Cleaning up the whole $HOME/<.pkgname>/ situation for individual app settings

Hey guys! Is there a way for me to force apps to treat e.g. $HOME/.config/ as their default directory to look for settings? I want to clear up my home directory because its getting quite messy and I don't even have that many packages installed yet.

Also, any way that would be easy and efficient for use with git for the purpose of backing up my dotfiles.

Thanks!