changing the landpoint files to use a new column "included", to filter for countries, rather than using the lat lon values to decide what to filter

Adding the functionality to group surveys and run source gen on each groups. Grouping is only run if it is defined in the config (otherwise it use all available surveys), and it is based on the 'Origin' column of the surveys. All unique 'Origin' will create its own group alongside the ones defined in the config. Groups can be ignored by defining 'GroupsToIgnore' in the config (this has no effect on 'Origin' types).

The model outputs were clipped to a smaller extent but the host map was
not. Because the epi model run grid is set by the host map, there is a big
time-saving by moving to a clipped host map. The epi partial integration
test passed on my machine, so now to check it passes in gitlab CI
pipeline.

Handle missing redundant columns and continue to set a common column
order at the same time.

This is useful for the new ODK form until the wheat rust toolbox is setup.

adding a page to the documentation for the setup of the IaaS server (not linked from within the docs)

changing the example landpoint files to be sorted lon,lat as the sort order gets enforced by the landpoint filter functions in postprocessing now.

adding a list of wildcards used when searching for nc file - useful if reporting that none are found

changing the optional SPATIAL_POINTS_FILE config parameter to SPATIAL_POINTS_FILE_TEMPLATE and allowing ${} value subsiitution in the paremeter value
removing some points from the ethiopia post processing landpoint file, to allow checking that the filtering for post-processing is working

It is possible to specify which spatial points file to use in the main config json. The default file will be used if not specified. This will allow us to perfrom historic runs with the old grid and specify manually.
The country-level points filtering used by the postprocessing steps (beofre plotting) now round down the acuracy when filtering points. This allows the country filtering to work with both the new and the old grid, as the differece is lost in the rounding

allowing the full iontegration pipeline for Surveys to use the standard deployment config, rather than trying to exclude WRSIS

making $PACKAGES_DIR a local variable and adding warnings about shared variable names at the pipeline level