Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx agentmods add commands/brain-bootstrap/claude-code-brain-bootstrap/researchgit clone --depth 1 https://github.com/brain-bootstrap/claude-code-brain-bootstrapWhat it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5 | $0.00011 | $0.00612 |
| Opus 5 | $0.00005 | $0.00306 |
| Sonnet 5 | $0.00002 | $0.00122 |
| Haiku 4.5 | $0.00001 | $0.00061 |
Grade A, and why
research scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 2d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 79 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Research and gather knowledge about: $ARGUMENTS
ultrathink — use extended reasoning for question formulation and knowledge synthesis.
Context
Read CLAUDE.md for project architecture and conventions.
Read claude/architecture.md for the tech stack.
Instructions
Phase 1: Analyze Information Gaps
Based on $ARGUMENTS and the project context:
- Identify what you already know from the codebase
- Identify knowledge gaps where external information would be valuable
- Categorize gaps: technical implementation, best practices, security, performance, alternatives
Phase 2: Generate Targeted Research Questions
Generate 5-7 focused research questions that are:
- Specific — target a distinct piece of information, not general knowledge
- Actionable — the answer should directly inform a design or implementation decision
- Prioritized — most critical questions first
- Diverse — cover different aspects (implementation patterns, pitfalls, performance, security)
Example questions:
- "What are the current best practices for [specific pattern] in [framework version]?"
- "What are common pitfalls when integrating [library A] with [library B]?"
- "How does [approach A] compare to [approach B] for [specific use case] in terms of performance and maintainability?"
Phase 3: Research
For each question:
- Check the codebase first — grep for existing patterns, read relevant files
- Check project docs —
claude/*.mdmay already have the answer - If MCP web search is available (check
.mcp.json): usemcp__SERVER_KEY__searchto find current information - If no web search: use your training knowledge, clearly marking confidence levels
Phase 4: Synthesize Findings
Present findings as a structured report:
## Research Report: [Topic]
### Question 1: [Question]
**Confidence:** [High/Medium/Low]
**Finding:** [Concise answer]
**Source:** [Codebase pattern / MCP search / Training knowledge]
**Recommendation:** [Actionable next step]
### Question 2: ...
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 2d ago First seen · 79 lines · 11 tokens per session scan A 599a824b668d
research is a command published in the GitHub repository brain-bootstrap/claude-code-brain-bootstrap (11 stars, last pushed 4mo ago), licensed MIT. It adds 11 tokens to every session and 612 once invoked, about $0.0001 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
Other commands, from other repositories
restart
Restart the claude-mnemonic worker process. Use this command when experiencing issues with the memory system.
checklist
Generate a custom checklist for the current feature based on user requirements.
clarify
Identify underspecified areas in the current feature spec by asking up to 5 highly targeted clarification questions and encoding answers back into the spec.
specify
Create or update the feature specification from a natural language feature description.
analyze
Perform a non-destructive cross-artifact consistency and quality analysis across spec.md, plan.md, and tasks.md after task generation.
converge
Assess the current codebase against the feature's spec, plan, and tasks, then append any remaining unbuilt work as new tasks to tasks.md so implement can complete it.