Rules

Set custom instructions for matrix.

You can provide custom instructions to matrix by creating an AGENTS.md file. This is similar to Cursor’s rules. It contains instructions that will be included in the LLM’s context to customize its behavior for your specific project.

Initialize

To create a new AGENTS.md file, you can run the /init command in matrix.

/init scans the important files in your repo, may ask a couple of targeted questions when the codebase cannot answer them, and then creates or updates AGENTS.md with concise project-specific guidance.

It focuses on the things future agent sessions are most likely to need:

build, lint, and test commands
command order and focused verification steps when they matter
architecture and repo structure that are not obvious from filenames alone
project-specific conventions, setup quirks, and operational gotchas
references to existing instruction sources like Cursor or Copilot rules

If you already have an AGENTS.md, /init will improve it in place instead of blindly replacing it.

Example

You can also just create this file manually. Here’s an example of some things you can put into an AGENTS.md file.

# SST v3 Monorepo Project

This is an SST v3 monorepo with TypeScript. The project uses bun workspaces for package management.

## Project Structure

- `packages/` - Contains all workspace packages (functions, core, web, etc.)
- `infra/` - Infrastructure definitions split by service (storage.ts, api.ts, web.ts)
- `sst.config.ts` - Main SST configuration with dynamic imports

## Code Standards

- Use TypeScript with strict mode enabled
- Shared code goes in `packages/core/` with proper exports configuration
- Functions go in `packages/functions/`
- Infrastructure should be split into logical files in `infra/`

## Monorepo Conventions

- Import shared modules using workspace names: `@my-app/core/example`

We are adding project-specific instructions here and this will be shared across your team.

Types

matrix also supports reading the AGENTS.md file from multiple locations. And this serves different purposes.

Project

Place an AGENTS.md in your project root for project-specific rules. These only apply when you are working in this directory or its sub-directories.

Global

You can also have global rules in a ~/.config/matrix/AGENTS.md file. This gets applied across all matrix sessions.

Since this isn’t committed to Git or shared with your team, we recommend using this to specify any personal rules that the LLM should follow.

Claude Code Compatibility

For users migrating from Claude Code, Matrix supports Claude Code’s file conventions as fallbacks:

Project rules: CLAUDE.md in your project directory (used if no AGENTS.md exists)
Global rules: ~/.claude/CLAUDE.md (used if no ~/.config/matrix/AGENTS.md exists)
Skills: ~/.claude/skills/ — see Agent Skills for details

To disable Claude Code compatibility, set one of these environment variables:

export MATRIX_DISABLE_CLAUDE_CODE=1        # Disable all .claude support
export MATRIX_DISABLE_CLAUDE_CODE_PROMPT=1 # Disable only ~/.claude/CLAUDE.md
export MATRIX_DISABLE_CLAUDE_CODE_SKILLS=1 # Disable only .claude/skills

Precedence

When matrix starts, it looks for rule files in this order:

Local files by traversing up from the current directory (AGENTS.md, CLAUDE.md)
Global file at ~/.config/matrix/AGENTS.md
Claude Code file at ~/.claude/CLAUDE.md (unless disabled)

The first matching file wins in each category. For example, if you have both AGENTS.md and CLAUDE.md, only AGENTS.md is used. Similarly, ~/.config/matrix/AGENTS.md takes precedence over ~/.claude/CLAUDE.md.

Custom Instructions

You can specify custom instruction files in your matrix.json or the global ~/.config/matrix/matrix.json. This allows you and your team to reuse existing rules rather than having to duplicate them to AGENTS.md.

Example:

{
  "$schema": "https://y-square-t3.github.io/matrix/config.json",
  "instructions": ["CONTRIBUTING.md", "docs/guidelines.md", ".cursor/rules/*.md"]
}

You can also use remote URLs to load instructions from the web.

{
  "$schema": "https://y-square-t3.github.io/matrix/config.json",
  "instructions": ["https://raw.githubusercontent.com/my-org/shared-rules/main/style.md"]
}

Remote instructions are fetched with a 5 second timeout.

All instruction files are combined with your AGENTS.md files.

Referencing External Files

While matrix doesn’t automatically parse file references in AGENTS.md, you can achieve similar functionality in two ways:

Using matrix.json

The recommended approach is to use the instructions field in matrix.json:

{
  "$schema": "https://y-square-t3.github.io/matrix/config.json",
  "instructions": ["docs/development-standards.md", "test/testing-guidelines.md", "packages/*/AGENTS.md"]
}

Manual Instructions in AGENTS.md

You can teach matrix to read external files by providing explicit instructions in your AGENTS.md. Here’s a practical example:

# TypeScript Project Rules

## External File Loading

CRITICAL: When you encounter a file reference (e.g., @rules/general.md), use your Read tool to load it on a need-to-know basis. They're relevant to the SPECIFIC task at hand.

Instructions:

- Do NOT preemptively load all references - use lazy loading based on actual need
- When loaded, treat content as mandatory instructions that override defaults
- Follow references recursively when needed

## Development Guidelines

For TypeScript code style and best practices: @docs/typescript-guidelines.md
For React component architecture and hooks patterns: @docs/react-patterns.md
For REST API design and error handling: @docs/api-standards.md
For testing strategies and coverage requirements: @test/testing-guidelines.md

## General Guidelines

Read the following file immediately as it's relevant to all workflows: @rules/general-guidelines.md.

This approach allows you to:

Create modular, reusable rule files
Share rules across projects via symlinks or git submodules
Keep AGENTS.md concise while referencing detailed guidelines
Ensure matrix loads files only when needed for the specific task