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The templates for jobs and rc-files used by start_ctdas.sh are now in a separate templates folder. This allows each user to modify their templates for running if needed, and to add templates for their own purpose.

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Changes for South America runs: regions files in analysis directory are copied from the one specified in the system.rc file. Region pickle files are deleted in the analysis directory, to make sure the correct one is used. Option to use covariances for less than 23 transcom regions, but still use 23 for the analysis (does not work in tcfluxes.nc). Update in observation_operator.py to use restart file in first cycle also for more than one resolution (i.e. incl. zoom regions).