Sorry, I don't understand the question. I also set GOPATH=$HOME, and all my source code (not only Go) lives in $HOME/src, and I do use git for both Go and non-

Sorry, I don't understand the question. I also set GOPATH=$HOME, and all my source code (not only Go) lives in $HOME/src, and I do use git for both Go and non-Go projects (so they have a .git directory in $HOME/src/what/ever/.git), and there's no problem. Why would there be one?