So I have an install script that I use to stow to symlink my dotfiles and today I am noticing that in my dotfiles config directory I am seeing all the folders that actually in $HOME/.config directory. Maybe something has changed as I do not remember this happening before. Here is an excerpt from the shell script:
DOTFILES="$(pwd)"
/usr/bin/stow --stow --ignore ".DS_Store" --target="$HOME" --dir="$DOTFILES" files
On my Mac I do not see this problem, it seems to only be my linux machine. Thoughts?