Hi Carin,
We have put that as a safety check for our developers installations, to avoid to install a package overwriting a git repository. Be reassured and keep calm, we didn't invent that check in our office. Many other extensions do similar (e.g. Kunena).
But I can see use-cases where a site is git-versioned and it makes full sense to install over a git checkout.
Fortunately, the error message is quite clear, and easy to grep, and would affect only knowledgeable developers.
I will improve that check to avoid checking for Joomla being git-versioned, but only CB itself when versioned through an aliased folder. Will do that hopefully for for next RC.
Thanks for the feedback, which allowed idea to improve this safety-check.
I've added a feature-tracker for it here:
forge.joomlapolis.com/issues/4599
Best Regards,