Migrate from a Previous Installation

June 26, 2026 · View on GitHub

If you set up the Simulink® Agentic Toolkit using an earlier version (the agent-driven "Set up the Simulink Agentic Toolkit" workflow), you should clean up the old installation before using setupAgenticToolkit. The old workflow installed files to different locations that the new setup script does not manage.

What to Remove

  1. Old toolkit data folder — delete ~/.simulink-agentic-toolkit/ (macOS/Linux) or %USERPROFILE%\.simulink-agentic-toolkit\ (Windows). This was the data directory used by the old agent-driven setup.

  2. MCP server binary — delete ~/.matlab/agentic-toolkits/bin/matlab-mcp-server (macOS/Linux) or %USERPROFILE%\.matlab\agentic-toolkits\bin\matlab-mcp-server.exe (Windows). Some earlier versions installed the binary as matlab-mcp-core-server or to ~/.local/bin/ or %USERPROFILE%\.local\bin\ — check both locations and names.

  3. MCP Add-On — delete ~/.local/share/MATLABMCPCoreServerToolbox.mltbx (macOS/Linux) or %USERPROFILE%\.local\share\MATLABMCPCoreServerToolbox.mltbx (Windows). If you already installed the toolbox in MATLAB, you can uninstall it via matlab.addons.uninstall or manually through the Add-On Manager — the new setup uninstalls any previous copy automatically before installing the latest .mltbx. (The toolbox was previously named "MATLAB MCP Core Server Toolbox" and is now "MATLAB MCP Server Toolbox".)

  4. Agent MCP configuration — remove the old matlab or simulink MCP server entry from your agent's config file. Your config should not reference any of the paths above. The location depends on your platform:

    • Claude Code: ~/.claude.json (%USERPROFILE%\.claude.json on Windows) — remove the entry from mcpServers
    • GitHub Copilot: VS Code user-profile mcp.json (remove the matlab or simulink server). File location: ~/Library/Application Support/Code/User/mcp.json (macOS), ~/.config/Code/User/mcp.json (Linux), %APPDATA%\Code\User\mcp.json (Windows)
    • OpenAI Codex: ~/.codex/config.toml (remove [mcp_servers.matlab] or [mcp_servers.simulink])
    • Gemini CLI: ~/.gemini/settings.json (remove the mcpServers entry)
    • Sourcegraph Amp: ~/.config/amp/settings.json (remove amp.mcpServers.matlab or amp.mcpServers.simulink and amp.skills.path)

  5. Skill registrations — remove old symlinks from ~/.agents/skills/ and ~/.claude/skills/ that point into your old toolkit clone. For Amp, also remove the amp.skills.path entry in ~/.config/amp/settings.json if it references your old toolkit path.

  6. Old toolkit clone — if you cloned the repository just for setup and no longer need it as a reference, you can delete it. The new setup script downloads toolkit files to ~/.matlab/agentic-toolkits/.

Tip: After removing the items above, you can ask your coding agent to search your home directory for any remaining references to the old toolkit (e.g., "matlab-mcp", "simulink-agentic-toolkit", or old paths like .local/bin) to catch anything we missed.

After cleaning up, follow the Automated Setup instructions in the README.