Most of my dotfiles have a
source $HOME/.local/conf/vimrc
type line in them so I can store messy settings I don't want to share on the internet.
The dotfiles check out directly to my $HOME without symlinks or anything using the method outlined at this blogpost.
On a new machine, I must
git clone --bare <git-repo-url> $HOME/.cfg
alias config='/usr/bin/git --git-dir=$HOME/.cfg/ --work-tree=$HOME'
config config --local status.showUntrackedFiles no
config checkout