Here you will find most classes and most of their methods (some might not be documented in case they're handled internally and should not be changed). All methods listed here are used somewhere at some point in the game code.
With that said, as long as you know what you're doing, you could create pretty much any mod. The game uses the LOVE2D framework, and is written in Lua. If you've worked with Lua before, you should feel right at home; if not, I invite you to take a look at the Lua 5.2 documentation, as well as the LuaJIT documentation, since the framework uses it.
You can download the game's source code here to look through how it all works, so that you can get a better understanding of how various systems work.