You say, I know how to set the home directory however for version control reasons I want to be able to set emacs to read from a different directory (so that I can have a directory specific to emacs).

Your init file goes in your home directory, which you can put anywhere. Apparently you want to have a different directory for stuff that Emacs loads. That's not a problem. Put your init file in your home directory, and have that file add another directory to the value of variable load-path and then require whatever other Emacs libraries you want to use. Put those libraries in that other directory.

IOW, your init file need not contain anything beyond setup of the directory where you keep the Emacs libraries that you want to load.

You say:

I know how to set the home directory however for version control reasons I want to be able to set emacs to read from a different directory (so that I can have a directory specific to emacs).

Your init file goes in your home directory, which you can put anywhere. Apparently you want to have a different directory for stuff that Emacs loads. That's not a problem. Put your init file in your home directory, and have that file add another directory to the value of variable load-path and then require whatever other Emacs libraries you want to use. Put those libraries in that other directory.

IOW, your init file need not contain anything beyond setup of the directory where you keep the Emacs libraries that you want to load.