I have some git repositories that were created with the --separate-git-dir flag (see https://www.kernel.org/pub/software/scm/git/docs/git-init.html) These are not recognized as valid by SourceTree. I have been using TortoiseGit to work with them but would like to switch.

When made this way, the main working folder contains a .git file that points to the real .git directory. For example, this setup could be created as:

cd \
git init --separate-git-dir foo-git foo

Then \foo would contain my files and \foo-git would contain the git files. This allows other tools that walk the directory tree from \foo to easily skip the git specific files.