agents

One config to rule them all.
Practical standard layer for multi-LLM development.

Quick Start · Integrations · Commands · FAQ

The Problem

Every AI coding tool wants its own config format:

	Codex	Claude Code	Claude Desktop	Gemini	Cursor	Copilot VS Code	Copilot CLI	Antigravity	Windsurf	OpenCode	Junie
Config	`.codex/config.toml`	CLI commands	Global `claude_desktop_config.json`	`.gemini/settings.json`	`.cursor/mcp.json`	`.vscode/mcp.json`	`.mcp.json`	`.agents/mcp_config.json`	Global `mcp_config.json`	`opencode.json`	`.junie/mcp/mcp.json`
Instructions	`AGENTS.md`	`CLAUDE.md`	—	`AGENTS.md`	`.cursorrules`	—	`AGENTS.md`	`AGENTS.md`	`AGENTS.md`	`AGENTS.md`	`AGENTS.md`
Format	TOML	JSON (via CLI)	JSON	JSON	JSON	JSON	JSON	JSON	JSON	JSON	JSON

Result: Duplicated configs, team drift, painful onboarding.

agents gives you one source of truth in .agents/ and syncs MCP servers, skills, and instructions to every tool automatically. For Claude Code, it keeps AGENTS.md canonical and generates a minimal root CLAUDE.md wrapper (@AGENTS.md) when the Claude integration is enabled. For Claude Desktop, it syncs local stdio MCP servers into the global claude_desktop_config.json while preserving non-agents entries already in that file. Remote Claude MCP servers are managed by Claude custom connectors, not by this file.

Quick Start

# 1. Install
npm install -g @agents-dev/cli

# 2. Interactive setup — picks integrations, adds MCP servers, syncs everything
agents start

# 3. Re-sync whenever config changes
agents sync

That's it. Your .agents/agents.json is now the single source of truth.

Using agents in this repository

This repository uses @agents-dev/cli to keep MCP servers, skills, and instructions aligned across supported AI tools.

Quick commands

agents status
agents mcp add <url-or-name>
agents mcp test --runtime
agents sync
agents sync --check

One MCP setup for all tools

Add a server once in .agents/agents.json, then run agents sync to materialize it for enabled integrations.

References

MCP Protocol Docs: https://modelcontextprotocol.io
MCP servers catalog: https://mcpservers.org
Project examples: docs/EXAMPLES.md

Supported Integrations

Integration	MCP Servers	Skills	Instructions	How it syncs
Codex	✅	✅	✅	Writes `.codex/config.toml`
Claude Code	✅	✅	✅	Calls `claude mcp add/remove` CLI + manages root `CLAUDE.md` wrapper
Claude Desktop	✅	—	—	Writes local stdio servers to global `claude_desktop_config.json` and preserves non-agents MCP entries
Gemini CLI	✅	✅	✅	Writes `.gemini/settings.json`
Cursor	✅	✅	✅	Writes `.cursor/mcp.json` + CLI enable
Copilot VS Code	✅	—	—	Writes `.vscode/mcp.json`
Copilot CLI	✅	✅	✅	Writes project `.mcp.json`; Copilot CLI reads `AGENTS.md` and `.agents/skills` natively
Antigravity	✅	✅	✅	Writes workspace `.agents/mcp_config.json` and an Antigravity-compatible physical flat skills bridge at `.gemini/skills`
Windsurf	✅	✅	✅	Writes to global user profile `~/.codeium/windsurf/mcp_config.json` and preserves unmanaged entries + workspace `.windsurf/skills`
OpenCode	✅	✅	✅	Writes project `opencode.json` (`mcp` block)
Junie	✅	✅	✅	Writes `.junie/mcp/mcp.json` + skills bridge `.junie/skills`

Antigravity note: agents manages the workspace MCP config used by Antigravity CLI and materializes a physical flat copy at .gemini/skills when Antigravity is enabled. Nested source skills remain under .agents/skills; duplicate skill names are rejected for the flat bridge. Global Antigravity editor/CLI profile files are left user-owned.

Project Layout

your-project/
├── AGENTS.md                        ← Canonical instructions for all tools
├── CLAUDE.md                        ← Generated Claude wrapper (`@AGENTS.md`)
├── .agents/
│   ├── agents.json                  ← MCP servers & config (commit this)
│   ├── local.json                   ← Secrets & overrides (gitignored)
│   ├── mcp_config.json              ← Generated Antigravity CLI MCP (gitignored in source-only mode)
│   ├── skills/                      ← Reusable workflow definitions
│   │   └── my-skill/SKILL.md
│   └── generated/                   ← Auto-generated artifacts (gitignored)
│       ├── codex.config.toml
│       ├── claude-desktop.mcp.json
│       ├── copilot.cli.mcp.json
│       ├── gemini.settings.json
│       ├── antigravity.mcp_config.json
│       ├── cursor.mcp.json
│       ├── windsurf.mcp.json
│       ├── opencode.json
│       └── ...
│
│  ┌─── Generated by `agents sync` ───┐
├── .codex/config.toml                │  Materialized tool configs
├── .gemini/settings.json             │  (gitignored in source-only mode)
├── .cursor/mcp.json                  │
├── .vscode/mcp.json                  │
├── .mcp.json                         │  Copilot CLI
├── .agents/mcp_config.json           │  Antigravity CLI
├── opencode.json                     │
├── .claude/skills/ → .agents/skills  │  Claude workspace bridges
├── .cursor/skills/ → .agents/skills  │
├── .gemini/skills/                  │  Gemini symlink; physical flat copy for Antigravity
├── .windsurf/skills/ → .agents/skills│
└── .junie/skills/ → .agents/skills   │

Git strategy: By default only .agents/agents.json, .agents/skills/, and AGENTS.md are committed. Generated CLAUDE.md and tool-specific outputs are gitignored in source-only mode and regenerated with agents sync. Claude Desktop MCP is materialized into the user's global claude_desktop_config.json, not into the project tree.

Command Overview

Setup & Sync

Command	Description
`agents start`	Interactive setup wizard — integrations, MCP servers, skills, first sync
`agents start --inject-docs`	Also upsert an agents guide block in `README.md` (+ `CONTRIBUTING.md` if present)
`agents start --reinit`	Reinitialize existing `.agents/agents.json` with fresh wizard/default choices
`agents init`	Scaffold `.agents/` directory without guided setup
`agents sync`	Regenerate and materialize all tool configs
`agents sync --check`	Strict read-only drift check — exits `2` if config is out of sync
`agents watch`	Auto-sync on `.agents/` file changes (`--once` exits non-zero on sync failure)

Diagnostics

Command	Description
`agents status`	Show integrations, MCP servers, file states, and live probes
`agents status --fast`	Skip external CLI probes for quicker output
`agents doctor`	Validate configs, check for issues, suggest fixes
`agents doctor --fix`	Auto-fix what can be fixed
`agents update`	Check for newer CLI version on npm

MCP Server Management

Command	Description
`agents mcp add <name>`	Add a server interactively
`agents mcp add <url>`	Import a server from URL (mcpservers.org, GitHub, etc.)
`agents mcp import --file config.json`	Bulk import from JSON/JSONC file
`agents mcp list`	List all configured servers
`agents mcp remove <name>`	Remove a server (`--no-sync` skips auto-sync for add/import/remove)
`agents mcp test`	Validate server definitions
`agents mcp test --runtime`	Live connectivity check via tool CLIs

Integrations

Command	Description
`agents connect --llm cursor,claude`	Add integrations to the currently enabled set
`agents disconnect --llm codex`	Disable integrations
`agents reset`	Remove generated files, keep `.agents/`
`agents reset --hard`	Full cleanup — removes all agents-managed setup

How It Works

┌──────────────────────────────────────────────────────────────┐
│                      agents sync                             │
├──────────────────────────────────────────────────────────────┤
│                                                              │
│   .agents/agents.json ─── merge ──→ Resolved    ──→ Codex   │
│         (shared)           ↑        Registry          TOML   │
│                            │           │                     │
│   .agents/local.json ──────┘           ├────────→ Claude     │
│      (secrets)                         │          CLI + root │
│                                        │          CLAUDE.md  │
│                                        ├────────→ Claude     │
│                                        │          Desktop    │
│                                        │          Global JSON│
│                                        ├────────→ Gemini     │
│   ${ENV_VARS} ─── resolve ─────────────┤          JSON       │
│   ${PROJECT_ROOT}                      ├────────→ Cursor     │
│                                        │          JSON + CLI │
│                                        ├────────→ Copilot    │
│                                        │          VS Code + CLI │
│                                        ├────────→ Antigravity│
│                                        │          .agents/   │
│                                        │          mcp_config │
│                                        ├────────→ Windsurf   │
│                                        │          Global MCP │
│                                        ├────────→ OpenCode   │
│                                        │          opencode.json │
│                                        └────────→ Junie      │
│                                                   .junie/mcp/ │
│                                                              │
│   .agents/skills/ ── symlink ──→ .claude/skills              │
│                                  .cursor/skills              │
│                                  .gemini/skills              │  (flat copy for Antigravity)
│                                  .junie/skills               │
│                                  .windsurf/skills            │
└──────────────────────────────────────────────────────────────┘

Load — reads .agents/agents.json + merges secrets from .agents/local.json
Resolve — expands ${PROJECT_ROOT}, ${ENV_VAR} placeholders, filters by enabled and requiredEnv
Route — sends each server to its target integrations (or all, if no targets specified)
Generate — renders tool-specific config formats (TOML for Codex, JSON for others)
Materialize — writes configs atomically (project-local and global targets), calls CLIs for Claude Code/Cursor, writes global configs with scoped merge/cleanup, and manages Claude Code's root CLAUDE.md wrapper
Bridge skills — creates symlinks from tool directories to .agents/skills/ where needed; Antigravity receives a physical flat copy at .gemini/skills so nested skills are discoverable

MCP Server Examples

Add from mcpservers.org

agents mcp add https://mcpservers.org/servers/context7-mcp

Add a stdio server

agents mcp add my-server \
  --command npx \
  --arg @my-org/mcp-server \
  --arg /path/to/project

Add an HTTP server with secrets

agents mcp add company-api \
  --url "https://api.company.com/mcp" \
  --secret-header "Authorization=Bearer YOUR_API_TOKEN"

Secrets are automatically detected and split: placeholders go to agents.json (committed), real values to local.json (gitignored).

Target specific tools

# Only for Claude Code
agents mcp add claude-only-server --url "https://..." --target claude

# Only for Claude Desktop
agents mcp add desktop-only-server --command npx --arg @my-org/server --target claude_desktop

# Only for Cursor and Copilot in VS Code
agents mcp add ide-server --command ide-mcp --target cursor --target copilot_vscode

# Only for Copilot CLI
agents mcp add copilot-cli-server --command npx --arg @my-org/server --target copilot_cli

Security

	What	Where
🔓	Server definitions, team config	`.agents/agents.json` — committed
🔒	API keys, tokens, secrets	`.agents/local.json` — gitignored

How secrets work:

When you add a server, agents detects secret-like values (API keys, tokens, JWTs)
Secrets are moved to local.json and replaced with ${PLACEHOLDER} in agents.json
agents doctor warns if it finds literal secrets in committed config
All env keys and header names are validated to prevent injection

Team Workflow

Lead sets up the project:

agents start
agents mcp add https://mcpservers.org/servers/context7-mcp
agents mcp add company-api --url "https://api.company.com/mcp" \
  --secret-header "Authorization=Bearer YOUR_API_TOKEN"
git add .agents/agents.json .agents/skills/ AGENTS.md && git commit -m "Add agents config"

New member onboards:

git clone <repo> && cd <repo>
agents start        # Preserves team config and syncs local tool files
# Add your local secrets in .agents/local.json if required by project MCP servers

One command. Same MCP servers, same skills, same instructions. No drift.

FAQ

Does this replace AGENTS.md?

No. It extends it. AGENTS.md is human-readable guidance for LLMs; agents handles machine-readable config (MCP servers, skills) and keeps everything in sync. When Claude integration is enabled, agents also generates a minimal root CLAUDE.md wrapper that references AGENTS.md.

Can I use this with only one tool?

Yes. You still get cleaner config management, safer git defaults, secret splitting, and easy MCP server management — even for a single tool.

Where should secrets live?

In .agents/local.json (gitignored by default). The CLI automatically splits secrets from public config when you add MCP servers.

What happens during agents sync?

It reads your .agents/ config, merges secrets, resolves placeholders, generates tool-specific files, and writes them atomically. For Claude Code and Cursor it also calls their CLIs to register servers. Claude Desktop stdio servers are synced by updating its global claude_desktop_config.json without touching non-agents MCP entries. The whole process is idempotent and safe to run repeatedly. For Claude Code it also maintains a root CLAUDE.md wrapper without duplicating the contents of AGENTS.md.

How do I keep configs in sync automatically?

Run agents watch — it polls .agents/ files and auto-syncs on changes. Or run agents sync manually after editing config.

Can I target an MCP server to specific tools only?

Yes. Add "targets": ["claude", "claude_desktop", "cursor"] to a server definition in agents.json, or use the --target flag with agents mcp add. Servers without targets stay universal and are included for integrations as they are enabled.

Any Claude Desktop caveats?

Yes. Claude Desktop local JSON sync is stdio-only. HTTP/SSE MCP servers should be added in Claude as custom connectors or wrapped by a stdio bridge. Prefer absolute paths in command/args, and avoid relying on cwd for Desktop-targeted servers.

Docs

	Resource
📖	Usage Examples — solo dev, teams, monorepos, scripting
🏗️	System Architecture — sync internals, file formats, security model
📋	Changelog — version history and migration notes

Name		Name	Last commit message	Last commit date
Latest commit History 69 Commits
.github/workflows		.github/workflows
bin		bin
docs		docs
fixtures/basic/.agents/mcp		fixtures/basic/.agents/mcp
src		src
templates/agents		templates/agents
tests		tests
.gitignore		.gitignore
AGENTS.md		AGENTS.md
CHANGELOG.md		CHANGELOG.md
CONTRIBUTING.md		CONTRIBUTING.md
LICENSE		LICENSE
NOTICE		NOTICE
README.md		README.md
eslint.config.js		eslint.config.js
package-lock.json		package-lock.json
package.json		package.json
tsconfig.json		tsconfig.json
vitest.config.ts		vitest.config.ts

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agents

The Problem

Quick Start

Using agents in this repository

Quick commands

One MCP setup for all tools

References

Supported Integrations

Project Layout

Command Overview

Setup & Sync

Diagnostics

MCP Server Management

Integrations

How It Works

MCP Server Examples

Add from mcpservers.org

Add a stdio server

Add an HTTP server with secrets

Target specific tools

Security

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FAQ

Docs

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agents

The Problem

Quick Start

Using agents in this repository

Quick commands

One MCP setup for all tools

References

Supported Integrations

Project Layout

Command Overview

Setup & Sync

Diagnostics

MCP Server Management

Integrations

How It Works

MCP Server Examples

Add from mcpservers.org

Add a stdio server

Add an HTTP server with secrets

Target specific tools

Security

Team Workflow

FAQ

Docs

Community

About

Resources

Contributing

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