Add support for nested classes/functions

[jbheard]

Currently we only look at the top level of the ast when getting class & function definitions. However, a class could contain a subclass, and functions could have helper functions defined inside of them.

For these reasons, finding class definitions should use a stack and collect all subclasses/inner functions.

subclass documentation should go in the same file as the parent class to keep them together. Inner functions may need a bit more thought, since functions don't have their own files.