Skills
skills/flora131/atomic/research-codebase

research-codebase

Installation
SKILL.md
Contains Shell Commands

This skill contains shell command directives (!`command`) that may execute system commands. Review carefully before installing.

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.

The user's research question/request is: $ARGUMENTS

Steps to follow after receiving the research query:

<EXTREMELY_IMPORTANT>

  • OPTIMIZE the research question using your prompt-engineer skill to refine phrasing and structure for maximum clarity and precision.
  • After research is complete and the research artifact(s) are generated, provide an executive summary of the research and path to the research document(s) to the user, and ask if they have any follow-up questions or need clarification.

</EXTREMELY_IMPORTANT>

  1. Read any directly mentioned files first:

    • If the user mentions specific files (tickets, docs, or other notes), read them FULLY first
    • IMPORTANT: Use the readFile tool WITHOUT limit/offset parameters to read entire files
    • CRITICAL: Read these files yourself in the main context before spawning any sub-tasks
    • This ensures you have full context before decomposing the research

  2. Analyze and decompose the research question:

    • Break the research question down into composable research areas
    • Take time to ultrathink about the underlying patterns, connections, and architectural implications the user might be seeking
    • Identify specific components, patterns, or concepts to investigate
    • Create a research plan using TodoWrite to track all subtasks
    • Consider which directories, files, or architectural patterns are relevant

  3. Spawn parallel sub-agent tasks:

    • Create multiple Task agents to research different aspects concurrently
    • We now have specialized agents that know how to do specific research tasks:

    For codebase research:

    • Use the codebase-locator agent to find WHERE files and components live
    • Use the codebase-analyzer agent to understand HOW specific code works (without critiquing it)
    • Use the codebase-pattern-finder agent to find examples of existing patterns (without evaluating them)
    • Output directory: research/docs/
    • Examples:
      • The database logic is found and can be documented in research/docs/2024-01-10-database-implementation.md
      • The authentication flow is found and can be documented in research/docs/2024-01-11-authentication-flow.md

    IMPORTANT: All agents are documentarians, not critics. They will describe what exists without suggesting improvements or identifying issues.

    For research directory:

    • Use the codebase-research-locator agent to discover what documents exist about the topic
    • Use the codebase-research-analyzer agent to extract key insights from specific documents (only the most relevant ones)

    For online search:

    • VERY IMPORTANT: In case you discover external libraries as dependencies, use the codebase-online-researcher agent for external documentation and resources
      • The agent fetches live web content using the playwright-cli skill (or bunx @playwright/cli / curl). Instruct it to apply the token-efficient fetch order: (1) try curl https://<site>/llms.txt for an AI-friendly index (see llmstxt.org), (2) try curl <url> -H "Accept: text/markdown" to get pre-converted Markdown (supported on Cloudflare-hosted docs via Markdown for Agents), (3) fall back to HTML parsing via playwright-cli
      • Instruct the agent to return LINKS with their findings and INCLUDE those links in the research document
      • The agent should persist reusable source documents under research/web/<YYYY-MM-DD>-<kebab-case-topic>.md (with frontmatter noting source_url, fetched_at, and fetch_method) so future research can reuse them without re-fetching
      • Output directory for the synthesized research artifact: research/docs/
      • Examples:
        • If researching Redis locks usage, the agent might find relevant usage and create a document research/docs/2024-01-15-redis-locks-usage.md with internal links to Redis docs and code references (and cache the fetched Redis docs under research/web/)
        • If researching OAuth flows, the agent might find relevant external articles and create a document research/docs/2024-01-16-oauth-flows.md with links to those articles

    The key is to use these agents intelligently:

    • Start with locator agents to find what exists
    • Then use analyzer agents on the most promising findings to document how they work
    • Run multiple agents in parallel when they're searching for different things
    • Each agent knows its job - just tell it what you're looking for
    • Don't write detailed prompts about HOW to search - the agents already know
    • Remind agents they are documenting, not evaluating or improving

  4. Wait for all sub-agents to complete and synthesize:

    • IMPORTANT: Wait for ALL sub-agent tasks to complete before proceeding
    • Compile all sub-agent results (both codebase and research findings)
    • Prioritize live codebase findings as primary source of truth
    • Use research findings as supplementary historical context
    • Connect findings across different components
    • Include specific file paths and line numbers for reference
    • Highlight patterns, connections, and architectural decisions
    • Answer the user's research question with concrete evidence
    • If findings reveal the original question was misframed (e.g., the system works differently than assumed, or the components don't exist where expected), flag this to the user before finalizing the document. This is valuable signal — don't bury it.

  5. Generate research document:

    • Follow the directory structure for research documents:
research/
├── tickets/
│   ├── YYYY-MM-DD-XXXX-description.md
├── docs/
│   ├── YYYY-MM-DD-topic.md
├── notes/
│   ├── YYYY-MM-DD-meeting.md
├── ...
└──

  • Naming conventions:

    • YYYY-MM-DD is today's date
    • topic is a brief kebab-case description of the research topic
    • meeting is a brief kebab-case description of the meeting topic
    • XXXX is the ticket number (omit if no ticket)
    • description is a brief kebab-case description of the research topic
    • Examples:
      • With ticket: 2025-01-08-1478-parent-child-tracking.md
      • Without ticket: 2025-01-08-authentication-flow.md

  • Structure the document with YAML frontmatter followed by content:

    ---
date: !`date '+%Y-%m-%d %H:%M:%S %Z'`
researcher: [Researcher name from thoughts status]
git_commit: !`git rev-parse --verify HEAD 2>/dev/null || echo "no-commits"`
branch: !`git branch --show-current 2>/dev/null || git rev-parse --abbrev-ref HEAD 2>/dev/null || echo "unborn"`
repository: !`basename "$(git rev-parse --show-toplevel 2>/dev/null)" 2>/dev/null || echo "unknown-repo"`
topic: "[User's Question/Topic]"
tags: [research, codebase, relevant-component-names]
status: complete
last_updated: !`date '+%Y-%m-%d'`
last_updated_by: [Researcher name]
---

# Research

## Research Question

[Original user query]

## Summary

[High-level documentation of what was found, answering the user's question by describing what exists]

## Detailed Findings

### [Component/Area 1]

- Description of what exists ([file.ext:line](link))
- How it connects to other components
- Current implementation details (without evaluation)

### [Component/Area 2]

...

## Code References

- `path/to/file.py:123` - Description of what's there
- `another/file.ts:45-67` - Description of the code block

## Architecture Documentation

[Current patterns, conventions, and design implementations found in the codebase]

## Historical Context (from research/)

[Relevant insights from research/ directory with references]

- `research/docs/YYYY-MM-DD-topic.md` - Information about module X
- `research/notes/YYYY-MM-DD-meeting.md` - Past notes from internal engineering, customer, etc. discussions
- ...

## Related Research

[Links to other research documents in research/]

## Open Questions

[Any areas that need further investigation]

  1. Add GitHub permalinks (if applicable):

    • Check if on main branch or if commit is pushed: git branch --show-current and git status
    • If on main/master or pushed, generate GitHub permalinks:
      • Get repo info: gh repo view --json owner,name
      • Create permalinks: https://github.com/{owner}/{repo}/blob/{commit}/{file}#L{line}
    • Replace local file references with permalinks in the document

  2. Present findings:

    • Present a concise summary of findings to the user
    • Include key file references for easy navigation
    • Ask if they have follow-up questions or need clarification

  3. Handle follow-up questions:

  • If the user has follow-up questions, append to the same research document
  • Update the frontmatter fields last_updated and last_updated_by to reflect the update
  • Add last_updated_note: "Added follow-up research for [brief description]" to frontmatter
  • Add a new section: ## Follow-up Research [timestamp]
  • Spawn new sub-agents as needed for additional investigation
  • Continue updating the document and syncing

Important notes:

  • Please DO NOT implement anything in this stage, just create the comprehensive research document

  • Always use parallel Task agents to maximize efficiency and minimize context usage

  • Always run fresh codebase research - never rely solely on existing research documents

  • The research/ directory provides historical context to supplement live findings

  • Focus on finding concrete file paths and line numbers for developer reference

  • Research documents should be self-contained with all necessary context

  • Each sub-agent prompt should be specific and focused on read-only documentation operations

  • Document cross-component connections and how systems interact

  • Include temporal context (when the research was conducted)

  • Link to GitHub when possible for permanent references

  • Keep the main agent focused on synthesis, not deep file reading

  • Have sub-agents document examples and usage patterns as they exist

  • Explore all of research/ directory, not just research subdirectory

  • CRITICAL: You and all sub-agents are documentarians, not evaluators

  • REMEMBER: Document what IS, not what SHOULD BE

  • NO RECOMMENDATIONS: Only describe the current state of the codebase

  • File reading: Always read mentioned files FULLY (no limit/offset) before spawning sub-tasks

  • Critical ordering: Follow the numbered steps exactly

    • ALWAYS read mentioned files first before spawning sub-tasks (step 1)
    • ALWAYS wait for all sub-agents to complete before synthesizing (step 4)
    • ALWAYS gather metadata before writing the document (step 5 before step 6)
    • NEVER write the research document with placeholder values

  • Frontmatter consistency:

    • Always include frontmatter at the beginning of research documents
    • Keep frontmatter fields consistent across all research documents
    • Update frontmatter when adding follow-up research
    • Use snake_case for multi-word field names (e.g., last_updated, git_commit)
    • Tags should be relevant to the research topic and components studied

Final Output

  • A collection of research files with comprehensive research findings, properly formatted and linked, ready for consumption to create detailed specifications or design documents.
  • IMPORTANT: DO NOT generate any other artifacts or files OUTSIDE of the research/ directory.
Weekly Installs
108
Repository
flora131/atomic
GitHub Stars
163
First Seen
Today
Security Audits
Gen Agent Trust HubWarn
SocketPass
SnykWarn