The main reason that ProofBuddy was started was the inability to find a proofing solution that could be easily customized to match our needs. From the ground up ProofBuddy was written to be as easy as possible to match your existing site.
With the release of version 2.0 that customization took a big step up. Yes, the ability to easily customize the client side of your site is still done by editing theme files. And theme files are just basic HTML. But 2.0 added the ability to write plugins that can read from the ProofBuddy database and gives the ability to do more on the client side and add functionality on the admin side.
Of course, with that comes a greater need for documentation; something which we felt was severely lacking.
One note, this section of our site is very much a liquid set of pages and will be under almost continual update. As of right now there's just this single page. But it will expand.
Basic customization of your site can be done through editing of the theme files, a set of template files that are basic HTML. It is also possible to put PHP code into your theme files.
Plugins are PHP files that can affect how ProofBuddy operates. This is done through a series of API commands, similar to how WordPress plugins work.
You can start your trip with plugins with getting started with plugins.