Refactor document parsing

[elinw]

Parsing of the documents has now been pulled out to a separate function, parse_one_document(). However there are still many levels of loops which are not the ideal approach for many situations in R. The code is also very complex.

What should happen is to simplify this code through a combination of creating some separate functions and by using lapply() and its relatives when appropriate.

[elinw]

This has been started but it is still a very long and complex function that is hard to read, so we should work on improving it.