It doesn't override git diff at all, sem is its own standalone CLI. git diff continues to work exactly as before. You do sem setup only when you want to change your default git diff behavior, other wise after installing sem you can use it straight away using sem commands.
Ah okay thankyou! Is the MCP server manually configured, or is there documentation on the suggested way to tell an agent to use sem? My guess was that setup was how to do that.
If I were you I'd remove setup/unsetup commands and replace with a note that if you want to use it for git diff here's what to put in your config, or suggest aliasing as git sdiff or whatever.