~/pkb/Dotfiles/ , what we want to do is to put your actual dotfiles in this folder, and then symlink them to where the applications are expecting to find them. Here's a very crude version of what this might look like:install.sh script above, which does the following:-f and -n flags are important), and so if you discover a new set of dotfiles to preserve, e.g. .my.cnf, move it into the Dotfiles folder, add the corresponding symlink command to the install script (ln -f -s $HOME/.my.cnf $DOTFILES_DIR/.my.cnf), and then re-run the install script.