9-use-mo-nc-files-rather-than-name

See merge request gilligan-epid/wheat-rusts/ews-coordinator!4

reading NAME.nc files rather than NAME.txt files (#19)

simplifying the import required to a single statement by putting generate_all_jobs within the job_runner file

reverting code to run in the standard way (running with overwrite as false, etc). Removing redundant code from EnvSuitPipeline.py

There are now three different functions used to download surveys from
three different server types: ODK, kobotoolbox and WRSIS. All three
functions can use past downloads if there is no connection currently, but
they have different hard-coded settings. This fix makes them
consistent and configurable with the config parameter
['Survey']['AcceptableDowntimeDays'].

import and shell script changes to use new plotting and met_extractor (now met_processing) package structures

An input argument config['Epidemiology']['Deposition']['VariableNames']
is expected as a list, so that a different variable name can be loaded
 for each listed disease. The list parsing has a bug, and is picked up
only now because the config file now provides a list of variable names.

The preparation of deposition data is quite long winded so it is moved
a standalone function.