remove no-longer-needed diagnostics.departures and rename jedi diagnostic files as jdiag*

[guoqing-noaa]

As discussed in issue #240 , we no longer need to specify diagnostics.departures in YAML files and JEDI will always output ombg, oman, innov1 for two outer loop minimization

Also, the JEDI diagnostic file contains much more information than hofx. It is better to rename the JEDI diagnostic files as jdiag*, for example jdiag_adpupa.nc4 to be consistent with the reality (the word jdiag has been used for a long time in the python plotting scripts).

[SamuelDegelia-NOAA]

Good changes, thanks for doing this @guoqing-noaa. Also glad to see more verification that the ombg and oman diagnostics are working correctly now.

[guoqing-noaa]

@ShunLiu-NOAA @SamuelDegelia-NOAA @delippi

I have merged the latest develop branch, resolved the conflicts, and updated the newly-added fv3jedi yaml files accordingly.

[SamuelDegelia-NOAA]

On a sort of unrelated note, do we know if anyone is using the yamls contained in rrfs-test/testinput_expr? This directory contains our older yamls from before updating the ctests to use more obs types. These yamls are copied into the run directory created by setup_experiment.sh, but I do not know if anyone is actually using the yamls (or just running setup_experiment.sh solely to create the run directory). If not, it would be best to remove testinput_expr to avoid having to keep updating these yamls for developments like this PR.

[delippi]

On a sort of unrelated note, do we know if anyone is using the yamls contained in rrfs-test/testinput_expr? This directory contains our older yamls from before updating the ctests to use more obs types. These yamls are copied into the run directory created by setup_experiment.sh, but I do not know if anyone is actually using the yamls (or just running setup_experiment.sh solely to create the run directory). If not, it would be best to remove testinput_expr to avoid having to keep updating these yamls for developments like this PR.

That is a good point @SamuelDegelia-NOAA. We need to open an issue to start cleaning out and cleaning up older yamls.

[guoqing-noaa]

On a sort of unrelated note, do we know if anyone is using the yamls contained in rrfs-test/testinput_expr? This directory contains our older yamls from before updating the ctests to use more obs types. These yamls are copied into the run directory created by setup_experiment.sh, but I do not know if anyone is actually using the yamls (or just running setup_experiment.sh solely to create the run directory). If not, it would be best to remove testinput_expr to avoid having to keep updating these yamls for developments like this PR.

@SamuelDegelia-NOAA The rrfs-test/testinput_expr directory contains the single obs test which is a very useful experiment to test lots of functionalities. The directory was renamed to its current form in PR #184. The directory is used by link_mpasjedi_expr.sh and this wiki. We need to keep this single obs test but we can combine them into the testinput directory if appropriate.

[SamuelDegelia-NOAA]

@guoqing-noaa It is worth keeping that directory since it contains the single obs test as you mention. Maybe it would be be better to rename testinput_expr to something else since "testinput" implies use for the ctests. But that is not a priority right now and I am fine with keeping it the way it is.