Stupidly large pull request

Backlog of changes I've made to my branch of the patentprocessor. Mostly fixes to the disambiguations and database handling. Output should be relatively invariant, and I've done my best to maintain the original interfaces to the scripts. Refer to [this document](https://github.com/funginstitute/publications/raw/master/weeklyupdate/weeklyupdate.pdf) for the interface.