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Research Doc Organization

Set up and keep a clean research folder in Markdown, with one note per question, a sources file, a decision log and an index, so research stays findable, citable and readable by both people and AI agents. Use when research is scattered across tabs, chats and docs, when starting research for a new product, when handing research to a teammate or AI agent, or when someone asks "how should I organize my research", "research notes template", or "where do I keep sources".

Beginner⏱ 30 min to set up, 5 min per note📂 researchv1.0.0

In 30 minutes you will have a research/ folder with an index, a sources list, a decision log and a note template, ready for your AI agent to read and add to.

Goal

Every piece of research answers a question, cites its sources and leads to a decision, and anyone (you in three months, a teammate, an AI agent) can find it in under a minute.

When to use

  • Research lives in 30 browser tabs, three chats and a notes app.
  • Starting a new product, market or feature.
  • An AI agent keeps re-researching things you already found.
  • Not for: finding sources → research-source-finding.

Inputs

  • The product repo (or any folder) where the research should live.
  • The 3–5 open questions you're researching right now.

The structure

research/
├── README.md            # index: open questions, finished notes, latest decisions
├── sources.md           # every source once: link, date, level, one-line summary
├── decisions.md         # decision log: date, decision, why, which notes
└── notes/
    ├── 2026-09-pricing-competitors.md
    ├── 2026-09-where-users-ask.md
    └── 2026-10-aso-keywords-us.md
  • One note = one question. The file name is YYYY-MM-<topic>.md, so notes sort by date and read like a sentence.
  • Frontmatter on every note (template in assets/research-note.md): question, status (open / answered / outdated), confidence (high / medium / low), updated, sources.
  • Link, don't copy. Notes link to sources.md#anchor and to each other with relative links. The links turn the folder into a map.
  • Answer first. Every note starts with a 2–3 line answer, then the evidence.

Steps

  1. Create the folder (5 min). Copy assets/research-note.md, assets/sources-template.md and assets/decisions-template.md into research/. Rename them to notes/_template.md, sources.md and decisions.md.
  2. Write the index (5 min). research/README.md has three lists: Open questions, Answered (with a link to each note), and Latest decisions.
  3. Move existing research in (15 min). For each open tab or chat worth keeping: which question does it answer? Add it to that note, and add its link to sources.md. Close the tab.
  4. Tell your AI agent (2 min). Add to your CLAUDE.md / AGENTS.md: "Research lives in research/. Read research/README.md first. New findings go in a note from notes/_template.md; cite sources from sources.md."
  5. Keep it alive (5 min a week). Set notes older than 6 months to outdated or re-check them. Every decision gets a line in decisions.md with links to the notes behind it.

Prompt (copy-paste)

Replace everything in {{ }}.

You are my research librarian. Organize my research into a Markdown folder.

Product: {{what it is}}
Open questions: {{3-5 questions}}
Raw research to sort (links, notes, chat excerpts): {{paste}}

1. Propose the file tree for research/ (README.md index, sources.md, decisions.md, notes/YYYY-MM-topic.md).
2. For each open question, create a note with this frontmatter:
   question, status (open/answered/outdated), confidence (high/medium/low), updated (today), sources (list).
   Start each note with a 2-3 line answer (or "Not answered yet" + what's missing), then evidence with links.
3. Put every link from my raw research into sources.md once: title, URL, publish date if known, date checked,
   level (1 official, 2 data, 3 users, 4 practitioners, 5 articles), one-line summary.
   Never invent a URL or a date. Write "unknown" instead.
4. Write research/README.md with Open / Answered / Latest decisions sections, all linked.
Output each file in its own code block with the file path as the heading.

Example output

Illustrative example. Fictional product, shown for format.

---
question: Which paid tier do competitors put "export to PDF" in?
status: answered
confidence: medium
updated: 2026-09-30
sources: [notion-pricing, obsidian-pricing, r-productivity-export-thread]
---

**Answer:** 3 of 4 competitors keep PDF export free; only one paywalls it. Keep it free and paywall sync instead.

## Evidence
| Competitor | Export PDF | Source |
|---|---|---|
| Notion | Free | [notion-pricing](../sources.md#notion-pricing) |
| ...

Common mistakes

  • One giant research.md. It can't be linked, dated or marked outdated piece by piece.
  • Notes without an answer at the top. Nobody reads 2 pages to find the conclusion.
  • Copying the same source into five notes. When it changes, four copies are wrong. Link to sources.md instead.
  • Research that never becomes a decision. If it didn't change a decision, ask whether it was worth doing.

Credits

Written by @nvminhtu.

Tool (made by the maintainer at OneClickTool): Markdown Everywhere (free, Mac) opens a research/ folder as a table, a map of which note links to which, or Finder-style columns, with ★ favorites for the notes you use most.