Quick bugfix to create super yamls before expr directories

[SamuelDegelia-NOAA]

Bug Fix Description

This PR resolves error messages when building RDASApp that occur due to the expr/ directories being set up before the super yamls are created. This was preventing the super yamls from being copied into the expr/mpas_2024052700 and expr/fv3_2024052700 directories.

Description of Current Behavior:

Running ./build.sh produces errors like:

Linking in test data for MPAS-JEDI case
expdir is at: /scratch2/NCEPDEV/fv3-cam/Donald.E.Lippi/RRFSv2/PRs/RDASApp.20250321/expr/mpas_2024052700
cp: cannot stat '/scratch2/NCEPDEV/fv3-cam/Donald.E.Lippi/RRFSv2/PRs/RDASApp.20250321/rrfs-test/testinput/rrfs_mpasjedi_2024052700_Ens3Dvar.yaml': No such file or directory
cp: cannot stat '/scratch2/NCEPDEV/fv3-cam/Donald.E.Lippi/RRFSv2/PRs/RDASApp.20250321/rrfs-test/testinput/rrfs_mpasjedi_2024052700_getkf_observer.yaml': No such file or directory
cp: cannot stat '/scratch2/NCEPDEV/fv3-cam/Donald.E.Lippi/RRFSv2/PRs/RDASApp.20250321/rrfs-test/testinput/rrfs_mpasjedi_2024052700_getkf_solver.yaml': No such file or directory
Linking in test data for FV3-JEDI case
expdir is at: /scratch2/NCEPDEV/fv3-cam/Donald.E.Lippi/RRFSv2/PRs/RDASApp.20250321/expr/fv3_2024052700
cp: cannot stat '/scratch2/NCEPDEV/fv3-cam/Donald.E.Lippi/RRFSv2/PRs/RDASApp.20250321/rrfs-test/testinput/rrfs_fv3jedi_2024052700_Ens3Dvar.yaml': No such file or directory
cp: cannot stat '/scratch2/NCEPDEV/fv3-cam/Donald.E.Lippi/RRFSv2/PRs/RDASApp.20250321/rrfs-test/testinput/rrfs_fv3jedi_2024052700_getkf_observer.yaml': No such file or directory
cp: cannot stat '/scratch2/NCEPDEV/fv3-cam/Donald.E.Lippi/RRFSv2/PRs/RDASApp.20250321/rrfs-test/testinput/rrfs_fv3jedi_2024052700_getkf_solver.yaml': No such file or directory

Description of Fixed Behavior:

Now gen_yaml_ctest.sh is run before link_mpasjedi_expr.sh and link_fv3jedi_expr.sh to prevent this error and correctly copy the super yamls into the expr directories.

Issue(s) addressed

None

Dependencies (if applicable)

None

Checklist

• I have performed a self-review of my own code.
• I have run rrfs tests before creating the PR (if applicable).

[SamuelDegelia-NOAA]

Added one more change to this PR to move the utilities for updating ctest inputs/refs into RDASApp/ush. That will make it easier to update and run the ctests all from one directory. I don't normally like using one PR for multiple goals like this but it made sense to throw it in here since the changes are so minor.

[ShunLiu-NOAA]

@hu5970 @guoqing-noaa Please review this PR if you have a chance.

[rrfsbot]

PASSED on jet

started build_and_test on jet at UTC time: Mon Mar 24 03:51:30 UTC 2025
finished at UTC time: Mon Mar 24 04:34:45 UTC 2025

Test project /lfs5/BMC/wrfruc/rrfsbot/PRs_RDASApp/337/build/rrfs-test
    Start 2: rrfs_fv3jedi_2024052700_getkf_observer
    Start 5: rrfs_mpasjedi_2024052700_getkf_observer
    Start 1: rrfs_fv3jedi_2024052700_Ens3Dvar
    Start 4: rrfs_mpasjedi_2024052700_Ens3Dvar
    Start 7: rrfs_mpasjedi_2024052700_bumploc
    Start 8: rrfs_bufr2ioda_msonet
1/8 Test #8: rrfs_bufr2ioda_msonet .....................   Passed   34.26 sec
2/8 Test #2: rrfs_fv3jedi_2024052700_getkf_observer ....   Passed  174.25 sec
    Start 3: rrfs_fv3jedi_2024052700_getkf_solver
3/8 Test #5: rrfs_mpasjedi_2024052700_getkf_observer ...   Passed  188.33 sec
    Start 6: rrfs_mpasjedi_2024052700_getkf_solver
4/8 Test #7: rrfs_mpasjedi_2024052700_bumploc ..........   Passed  393.71 sec
5/8 Test #4: rrfs_mpasjedi_2024052700_Ens3Dvar .........   Passed  394.49 sec
6/8 Test #1: rrfs_fv3jedi_2024052700_Ens3Dvar ..........   Passed  414.76 sec
7/8 Test #3: rrfs_fv3jedi_2024052700_getkf_solver ......   Passed  327.43 sec
8/8 Test #6: rrfs_mpasjedi_2024052700_getkf_solver .....   Passed  420.00 sec

100% tests passed, 0 tests failed out of 8

Label Time Summary:
mpi            = 2347.23 sec*proc (8 tests)
rdas-bundle    = 2347.23 sec*proc (8 tests)
script         = 2347.23 sec*proc (8 tests)

Total Test time (real) = 608.40 sec

workdir: /lfs5/BMC/wrfruc/rrfsbot/PRs_RDASApp/337

[rrfsbot]

PASSED on hera

started build_and_test on hera at UTC time: Mon Mar 24 03:53:48 UTC 2025
finished at UTC time: Mon Mar 24 04:36:11 UTC 2025

Test project /scratch1/NCEPDEV/fv3-cam/rrfsbot/PRs_RDASApp/337/build/rrfs-test
    Start 2: rrfs_fv3jedi_2024052700_getkf_observer
    Start 5: rrfs_mpasjedi_2024052700_getkf_observer
    Start 1: rrfs_fv3jedi_2024052700_Ens3Dvar
    Start 4: rrfs_mpasjedi_2024052700_Ens3Dvar
    Start 7: rrfs_mpasjedi_2024052700_bumploc
    Start 8: rrfs_bufr2ioda_msonet
1/8 Test #8: rrfs_bufr2ioda_msonet .....................   Passed   36.48 sec
2/8 Test #2: rrfs_fv3jedi_2024052700_getkf_observer ....   Passed  228.18 sec
    Start 3: rrfs_fv3jedi_2024052700_getkf_solver
3/8 Test #5: rrfs_mpasjedi_2024052700_getkf_observer ...   Passed  255.80 sec
    Start 6: rrfs_mpasjedi_2024052700_getkf_solver
4/8 Test #7: rrfs_mpasjedi_2024052700_bumploc ..........   Passed  416.71 sec
5/8 Test #1: rrfs_fv3jedi_2024052700_Ens3Dvar ..........   Passed  429.50 sec
6/8 Test #4: rrfs_mpasjedi_2024052700_Ens3Dvar .........   Passed  483.60 sec
7/8 Test #3: rrfs_fv3jedi_2024052700_getkf_solver ......   Passed  476.69 sec
8/8 Test #6: rrfs_mpasjedi_2024052700_getkf_solver .....   Passed  542.26 sec

100% tests passed, 0 tests failed out of 8

Label Time Summary:
mpi            = 2869.21 sec*proc (8 tests)
rdas-bundle    = 2869.21 sec*proc (8 tests)
script         = 2869.21 sec*proc (8 tests)

Total Test time (real) = 798.10 sec

workdir: /scratch1/NCEPDEV/fv3-cam/rrfsbot/PRs_RDASApp/337

[rrfsbot]

PASSED on hercules

started build_and_test on hercules at UTC time: Mon Mar 24 03:50:54 UTC 2025
finished at UTC time: Mon Mar 24 05:06:13 UTC 2025

Test project /work/noaa/wrfruc/rrfsbot/PRs_RDASApp/337/build/rrfs-test
    Start 2: rrfs_fv3jedi_2024052700_getkf_observer
    Start 5: rrfs_mpasjedi_2024052700_getkf_observer
    Start 1: rrfs_fv3jedi_2024052700_Ens3Dvar
    Start 4: rrfs_mpasjedi_2024052700_Ens3Dvar
    Start 7: rrfs_mpasjedi_2024052700_bumploc
    Start 8: rrfs_bufr2ioda_msonet
1/8 Test #8: rrfs_bufr2ioda_msonet .....................   Passed  146.81 sec
2/8 Test #2: rrfs_fv3jedi_2024052700_getkf_observer ....   Passed  228.80 sec
    Start 3: rrfs_fv3jedi_2024052700_getkf_solver
3/8 Test #5: rrfs_mpasjedi_2024052700_getkf_observer ...   Passed  235.43 sec
    Start 6: rrfs_mpasjedi_2024052700_getkf_solver
4/8 Test #7: rrfs_mpasjedi_2024052700_bumploc ..........   Passed  291.61 sec
5/8 Test #4: rrfs_mpasjedi_2024052700_Ens3Dvar .........   Passed  371.49 sec
6/8 Test #3: rrfs_fv3jedi_2024052700_getkf_solver ......   Passed  181.70 sec
7/8 Test #6: rrfs_mpasjedi_2024052700_getkf_solver .....   Passed  327.07 sec
8/8 Test #1: rrfs_fv3jedi_2024052700_Ens3Dvar ..........   Passed  795.61 sec

100% tests passed, 0 tests failed out of 8

Label Time Summary:
mpi            = 2578.53 sec*proc (8 tests)
rdas-bundle    = 2578.53 sec*proc (8 tests)
script         = 2578.53 sec*proc (8 tests)

Total Test time (real) = 795.62 sec

workdir: /work/noaa/wrfruc/rrfsbot/PRs_RDASApp/337