An option is to use symbolic links. For example, say I have my git checkout out in ~/.dotfiles. I might have:

.vimrc -> ~/.dotfiles/vimrc .bashrc -> ~/.dotfiles/bashrc .bash_login _. ~/.dotfiles/bash_profile ... 

I would not, personally, check my home directory itself into the repo.

An option is to use symbolic links. For example, say I have my git checkout out in ~/.dotfiles. I might have:

.vimrc -> ~/.dotfiles/vimrc .bashrc -> ~/.dotfiles/bashrc .bash_login -> ~/.dotfiles/bash_profile ... 

I would not, personally, check my home directory itself into the repo.