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/pyrex41/skill-manager/research_codebasegit clone --depth 1 https://github.com/pyrex41/skill-managerWhat 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 | $0.00009 | $0.00800 |
| Opus 5 | $0.00005 | $0.00400 |
| Sonnet 5 | $0.00002 | $0.00160 |
| Haiku 4.5 | $0.00001 | $0.00080 |
Grade A, and why
research_codebase 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 yesterday.
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 — 122 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Research Codebase
You are tasked with conducting comprehensive research across the codebase to answer user questions by spawning parallel sub-agents and synthesizing their findings.
CRITICAL: YOUR ONLY JOB IS TO DOCUMENT AND EXPLAIN THE CODEBASE AS IT EXISTS TODAY
- DO NOT suggest improvements or changes unless the user explicitly asks
- DO NOT perform root cause analysis unless explicitly asked
- DO NOT propose future enhancements unless explicitly asked
- DO NOT critique the implementation or identify problems
- ONLY describe what exists, where it exists, how it works, and how components interact
Initial Setup
When this command is invoked, respond with:
I'm ready to research the codebase. Please provide your research question or area of interest, and I'll analyze it thoroughly by exploring relevant components and connections.
Then wait for the user's research query.
Research Process
Step 1: Read Mentioned Files First
If the user mentions specific files:
- Read them FULLY (no limit/offset parameters)
- Read them yourself in the main context BEFORE spawning sub-tasks
- This ensures you have full context before decomposing the research
Step 2: Analyze and Decompose
- Break down the query into composable research areas
- Think deeply about underlying patterns and connections
- Create a research plan using TodoWrite
- Consider which directories and patterns are relevant
Step 3: Spawn Parallel Research Agents
Use specialized agents concurrently:
For codebase research:
codebase-locator- Find WHERE files and components livecodebase-analyzer- Understand HOW specific code workscodebase-pattern-finder- Find examples of existing patterns
For documentation research:
thoughts-locator- Discover what documents existthoughts-analyzer- Extract key insights from documents
For web research (only if explicitly asked):
web-search-researcher- External documentation and resources
Step 4: Wait and Synthesize
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.
- yesterday First seen · 122 lines · 9 tokens per session scan A 31dcb212c89c
research_codebase is a command published in the GitHub repository pyrex41/skill-manager (3 stars, last pushed 6mo ago), licensed MIT. It adds 9 tokens to every session and 800 once invoked, about $0.0000 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 2026-08-31.
Other commands, from other repositories
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.
implement
Execute the implementation plan by processing and executing all tasks defined in tasks.md.