# Research Resources

Resources that contain research that can be used to build plugins.

## List

[][YOLO Mode (You Only Look Once) automates your entire Phases workflow](https://docs.traycer.ai/tasks/yolo-mode) - Claude have `--dangerously-skip-permissions` flag to skip permissions check, so it can be used to run YOLO Mode without permissions check.
[][Agent0](https://huggingface.co/papers/2511.16043) - Unleashing Self-Evolving Agents from Zero Data via Tool-Integrated Reasoning
- <https://github.com/aiming-lab/Agent0>
[][Solving a Million-Step LLM Task with Zero Errors](https://arxiv.org/abs/2511.09030) - using `cat file | claude -p "query" --output-format` will run Query via SDK, then exit with json output. 
- Adding `--max-turns 3` will limit amount of turns to 3.
- `--json-schema '{"type":"object","properties":{...}}' "query"` will validate the output against a JSON schema.
- `--model` flag to specify the model to use.
- `--permission-mode plan` will run agent in specified permissions mode <https://code.claude.com/docs/en/iam#permission-modes>

```bash
claude --agents '{
  "code-reviewer": {
    "description": "Expert code reviewer. Use proactively after code changes.",
    "prompt": "You are a senior code reviewer. Focus on code quality, security, and best practices.",
    "tools": ["Read", "Grep", "Glob", "Bash"],
    "model": "sonnet"
  },
  "debugger": {
    "description": "Debugging specialist for errors and test failures.",
    "prompt": "You are an expert debugger. Analyze errors, identify root causes, and provide fixes."
  }
}'
```
[][Agent OS](https://buildermethods.com/agent-os) - Agent OS is a spec-driven development system that gives AI agents the structured context they need to write production-quality code.
[x][codemap](https://github.com/JordanCoin/codemap) - map codebase structure
[][Effective harnesses for long-running agents](https://www.anthropic.com/engineering/effective-harnesses-for-long-running-agents)
[][mgrep](https://github.com/mixedbread-ai/mgrep)
[x][arxhiv MCP](https://hub.docker.com/mcp/server/arxiv-mcp-server/overview)
[][Docker MCP Toolkit](https://docs.docker.com/ai/mcp-catalog-and-toolkit/toolkit/)
[][Arc42 specification template] - Research Arc42 and adapt it for use in Spec Driven Development.
[][Opus soul document](https://gist.github.com/Richard-Weiss/efe157692991535403bd7e7fb20b6695)
[][YAGNI](https://martinfowler.com/bliki/Yagni.html) - Yagni originally is an acronym that stands for “You Aren't Gonna Need It”. It is a mantra from ExtremeProgramming.
[][Extreme Programming](https://martinfowler.com/bliki/ExtremeProgramming.html)
[][Beads task traker cli](https://github.com/steveyegge/beads) - maybe better to create new cli with simplified architecture, that useses only TASKS.md file.
[][Building the 14 Key Pillars of Agentic AI](https://levelup.gitconnected.com/building-the-14-key-pillars-of-agentic-ai-229e50f65986)
[] Three of Thought and etc - Expand papers that used in reflect plugin as separate comamnds/skills/hooks
[][Building Reliable RAG Pipelines Is Still Hard In 2025](https://medium.com/aiguys/building-reliable-rag-pipelines-is-still-hard-in-2025-9ba5fd92601c)
[] LSP server integration with Claude Code
[][Conductor: Google spec driven development kit](https://github.com/gemini-cli-extensions/conductor)
[] Task tracking: https://github.com/hmans/beans https://github.com/rrnewton/minibeads https://github.com/steveyegge/beads
[x][Agent Skills for Context Engineering](https://github.com/muratcankoylan/Agent-Skills-for-Context-Engineering)
[][Agent search MCP](https://github.com/exa-labs/exa-mcp-server)
[][First Principles Framework](https://github.com/m0n0x41d/quint-code)
[] Think about way to make reflection work as continues-learning agent. It can trigger on words like "You absolutily right", analyse it and save to CLAUDE.md file correction that user provided.
[][Hookify](https://github.com/anthropics/claude-code/tree/main/plugins/hookify) - advanced hook configuration, that using python skills.
[][Ralph](https://github.com/anthropics/claude-code/tree/main/plugins/ralph-wiggum) - continus iteration plugin and orcestrator verision https://github.com/mikeyobrien/ralph-orchestrator
[][Security Reminder](https://github.com/anthropics/claude-code/tree/main/plugins/security-guidance/hooks) - hook that reminds about security best practices.
[] Add git workspaces usage for competitive model writing
[] Research how git notes can be used during code writing and review
[] Research how to add RAG style pipline with vector search to prepent relevant code to context window before code writing
[] Check "Prompting Science" series. https://arxiv.org/abs/2503.04818, https://arxiv.org/abs/2512.05858, https://chatpaper.com/paper/172346, https://arxiv.org/abs/2508.00614, https://www.researchgate.net/publication/392530384_Prompting_Science_Report_2_The_Decreasing_Value_of_Chain_of_Thought_in_Prompting
[] https://arxiv.org/html/2602.16666v1 - Towards a Science of AI Agent Reliability
[] https://arxiv.org/html/2601.06112v1 - ReliabilityBench: Evaluating LLM Agent Reliability Under Production-Like Stress Conditions
