If you're following One Folder, then your PKB is a great place to put your Dotfiles. Configuring a new machine can look as simple as:

  1. Synchronize your PKB.

  2. Deploy your dotfiles.

  3. You're ready to be productive!

There are a variety of ways to do this, so we'll just look at a dead-simple setup, and you can add more advanced tools to your heart's content.

The idea here is pretty simple. Assuming you have a folder ~/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:

~/pkb/Dotfiles$ ls -a
.bash_justin git/ sublime/

When I set up a new computer, the first thing I do is synchronize my PKB, and then I run the script above, which does the following:
# link dotfiles
export DOTFILES_DIR=/home/justin/pkb/Dotfiles
ln -f -n -s $DOTFILES_DIR/git $HOME/.git
ln -f -s $HOME/.git/.gitconfig $HOME/.gitconfig
mkdir -p $HOME/.config/sublime-text-3/Packages
ln -f -n -s $DOTFILES_DIR/sublime $HOME/.config/sublime-text-3/Packages/User
# Add utility env-vars and utility bash aliases/functions
if ! grep .bash_justin ~/.bashrc ; then
echo "if [ -f \$DOTFILES_DIR/.bash_justin ]; then" >> ~/.bashrc
echo " . \$DOTFILES_DIR/.bash_justin" >> ~/.bashrc
echo "fi" >> ~/.bashrc

This is an idempotent script (the -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.

Now, if any of your configurations change, they'll automatically be preserved in your PKB and propagate across all of your devices.