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IWE: a Markdown knowledge base you and your AI agent work on together

Memory serverOfficial IWE project

Created by IWE

Published in iwe-org/iwe. Publisher page

1,821 GitHub stars

What it is

Markdown knowledge graph — LSP for your editor, CLI + MCP memory for your AI agents
— the description by IWE

AutoGineer overview, from the brain’s own files

IWE provides a shared workspace for humans and AI agents to collaborate on project documentation, specs, and decision logs. By treating a folder of Markdown files as a structured knowledge graph, it allows agents to read, write, and organize information that persists across sessions. It functions as a memory server via the Model Context Protocol (MCP), enabling compatibility with various AI agents while remaining accessible to users through a native Mac app, CLI, or standard text editors like Neovim and VS Code.

How it works

Memory model: Not stated

AutoGineer overview, from the brain’s own files

IWE organizes notes as a collection of Markdown files within a project folder. It uses a CLI and an MCP server to expose these files to AI agents, allowing them to perform operations like searching, creating, and updating notes. The system supports features such as backlinks, link autocomplete, and graph visualization, ensuring that both the user and the AI agent interact with the same underlying document structure.

Folders
FolderRoleFiles
.githubagent-config4
docsdocs70
.githooksfolder1
cratesfolder381
npmfolder15

Requirements

Runtimes: Rust

Works with: Claude Code, Claude apps, OpenAI Codex, GitHub Copilot, Cursor, Gemini CLI, Google Antigravity, Kiro, OpenCode, Amp, Roo Code, Cline, JetBrains Junie, Devin (ex-Windsurf)

Set it up

  1. This brain runs code automatically: 1 script. Review .githooks/pre-commit before opening the folder in Claude Code. No step below turns a hook on for you.

    • .githooks/pre-commit: runs on git pre-commit
  2. Not scanned by AutoGineerAutoGineer could not scan everything it runs. https://www.npmjs.com/package/@iwe-org/mcp

  3. Created by IWE. Published in iwe-org/iwe. Licence: Apache License 2.0.

Usage

AutoGineer overview, from the brain’s own files

  • Connect an AI agent to your project notes using the MCP server.
  • Use the CLI to search, create, or reorganize notes from the terminal.
  • Write and browse notes in the native Mac app while an agent works alongside you.
  • Integrate note navigation and autocomplete into your preferred text editor.
  • Maintain a persistent record of project decisions and lessons learned that both you and your agent can access.
“Explore my IWE notes and summarize what's here.”
The agent reads the Markdown files in the designated folder and provides a summary of the project context, decisions, or documentation found.
“Save the decision we just made about the database schema.”
The agent creates or updates a Markdown note in the IWE folder containing the details of the decision for future reference.

Documentation by IWE

IWE: a Markdown knowledge base you and your AI agent work on together

English · 简体中文 · 한국어

Your notes are your agent’s memory. IWE is where you work on them together.

iwe.md · Download for Mac · Docs · Reddit

Image: Crates.io Image: License Image: Documentation

Too many AI conversations start from zero. You explain your project, your decisions, your reasoning — then find yourself explaining it all again next session. Your own notes live somewhere else, out of the agent's reach.

Or worse, the agent “remembers” something in its own internal memory, but you can't easily see what it saved or correct what it got wrong. And that memory doesn't travel with you to the other agents you work with.

IWE gives you and your AI agents one shared place to work, right inside your project: a folder of connected Markdown documents — specs, plans, decisions, and more. Keep your own ideas there, ask your agent to save what you learn together, and return to that context as your work grows. You can read, edit, and organize those documents yourself — and they stay yours.

<br/> <p align="center"> <a href="https://www.youtube.com/watch?v=D58bPkOvbxE"> <img src="https://iwe.md/images/video-thumbnail.jpg" alt="Watch the IWE intro video on YouTube" width="600"> </a> </p> <br/>

Choose how you work

There are four ways to work with IWE. Mix and match them to fit your day:

ToolHow you'll use it
iWe for MacWrite and browse in a native app, and connect your existing Claude/Codex agent.
Your own editorStay in Neovim, Helix, VS Code, or Zed, with note navigation, backlinks, and autocomplete.
CLISearch and manage your notes from the terminal or scripts.
Claude/CodexLet your agent read, write, and organize memory while you work through conversation.

All four work with the same Markdown documents. Draft a spec in your editor, develop it with Claude/Codex, browse it in the iWe app, or search it from the CLI. Use any combination you like; each tool also works independently.

Bring your own AI. Neither the IWE CLI nor the iWe Mac app includes an AI model. Both work on their own as tools for your notes. When you want AI help, use your existing Claude/Codex agent — in terminal or directly in the Mac app.

<a href="https://iwe.md/?ref=readme-shot"><img src="https://iwe.md/images/app/GH-screen-1.1.png" alt="iWe for Mac showing project plans and connected documents" width="820"></a>

<p> <a href="https://iwe.md/?ref=readme-shot"><img src="https://iwe.md/images/app/GH-screen-2.png" alt="Bug tracking with charts" width="32%"></a> <a href="https://iwe.md/?ref=readme-shot"><img src="https://iwe.md/images/app/GH-screen-3.png" alt="Technical documents with code" width="32%"></a> <a href="https://iwe.md/?ref=readme-shot"><img src="https://iwe.md/images/app/GH-screen-4.png" alt="Release documents" width="32%"></a> </p>

Plans · Charts · Technical documents · Releases — click a screenshot to see the iWe app in action on iwe.md.

Why IWE

  • Shared context. Your agent can use the same notes you write for yourself. Notes link to each other, and one note can belong to several topics, so you can follow an idea wherever it connects.

  • Memory you can read. Decisions and lessons saved by your agent are ordinary notes you can browse, correct, or delete.

  • Your notes stay yours. Everything is Markdown in a folder on your machine. Back it up, sync it, or keep it in git. You don't need an IWE cloud account to keep your notes; connecting an AI agent involves that agent's own setup and account requirements.

See it working on iwe.md →

iWe for Mac

If you'd like a dedicated space for your notes, use the native Mac app. Open a folder of notes and you get a fast, keyboard-friendly space to write and browse. You can also connect your existing Claude/Codex agent to work alongside you.

  • Works with your Claude/Codex agent. Connect the agent you already use, ask questions about your notes, and have it draft or reorganize them. Watch its edits appear in the document as it works.

  • Room to experiment. Each agent run is one undo step — try an idea, and roll it back if you don't like it.

  • Follow your ideas. Jump between related notes, search in a few keystrokes, and view Mermaid diagrams right in your documents. Your editor and other tools can keep working on the same files.

See iWe for Mac on iwe.md →

Open a notes folder and start with a note about something you're working on. Once Claude/Codex is connected, try asking it to summarize that note or help you develop an idea.

Your Own Editor

Keep writing in Neovim, Helix, VS Code, or Zed. IWE adds link autocomplete, backlinks, search, and safe renaming across your notes.

Follow the guide for your editor, open your notes folder, and try linking two notes with autocomplete. You can use IWE for your own writing without connecting an AI agent.

CLI

Prefer the terminal? Use IWE to search, create, and reorganize notes, or work it into your scripts. The CLI has no AI built in: these commands work on their own. Your existing Claude/Codex agent can use IWE's tools too.

Install with Homebrew, or choose another option from the installation guide:

brew install iwe-org/iwe/iwe

Then run these commands inside your notes folder:

iwe init
iwe find
iwe find --lexical "project decisions"

iwe find lists your notes; --lexical searches their content. Explore more in the CLI reference and workflow examples.

Claude/Codex

You can use IWE entirely through your agent. Ask Claude/Codex to save decisions, look up past work, and organize what you've learned. The agent works with your notes through IWE, and you can open those files yourself whenever you want.

IWE isn't tied to one AI. The same notes work with Claude Code, Claude Desktop, Codex, Gemini, Cursor, and any tool that supports the Model Context Protocol.

Give Claude/Codex a memory — for Claude Code, install the plugin, then run /iwe:init in any project you want remembered. For Codex, follow the agent connection steps below.

/plugin marketplace add iwe-org/skills
/plugin install iwe@iwe-org
/iwe:init

Then ask it to save a decision from your current work, and open the note it creates in your project.

Connect another agent — with Homebrew installed, install IWE:

brew install iwe-org/iwe/iwe

Run iwe init in your notes folder, then follow the agent connection guide to add the iwec MCP server with that folder as its working directory. For other installation options, see the installation guide.

Once connected, ask your agent: “Explore my IWE notes and summarize what's here.”

Or let the agent set itself up — paste this into any agent that can run commands:

Set up IWE for my notes: install it (brew install iwe-org/iwe/iwe,
npm install -g @iwe-org/iwe, or cargo install iwe iwes iwec), run `iwe init`
in my notes directory, then add the `iwec` MCP server with its working
directory set to that folder.
Docs: https://iwe.md/docs/agentic/

Learn More

Ready-made workspaces: dev-workspace — project memory for a coding agent · marketing-workspace — campaign memory for a marketing agent.

Get Involved

Trying IWE with your own notes? Tell us what felt useful and where you got stuck. Questions, rough edges, and examples of how you use it are all welcome in Discussions.

IWE is open source. You can also report a bug or help improve the documentation.

Community: Twitter/X · Reddit · Discussions

Building on IWE? The CLI and MCP server are the supported ways to integrate today. Tell us what you depend on so we know what not to break.

License

Apache License 2.0

docs/inclusion-links.md

Inclusion Links

When you place a markdown link on its own line, IWE treats it as a structural relationship—the current document becomes the "parent" of the linked document. This lets you organize knowledge into hierarchies without folders, and a single document can have multiple parents.

Why Hierarchy Matters

Hierarchy is one of the most natural ways humans organize knowledge. We instinctively break complex information into nested structures:

  • Living things are classified into kingdoms, classes, orders, and species

  • Places nest from continents to countries to cities to neighborhoods

  • Organizations have companies, departments, teams, and roles

  • Projects break down into epics, features, and tasks

This isn't arbitrary—hierarchical thinking is how we manage complexity. It lets us zoom out to see the big picture or zoom in to focus on specifics—and switch between these views effortlessly. It provides context: knowing something is "under" a topic tells you what it relates to.

What makes knowledge truly interesting is where hierarchies intersect. "Color Theory" belongs under both Art and Physics. "Game Theory" connects Mathematics and Economics. "Nutrition" bridges Chemistry and Health. These intersections are where insight lives.

Good knowledge systems should support this natural way of thinking.

The Problem

Traditional ways of organizing information don't match how knowledge actually works.

Directories: One Place Only

File systems force everything into a single hierarchy. A note about "Meditation" must live in either /health/ or /productivity/—it can't naturally exist in both.

This leads to:

  • Arbitrary placement decisions

  • Broken references when folders change

  • Duplicates or "misc" folders when nothing fits

But knowledge isn't a single tree—it's interconnected.

Tags: Flexible but Shallow

Tags allow multiple categories, but they lack structure:

  • No order or priority

  • No explanation of relationships

  • No hierarchy

  • No grouping within a category

A note tagged #health #productivity #mindfulness doesn't explain how these topics relate or which one is primary.

The Solution: Inclusion Links

An inclusion link is a markdown link placed on its own line:

# Photography

[Composition](composition.md)

[Lighting](lighting.md)

[Post-Processing](post-processing.md)

When a link appears on its own line, it defines structure: "Photography" becomes the parent of the linked documents.

This simple rule turns plain markdown into a structured, navigable system.

What This Enables

Multiple Contexts (Polyhierarchy)

A document can belong to multiple parents.

In health-practices.md:

# Health Practices

[Meditation](meditation.md)

In productivity-tools.md:

# Productivity Tools

[Meditation](meditation.md)

The same document appears in both contexts without duplication.

Structure with Meaning

Unlike tags, inclusion links allow ordering, grouping, and explanation:

# Psychology

## Cognitive

How we encode, store, and retrieve information

[Memory](memory.md)

Biases, heuristics, and rational choice

[Decision Making](decision-making.md)

## Behavioral

Cue, routine, reward loops

[Habit Formation](habit-formation.md)

You're not just grouping items—you're adding context.

Navigable Hierarchies

By linking documents together, you naturally create paths through your knowledge:

Knowledge Base > Psychology > Cognitive > Memory
Knowledge Base > Photography > Composition

This makes navigation and search more meaningful—you see not just what matches, but where it fits.

Context Flows Downward

When a document appears under a parent, it inherits meaning from that relationship. A "Memory" note under "Psychology" is understood differently than "Memory" under "Computer Architecture."

The parent page can also add explicit context:

# Cognitive Psychology

Foundation of learning and recall

[Memory](memory.md)

Selective focus and its limits

[Attention](attention.md)

These descriptions aren't part of the child documents—they live in the parent, explaining why each child belongs here.

Flexible Level of Detail

You can control how much information is visible. With --depth 1, you see only immediate children:

# Psychology
- Memory
- Decision Making
- Habit Formation

With --depth 3, the full subtree expands:

# Psychology
- Memory
  - Working Memory
    - Capacity Limits
    - Chunking Strategies
  - Long-term Memory
- Decision Making
- Habit Formation

Use Extract Actions to move details into separate documents, or Inline Notes to expand linked content in place.

Inclusion Links vs Inline Links

Inclusion Links (Structure)

Inclusion links define parent-child relationships and are used for:

  • Navigation

  • Hierarchical traversal (--depth)

  • Structured views

Inline Links (References)

Links inside text create conceptual connections:

# Habit Formation

The [Habit Loop](habit-loop.md) consists of cue, routine, and reward.
This process is driven by [Dopamine Pathways](dopamine.md) in the brain.

These links:

  • Create backlinks

  • Show relationships between ideas

  • Do not affect structure

Why This Distinction Matters

When retrieving content with depth:

iwe retrieve psychology --depth 2

The --depth flag controls how many levels of inclusion links to expand. See IWE Retrieve for details.

  • Inclusion links expand into full content

  • Inline links remain references only

This keeps structure clean while preserving connections between ideas.

Summary

Inclusion links give you structure without rigidity:

  • Documents can exist in multiple contexts

  • Ordering, grouping, and meaning are explicit

  • Navigation becomes contextual

For a deeper understanding of how IWE represents these relationships internally, see Data Model.

485 files · 414 not served here

Advantages

  • Shared context allows agents to access and build upon the same notes written by the user. evidence: README.md
  • Memory is stored as human-readable Markdown files that can be easily browsed, corrected, or deleted. evidence: README.md
  • Data remains under user control in local folders, avoiding dependency on proprietary cloud storage. evidence: README.md

Limitations

  • Requires manual setup of the MCP server or CLI tools to enable agent connectivity. evidence: README.md
  • The system does not include an AI model, requiring the user to bring their own agent. evidence: README.md

Security

Risk level: Low risk

This brain runs

Git hooks (1)

  • .githooks/pre-commit (pre-commit): runs on git pre-commit
  • Low risk: scripts-present (.githooks/pre-commit)

Attribution and licence

Created by
IWE
Publisher
IWE (Official IWE project)
Source
iwe-org/iwe · commit b733afe
Licence
Apache License 2.0 (files served here)
  • ATTRIBUTION.md (written by AutoGineer)
Synced

AutoGineer is not affiliated with or endorsed by IWE.

Install from source

414 of its files are not served here, so there is no ZIP. iwe-org/iwe at b733afe