Feature refactor harvester into develop

This set of commits provides a refactoring of the controller/harvest.py and modules/harvest_tools.py.

The refactoring was implemented before the recent changes for release 0.8.9, so there was many conflicts. I solved them manually and I'm not sure the result is perfect.

A quick test showed that normal harvesting works, but I'm not sure if the output is the one to expect.

A quick test with pylint didn't show any serious problem. The only problem with the proposed code is that the class PublicationsTool has apparently too many member variables. 7 is apparently a maximum.