Cycle](#verification-cycle-workflow)
+
+---
+
+## API Keys (Optional)
+
+Set these for enhanced functionality:
+
+| Key | Purpose |
+|-----|---------|
+| `GEMINI_API_KEY` | Web search (Google grounding), vision analysis |
+| `OPENAI_API_KEY` | Alternative search/vision provider |
+| `GITHUB_TOKEN` | Higher rate limits (5000/hr vs 60/hr) |
+| `ANTHROPIC_API_KEY` | Alternative vision provider |
+
+**→ Quick Refs:** Check what's available: `setup_local_env({ checkSdks: true })` | Vision capabilities: `discover_vision_env()` | See [Environment Setup](#environment-setup)
+
+---
+
+## Vision Analysis
+
+For UI/UX verification:
+
+```
+1. capture_ui_screenshot({ url: "http://localhost:3000", viewport: "desktop" })
+2. analyze_screenshot({ imageBase64: "...", prompt: "Check accessibility" })
+3. capture_responsive_suite({ url: "...", label: "homepage" })
+```
+
+**→ Quick Refs:** Check capabilities: `discover_vision_env()` | UI QA methodology: `getMethodology({ topic: "ui_ux_qa" })` | Agentic vision: `getMethodology({ topic: "agentic_vision" })` | See [Quality Gates](#quality-gates)
+
+---
+
+## Post-Implementation Checklist
+
+After every implementation, answer these 3 questions:
+
+1. **MCP gaps?** — Were all relevant tools called? Any unexpected results?
+2. **Implementation gaps?** — Dead code? Missing integrations? Hardcoded values?
+3. **Flywheel complete?** — All 7 steps passed including E2E test?
+
+If any answer reveals a gap: fix it before proceeding.
+
+**→ Quick Refs:** Run self-check: `run_self_maintenance({ scope: "quick" })` | Record learnings: `record_learning` | Update docs: `update_agents_md` | See [AI Flywheel](#the-ai-flywheel-mandatory)
+
+---
+
+## Agent Self-Bootstrap System
+
+For agents to self-configure and validate against authoritative sources.
+
+### 1. Discover Existing Infrastructure
+```
+discover_infrastructure({
+  categories: ["agent_loop", "telemetry", "evaluation", "verification"],
+  depth: "thorough"
+})
+```
+
+Returns: discovered patterns, missing components, bootstrap plan.
+
+### 2. Triple Verification (with Source Citations)
+
+Run 3-layer verification with authoritative sources:
+
+```
+triple_verify({
+  target: "my-feature",
+  scope: "full",
+  includeWebSearch: true,
+  generateInstructions: true
+})
+```
+
+**V1: Internal Analysis** — Checks codebase patterns
+**V2: External Validation** — Cross-references Anthropic, OpenAI, LangChain, MCP spec
+**V3: Synthesis** — Generates recommendations with source citations
+
+### 3. Self-Implement Missing Components
+```
+self_implement({
+  component: "telemetry",  // or: agent_loop, evaluation, verification, multi_channel
+  dryRun: true
+})
+```
+
+Generates production-ready templates based on industry patterns.
+
+### 4. Generate Self-Instructions
+```
+generate_self_instructions({
+  format: "skills_md",  // or: rules_md, guidelines, claude_md
+  includeExternalSources: true
+})
+```
+
+Creates persistent instructions with authoritative source citations.
+
+### 5. Multi-Channel Information Gathering
+```
+connect_channels({
+  channels: ["web", "github", "slack", "docs"],
+  query: "agent verification patterns",
+  aggressive: true
+})
+```
+
+Aggregates findings from multiple sources.
+
+### Authoritative Sources (Tier 1)
+- https://www.anthropic.com/research/building-effective-agents
+- https://openai.github.io/openai-agents-python/
+- https://www.langchain.com/langgraph
+- https://modelcontextprotocol.io/specification/2025-11-25
+
+**→ Quick Refs:** Full methodology: `getMethodology({ topic: "agent_bootstrap" })` | After bootstrap: See [Autonomous Maintenance](#autonomous-self-maintenance-system) | Before implementing: `assess_risk` | See [Triple Verification](#2-triple-verification-with-source-citations)
+
+---
+
+## Autonomous Self-Maintenance System
+
+Aggressive autonomous self-management with risk-aware execution. Based on OpenClaw patterns and Ralph Wiggum stop-hooks.
+
+### 1. Risk-Tiered Execution
+
+Before any action, assess its risk tier:
+
+```
+assess_risk({ action: "push to remote" })
+```
+
+Risk tiers:
+- **Low**: Reading, analyzing, searching — auto-approve
+- **Medium**: Writing local files, running tests — log and proceed
+- **High**: Pushing to remote, posting externally — require confirmation
+
+### 2. Re-Update Before Create
+
+**CRITICAL:** Before creating new files, check if updating existing is better:
+
+```
+decide_re_update({
+  targetContent: "New agent instructions",
+  contentType: "instructions",
+  existingFiles: ["AGENTS.md", "README.md"]
+})
+```
+
+This prevents file sprawl and maintains single source of truth.
+
+### 3. Self-Maintenance Cycles
+
+Run periodic self-checks:
+
+```
+run_self_maintenance({
+  scope: "standard",  // quick | standard | thorough
+  autoFix: false,
+  dryRun: true
+})
+```
+
+Checks: TypeScript compilation, documentation sync, tool counts, test coverage.
+
+### 4. Directory Scaffolding (OpenClaw Style)
+
+When adding infrastructure, use standardized scaffolding:
+
+```
+scaffold_directory({
+  component: "agent_loop",  // or: telemetry, evaluation, multi_channel, etc.
+  includeTests: true,
+  dryRun: true
+})
+```
+
+Creates organized subdirectories with proper test structure.
+
+### 5. Autonomous Loops with Guardrails
+
+For multi-step autonomous tasks, use controlled loops:
+
+```
+run_autonomous_loop({
+  goal: "Verify all tools pass static analysis",
+  maxIterations: 5,
+  maxDurationMs: 60000,
+  stopOnFirstFailure: true
+})
+```
+
+Implements Ralph Wiggum pattern with checkpoints and stop conditions.
+
+**→ Quick Refs:** Full methodology: `getMethodology({ topic: "autonomous_maintenance" })` | Before actions: `assess_risk` | Before new files: `decide_re_update` | Scaffold structure: `scaffold_directory` | See [Self-Bootstrap](#agent-self-bootstrap-system)
+
+---
+
+## Methodology Topics
+
+Available via `getMethodology({ topic: "..." })`:
+
+| Topic | Description | Quick Ref |
+|-------|-------------|-----------|
+| `overview` | See all methodologies | Start here |
+| `verification` | 6-phase development cycle | [AI Flywheel](#the-ai-flywheel-mandatory) |
+| `eval` | Test case management | [Quality Gates](#quality-gates) |
+| `flywheel` | Continuous improvement loop | [AI Flywheel](#the-ai-flywheel-mandatory) |
+| `mandatory_flywheel` | Required verification for changes | [AI Flywheel](#the-ai-flywheel-mandatory) |
+| `reconnaissance` | Codebase discovery | [Self-Bootstrap](#agent-self-bootstrap-system) |
+| `quality_gates` | Pass/fail checkpoints | [Quality Gates](#quality-gates) |
+| `ui_ux_qa` | Frontend verification | [Vision Analysis](#vision-analysis) |
+| `agentic_vision` | AI-powered visual QA | [Vision Analysis](#vision-analysis) |
+| `closed_loop` | Build/test before presenting | [Closed Loop](#closed-loop-principle) |
+| `learnings` | Knowledge persistence | [Recording Learnings](#recording-learnings) |
+| `project_ideation` | Validate ideas before building | [Project Ideation](#project-ideation-workflow) |
+| `tech_stack_2026` | Dependency management | [Environment Setup](#environment-setup) |
+| `agents_md_maintenance` | Keep docs in sync | [Auto-Update](#auto-update-this-file) |
+| `agent_bootstrap` | Self-discover, triple verify | [Self-Bootstrap](#agent-self-bootstrap-system) |
+| `autonomous_maintenance` | Risk-tiered execution | [Autonomous Maintenance](#autonomous-self-maintenance-system) |
+| `parallel_agent_teams` | Multi-agent coordination, task locking, oracle testing | [Parallel Agent Teams](#parallel-agent-teams) |
+| `self_reinforced_learning` | Trajectory analysis, self-eval, improvement recs | [Self-Reinforced Learning](#self-reinforced-learning-loop) |
+| `toolset_gating` | 4 presets (meta, lite, core, full) and self-escalation | [Toolset Gating & Presets](#toolset-gating--presets) |
+
+**→ Quick Refs:** Find tools: `findTools({ query: "..." })` | Get any methodology: `getMethodology({ topic: "..." })` | See [MCP Tool Categories](#mcp-tool-categories)
+
+---
+
+## Parallel Agent Teams
+
+Based on Anthropic's ["Building a C Compiler with Parallel Claudes"](https://www.anthropic.com/engineering/building-c-compiler) (Feb 2026).
+
+Run multiple AI agents in parallel on a shared codebase with coordination via task locking, role specialization, context budget management, and oracle-based testing.
+
+### Quick Start — Parallel Agents
+
+```
+1. get_parallel_status({ includeHistory: true })     // Orient: what's happening?
+2. assign_agent_role({ role: "implementer" })         // Specialize
+3. claim_agent_task({ taskKey: "fix_auth" })           // Lock task
+4. ... do work ...
+5. log_context_budget({ eventType: "test_output", tokensUsed: 5000 })  // Track budget
+6. run_oracle_comparison({ testLabel: "auth_output", actualOutput: "...", expectedOutput: "...", oracleSource: "prod_v2" })
+7. release_agent_task({ taskKey: "fix_auth", status: "completed", progressNote: "Fixed JWT, added tests" })
+```
+
+### Predefined Agent Roles
+
+| Role | Focus |
+|------|-------|
+| `implementer` | Primary feature work. Picks failing tests, implements fixes. |
+| `dedup_reviewer` | Finds and coalesces duplicate implementations. |
+| `performance_optimizer` | Profiles bottlenecks, optimizes hot paths. |
+| `documentation_maintainer` | Keeps READMEs and progress files in sync. |
+| `code_quality_critic` | Structural improvements, pattern enforcement. |
+| `test_writer` | Writes targeted tests for edge cases and failure modes. |
+| `security_auditor` | Audits for vulnerabilities, logs CRITICAL gaps. |
+
+### Key Patterns (from Anthropic blog)
+
+- **Task Locking**: Claim before working. If two agents try the same task, the second picks a different one.
+- **Context Window Budget**: Do NOT print thousands of useless bytes. Pre-compute summaries. Use `--fast` mode (1-10% random sample) for large test suites. Log errors with ERROR prefix on same line for grep.
+- **Oracle Testing**: Compare output against known-good reference. Each failing comparison is an independent work item for a parallel agent.
+- **Time Blindness**: Agents can't tell time. Print progress infrequently. Use deterministic random sampling per-agent but randomized across VMs.
+- **Progress Files**: Maintain running docs of status, failed approaches, and remaining tasks. Fresh agent sessions read these to orient.
+- **Delta Debugging**: When tests pass individually but fail together, split the set in half to narrow down the minimal failing combination.
+
+### Bootstrap for External Repos
+
+When nodebench-mcp is connected to a project that lacks parallel agent infrastructure, it can auto-detect gaps and scaffold everything needed:
+
+```
+1. bootstrap_parallel_agents({ projectRoot: "/path/to/their/repo", dryRun: true })
+   // Scans 7 categories: task coordination, roles, oracle, context budget,
+   // progress files, AGENTS.md parallel section, git worktrees
+
+2. bootstrap_parallel_agents({ projectRoot: "...", dryRun: false, techStack: "TypeScript/React" })
+   // Creates .parallel-agents/ dir, progress.md, roles.json, lock dirs, oracle dirs
+
+3. generate_parallel_agents_md({ techStack: "TypeScript/React", projectName: "their-project", maxAgents: 4 })
+   // Generates portable AGENTS.md section — paste into their repo
+
+4. Run the 6-step flywheel plan returned by the bootstrap tool to verify
+5. Fix any issues, re-verify
+6. record_learning({ key: "bootstrap_their_project", content: "...", category: "pattern" })
+```
+
+The generated AGENTS.md section is framework-agnostic and works with any AI agent (Claude, GPT, etc.). It includes:
+- Task locking protocol (file-based, no dependencies)
+- Role definitions and assignment guide
+- Oracle testing workflow with idiomatic examples
+- Context budget rules
+- Progress file protocol
+- Anti-patterns to avoid
+- Optional nodebench-mcp tool mapping table
+
+### MCP Prompts for Parallel Agent Teams
+
+- `parallel-agent-team` — Full team setup with role assignment and task breakdown
+- `oracle-test-harness` — Oracle-based testing setup for a component
+- `bootstrap-parallel-agents` — Detect and scaffold parallel agent infra for any external repo
+
+**→ Quick Refs:** Full methodology: `getMethodology({ topic: "parallel_agent_teams" })` | Find parallel tools: `findTools({ category: "parallel_agents" })` | Bootstrap external repo: `bootstrap_parallel_agents({ projectRoot: "..." })` | See [AI Flywheel](#the-ai-flywheel-mandatory)
+
+---
+
+## Auto-Update This File
+
+Agents can self-update this file:
+
+```
+update_agents_md({
+  operation: "update_section",
+  section: "Custom Section",
+  content: "New content here...",
+  projectRoot: "/path/to/project"
+})
+```
+
+Or read current structure:
+```
+update_agents_md({ operation: "read", projectRoot: "/path/to/project" })
+```
+
+**→ Quick Refs:** Before updating: `decide_re_update({ contentType: "instructions", ... })` | After updating: Run flywheel Steps 1-7 | See [Re-Update Before Create](#2-re-update-before-create)
+
+---
+
+## License
+
+MIT — Use freely in any project.