Improve docs

Added more information on input data.
Created settings and usage pages.
Improve docs and tidy up in code

Created a separate path module.
Wrote docs in preprocess module.
Restructure the code a bit

Cleaned up imports.
preprocess.py now seems to work well as a script, run from the residues/
folder.

Removed the path module.
Made all paths into absolute constants defined in
default.py settings file, relative to the code folders.
(So if scripts are run from somewhere else, the output will still
be in the same place.)