Ignore .git directories when updating a repository

[kit-ty-kate]

In some cases (e.g. #6448), a .git directory can make its way into $OPAMROOT/repo/<repo-name>. Currently our internal implementation of diff doesn't do anything clever and will simply diff everything. However this can take a while depending on the hardware and take a significant amount of memory.

We should try to make sure that:

• every commands do ignore VCS directories
• the internal diff does ignore it if that repository was already present