setup_linux.sh: Fix bad refactoring

In a previous commit, I added some logic to run patch_{before,after}_file()
functions. However, in the process I ended up having the function
patch_after_devel.pp() duplicated.

This commit moves the logic that used to be in the original function into
the new one and gets rid of the duplicated (old) one.
setup_linux.sh: Print "patch" debugging lines from just one place

Simple refactoring to avoid having to remember to add echo statements in
every single function.
setup_linux.sh: Add patch to backup ~/bin/backup

Because this file is not too flexible and needs customisation.