mcpmatrix

Define MCP servers once and generate client configs from a single canonical configuration.

This version supports:

• Codex CLI
• Claude Code CLI
• Gemini CLI
• config import from existing client files
• explicit config validation
• doctor diagnostics
• interactive TUI
• versioned backups with retention

Install

Global install from npm:

npm install -g @mokivan/mcpmatrix

Available binaries:

• mcpmatrix
• mmx

Minimum Node.js version:

• 20

Package contract:

• supported public interface: mcpmatrix, mmx, and documented CLI flags
• unsupported: programmatic imports from package internals or dist/*

Quick Start

1. Create the default config:

mcpmatrix init

2. Edit ~/.mcpmatrix/config.yml with your MCP servers and scopes:

servers:
  github:
    transport: stdio
    command: npx
    args: ["-y", "@modelcontextprotocol/server-github"]
    env:
      GITHUB_TOKEN: ${env:GITHUB_TOKEN}

  medusa:
    transport: remote
    protocol: http
    url: https://docs.medusajs.com/mcp

scopes:
  global:
    enable:
      - github

  tags:
    ecommerce:
      enable:
        - medusa

  repos:
    "/Users/ivan/dev/store":
      tags: ["ecommerce"]
      enable: []

3. Validate, preview, and apply:

mcpmatrix validate
mcpmatrix doctor
mcpmatrix schema
mcpmatrix plan
mcpmatrix apply
mcpmatrix backups list
mcpmatrix rollback --client codex

Optional interactive workflow:

mcpmatrix tui

Import Existing Configs

Import MCP servers from the supported client files into ~/.mcpmatrix/config.yml:

mcpmatrix import

Detected sources:

• Codex: ~/.codex/config.toml
• Claude Code: ~/.claude.json
• Gemini: ~/.gemini/settings.json

Import rules:

• import fails if ~/.mcpmatrix/config.yml already exists
• imported servers become servers
• imported server names are enabled in scopes.global.enable
• Codex imports command as transport: stdio and url as transport: remote
• Claude imports stdio, remote HTTP, and remote SSE entries
• Gemini imports stdio and remote HTTP entries using httpUrl
• conflicting canonical definitions for the same server name cause import to fail

Commands

mcpmatrix init

Creates the initial config file at ~/.mcpmatrix/config.yml.

mcpmatrix import

Imports existing MCP client configs into the canonical YAML file.

mcpmatrix schema

Prints the packaged JSON Schema path and file:// URI for ~/.mcpmatrix/config.yml.

This is useful when your editor does not automatically pick up the schema header or when you want to configure schema association manually.

mcpmatrix validate

Validates:

• YAML syntax
• env reference syntax
• scope references to defined servers
• stdio commands available in PATH or by executable path
• remote MCP URLs and auth structure

mcpmatrix doctor [--repo <path>]

Runs a fuller diagnostic pass:

• MCP commands resolve locally
• remote MCP URLs are structurally valid
• referenced environment variables are defined
• configured repo paths are accessible
• the detected repo can be resolved and inspected
• stack files suggest tags without modifying config automatically
• compatibility is reported for Codex, Claude, and Gemini

Suggested stack tags:

• package.json -> node
• pom.xml -> java
• .csproj -> dotnet

mcpmatrix plan [--repo <path>]

Resolves the active server set for the current repository and shows:

• detected repo path
• active tags
• active servers
• global vs repo-scoped server partitions
• transport and per-client compatibility
• files that would be updated
• estimated diff size

Repository detection order:

1. --repo <path>
2. search upward for .git
3. current working directory

mcpmatrix apply [--repo <path>]

Resolves the same server set and writes client configs.

Client outputs:

• Codex global: ~/.codex/config.toml
• Codex repo-scoped: <repo>/.codex/config.toml
• Claude Code global: ~/.claude.json
• Claude Code repo-scoped: <repo>/.mcp.json
• Gemini global: ~/.gemini/settings.json
• Gemini repo-scoped: <repo>/.gemini/settings.json

Write behavior:

• global scope writes only servers resolved from scopes.global.enable
• repo scope writes only servers resolved from the matched repo's tags and enable, excluding names already active globally
• Codex updates only a managed mcpmatrix block inside each config.toml, using named TOML tables under mcp_servers
• Claude updates only the mcpServers section inside .claude.json and .mcp.json
• Gemini updates only the mcpServers section inside settings.json
• stdio and supported remote transports are rendered per client format
• apply fails before writing if any active server cannot be represented by Codex, Claude, or Gemini
• existing content outside those managed areas is preserved
• existing files are backed up before overwrite
• apply is transactional across all selected targets: either all global and repo-scoped files are updated or the previous state is restored

Backup files:

• stored in ~/.mcpmatrix/backups/
• filenames are versioned by client and scope, for example codex-global-YYYY-MM-DD-HH-MM.toml
• each backup stores metadata for the exact live target path
• latest 3 backups are retained per exact target file

Rollback behavior:

• if any target write fails, mcpmatrix apply exits non-zero
• mcpmatrix restores all selected client files to their pre-apply state
• a failed apply should never leave a mixed client state behind

Compatibility note:

• mcpmatrix tolerates UTF-8 BOM-prefixed YAML, TOML, and JSON config files when loading canonical config or importing/updating client configs

mcpmatrix backups list [--client <codex|claude|gemini>] [--repo <path>]

Lists versioned backups stored in ~/.mcpmatrix/backups/.

Output includes:

• client group
• scope
• backup file name
• inferred timestamp
• live target path
• full backup path

If no backups exist, the command prints an empty-state message and exits successfully.

mcpmatrix rollback [--client <codex|claude|gemini>] [--backup <name-or-path>] [--repo <path>]

Restores versioned backups into the live client config files.

Behavior:

• without flags, restores the latest global backup for Codex, Claude, and Gemini
• with --client, restores only the latest backup for that client in the selected scope
• with --repo, restores the latest repo-scoped backups for that repository
• with --backup, restores a specific backup file by base name from ~/.mcpmatrix/backups/ or by absolute path
• when --backup and --client are both provided, the backup must belong to that client
• when --backup and --repo are both provided, the backup must belong to that repo and be repo-scoped

Failure rules:

• global rollback is strict: if any required client backup is missing, nothing is restored
• repo rollback is strict: if any required repo-scoped client backup is missing, nothing is restored
• single-client rollback fails when no backup exists for that client
• an invalid or mismatched backup argument exits non-zero
• rollback does not create a new backup entry for the restored files

mcpmatrix tui [--repo <path>]

Opens an interactive terminal UI for the detected repo. The TUI can:

• visualize active MCP servers
• inspect repo status and doctor output
• open ~/.mcpmatrix/config.yml in $EDITOR
• enable or disable repo-local MCPs in scopes.repos.<repo>.enable

Keyboard shortcuts:

• ↑ / ↓ move the selection
• Enter or Space toggles the selected repo-local MCP
• / filters the server list by name
• d opens the structured doctor report
• e opens the canonical config in $EDITOR and reloads on exit
• r refreshes repo detection and resolved server state
• q or Esc exits the current view or closes the TUI

Current limitation from the canonical schema:

• inherited servers from global or tags are visible in the TUI but cannot be disabled there, because scope merging is additive only

Configuration

Global config location:

~/.mcpmatrix/config.yml

Autocomplete support:

• mcpmatrix init writes a yaml-language-server schema header into the generated config file
• mcpmatrix schema prints the packaged schema path and URI for manual editor setup
• packaged schema file: schemas/mcpmatrix-config.schema.json

Public schema:

servers:
  <server-name>:
    transport: stdio
    command: string
    args: string[]
    env:
      <ENV_NAME>: string

  <server-name>:
    transport: remote
    protocol: auto | http | sse
    url: string
    headers:
      <HEADER_NAME>: string
    auth:
      type: none | bearer | oauth

scopes:
  global:
    enable: string[]

  tags:
    <tag-name>:
      enable: string[]

  repos:
    <absolute-path>:
      tags: string[]
      enable: string[]

Rules:

• server names must be unique
• stdio servers use command, args, and env
• remote servers use protocol, url, headers, and auth
• scopes are additive
• resolution order is global -> tags -> repo
• duplicate server names are removed while preserving first appearance
• env references must use ${env:VAR_NAME} when interpolation syntax is used
• interpolation may appear in any string field
• repo matching uses normalized absolute paths across Windows, Linux, and macOS

Development

Install dependencies:

npm install

Build:

npm run build

Run checks:

npm run lint
npm run typecheck
npm test
npm run test:docs
npm run test:release
npm run test:smoke
npm run pack:check

Release

The public scoped package @mokivan/mcpmatrix is published from GitHub Actions, either after merges to master or from a manual run of the Release workflow. The workflow is guarded by version and registry checks. Release workflow details live in docs/releasing.md.

Compatibility

• supported runtime: Node.js 20+
• supported clients: Codex CLI, Claude Code CLI, Gemini CLI
• semver applies to the documented CLI only
• importing package internals is outside the support contract and may break without notice

Troubleshooting

• validate failing on a command usually means the executable is not available in local PATH or is not an executable file path
• validate failing on a remote server usually means the url, protocol, or auth block is malformed
• doctor fails when a referenced env var is missing or a configured repo path no longer exists
• doctor also reports active servers that cannot be applied to Codex, Claude, or Gemini
• import fails when ~/.mcpmatrix/config.yml already exists or when the same server name has conflicting canonical definitions across clients
• apply failures should restore the previous client state; inspect the reported target path and backup files if the error persists
• if a client config contains a UTF-8 BOM on Windows, mcpmatrix should still parse it correctly; if it does not, treat that as a bug
• use mcpmatrix backups list to inspect available restore points before running mcpmatrix rollback

Documentation Guard

When a roadmap phase is implemented or the supported client matrix changes, update this README in the same change.

Minimum README updates for that case:

• supported clients
• user-facing commands or setup changes
• release and install instructions if package metadata changes
• keep docs/specs/spec-cli.md aligned with the public CLI surface
• keep npm run test:docs passing
• when package.json.version changes, add the matching CHANGELOG.md section and keep npm run test:release passing

Source of Truth

Implementation follows this order:

1. roadmap documents in docs/
2. canonical specifications in docs/specs/
3. code in src/

Canonical specs are the files prefixed with spec-.