Reconciliation from production/RRFS.v1 branch to main

[grantfirl]

This PR copies the changes for the production/RRFS.v1 branch back to the main branch for the purposes of full UFS testing.

The only divergent PR in the production/RRFS.v1 branch was #536.
This is @climbfuji 's work. Given #529, I'm not sure if this is needed
or not. I recall that this was part of a "temporary" solution to the RRFSv1 release branch, but I'm not sure if
subsequent solutions made their way into main yet.

User interface changes?: No

Fixes:

Testing:
test removed:
unit tests:
system tests:
manual testing:

[grantfirl]

@dustinswales @climbfuji I can't recall if this is needed or not (whether other optional argument work has already made its way into the main branch such that -check all can successfully be used in UFS without this). It's been a while since I paid attention to this.

[climbfuji]

I believe these changes are not intended to go into main.

[grantfirl]

I believe these changes are not intended to go into main.

Thanks, I thought that was the case, but couldn't remember. I need to run some tests with UFS with -check all on the main branch without these changes to make sure, I guess.

[climbfuji]

I believe these changes are not intended to go into main.

Thanks, I thought that was the case, but couldn't remember. I need to run some tests with UFS with -check all on the main branch without these changes to make sure, I guess.

The development in main (redo how opt args are done) should take care of this - eventually if not already.

This code in the RRFS branch was a quick-n-dirty workaround for being able to compile with -check all. THe associated metadata changes (in_inactive, out_inactive) must also be kept out from ccpp-physics main.