After running into a few bugs do to the use of symlinks I decided to write my own that was really just a wrapper around Git. After installing [gitsick][1] you could add one of your existing repos,
gitsick clone <name> <url>
The files will be deployed directly to your $HOME, without symlinks, and from then on `gitsick <name>` is just a wrapper around Git such that the $GIT_DIR is stored in one place and your $WORK_TREE is $HOME.