skills/33-Galaxy-Dawn-claude-scholar/skills/planning-with-files/SKILL.md
Transforms workflow to use Manus-style persistent markdown files for planning, progress tracking, and knowledge storage. Use when starting complex tasks, multi-step projects, research tasks, or when the user mentions planning, organizing work, tracking progress, or wants structured output.
npx skillsauth add brycewang-stanford/Awesome-Agent-Skills-for-Empirical-Research planning-with-filesInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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Work like Manus: Use persistent markdown files as your "working memory on disk."
Before ANY complex task:
task_plan.md in the working directoryFor every non-trivial task, create THREE files:
| File | Purpose | When to Update |
|------|---------|----------------|
| task_plan.md | Track phases and progress | After each phase |
| notes.md | Store findings and research | During research |
| [deliverable].md | Final output | At completion |
Loop 1: Create task_plan.md with goal and phases
Loop 2: Research → save to notes.md → update task_plan.md
Loop 3: Read notes.md → create deliverable → update task_plan.md
Loop 4: Deliver final output
Before each major action:
Read task_plan.md # Refresh goals in attention window
After each phase:
Edit task_plan.md # Mark [x], update status
When storing information:
Write notes.md # Don't stuff context, store in file
Create this file FIRST for any complex task:
# Task Plan: [Brief Description]
## Goal
[One sentence describing the end state]
## Phases
- [ ] Phase 1: Plan and setup
- [ ] Phase 2: Research/gather information
- [ ] Phase 3: Execute/build
- [ ] Phase 4: Review and deliver
## Key Questions
1. [Question to answer]
2. [Question to answer]
## Decisions Made
- [Decision]: [Rationale]
## Errors Encountered
- [Error]: [Resolution]
## Status
**Currently in Phase X** - [What I'm doing now]
For research and findings:
# Notes: [Topic]
## Sources
### Source 1: [Name]
- URL: [link]
- Key points:
- [Finding]
- [Finding]
## Synthesized Findings
### [Category]
- [Finding]
- [Finding]
Never start a complex task without task_plan.md. This is non-negotiable.
Before any major decision, read the plan file. This keeps goals in your attention window.
After completing any phase, immediately update the plan file:
Large outputs go to files, not context. Keep only paths in working memory.
Every error goes in the "Errors Encountered" section. This builds knowledge for future tasks.
Use 3-file pattern for:
Skip for:
| Don't | Do Instead |
|-------|------------|
| Use TodoWrite for persistence | Create task_plan.md file |
| State goals once and forget | Re-read plan before each decision |
| Hide errors and retry | Log errors to plan file |
| Stuff everything in context | Store large content in files |
| Start executing immediately | Create plan file FIRST |
See reference.md for:
See examples.md for:
tools
Recommend AND run open-source AI tools, agents, Claude Code / Codex skills, and MCP servers for any stage of a literature review — searching, reading, extracting, synthesizing, screening, citation-checking, and paper writing. Use when the user asks "what tool should I use to..." OR "install/run/use <tool> to ..." for research/lit-review work: automating a survey or related-work section, PDF→Markdown extraction for LLMs (MinerU/marker/docling), PRISMA / systematic review (ASReview), citation-backed Q&A over PDFs (PaperQA2), wiring papers into Claude/Cursor via MCP (arxiv/paper-search/zotero servers), or chatting with a Zotero library. Ships a launcher (scripts/litrun.py) that installs each tool in an isolated venv and runs it. Curated catalog of 70+ vetted projects. 支持中英文(用于「文献综述工具选型」与「一键安装/运行」)。
development
Route empirical-research requests through the Auto-Empirical Research Skills catalog when this whole repository is installed as one skill in Codex, CodeBuddy, Claude Code, or another IDE. Use to choose and load the right vendored AERS skill for causal inference, econometrics, replication, data acquisition, manuscript writing, peer review and referee responses, citation checking, de-AIGC editing, or full empirical-paper workflows without reading the entire repository at once.
documentation
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tools
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