Claude/Code/Q/Why do I have multiple installations when using mise?

• Why does Claude Code warn about multiple installations when managed via mise?

  • Symptom

    • Claude Code shows this warning at startup:

      ⚠ Multiple installations found
      ├ npm-global at ~/.local/bin/claude
      └ native at ~/.local/bin/claude

    • Both entries point to the same symlink — so only one Claude Code is actually running.

  • Root cause

    • The warning is triggered by an orphaned mise install directory left behind when switching from the npm mise backend to the native mise backend.
    • Before (npm backend in ~/.config/mise/config.toml):
      toml

      "npm:@anthropic-ai/claude-code" = "latest"

    • After (native backend):
      toml

      claude-code = "latest"

    • Changing the tool entry installs the native version but does not uninstall the old npm version. The orphaned directory remains at:

      ~/.local/share/mise/installs/npm-anthropic-ai-claude-code/

    • Claude Code scans mise's installs directory and finds both, triggering the warning.

  • Fix

    • Option A — mise task (if your dotfiles include tool:missing:uninstall)

      • Preview orphans first:
        sh

        mise run tool:missing:ls

      • Remove them:
        sh

        mise run tool:missing:uninstall

      • This task finds all installed tools with no config source (source == null) and uninstalls them.

    • Option B — direct removal

      • mise uninstall npm:@anthropic-ai/claude-code will return "no versions found" because the tool is no longer in any config.
      • Remove the orphaned directory manually:
        sh

        rm -rf ~/.local/share/mise/installs/npm-anthropic-ai-claude-code

  • How to verify

    • Run claude --version — should start without the multiple-installations warning.