make documentation work again

The documentation is horribly outdated. Also, some parts are not working, like the automated documentation of the Python routines.

Topics to revisit:

• Documentation can now be built again, fixing #10 (closed)

• Installation Manual: Referencing ReadMe
• Fix Python module documentation (at least to some regard)
• Add documentation on dorie wrapper routine.

Issues and problems:

• Python modules are not found automatically. Error message by Sphinx:

  WARNING: autodoc: failed to import module 'dorie.utilities'; the following exception was raised:
  Traceback (most recent call last):
  File "/usr/local/lib/python3.6/site-packages/sphinx/ext/autodoc.py", line 551, in import_object
  __import__(self.modname)
  ModuleNotFoundError: No module named 'dorie'
  

  Python modules are found now because Sphinx is called in dune-env.