I’m developing WordPress themes using multiple repos (git and svn) and found that using symlinks to be the simplest way to manage it.
Here is my memo how I did what and how to check/re-do symlinks.
To create symlinks from from wp-config/themes
$ ln -s ../../../path/to/my/repo/mytheme mytheme
To check what is linked
$ ls -l
lrwxr-xr-x 1 daigo localhost Users 44 Oct 15 16:07 mytheme -> ../../../path/to/my/repo/mytheme