Sync with community code in prep for new build structure

[fossell]

This PR contains cherry-picked commits from our DTC_post branch that include:

• Bug fixes from our recent bug fix release version v4.0.1
• Adding some community control files to the parm/ directory
• Bug fix suggestions from recent merge with develop.

Merging these mods to develop will sync up the community and emc source codes and allow us to make the final switch and hand off for the new build structure.
Comments on specific code sections can be found in files changed.

[WenMeng-NOAA]

Kate,

Can you sync the recent changes from develop at original repos. so that I can run regression tests.
Thanks,

[fossell]

Wen,
I addressed your comments and pushed the requested mods. I did not modify the post_avblflds.xml MXUPHL file yet, but did comment, waiting for your response and final guidance.
I merged the top of develop into this PR as well so you can run regression tests.

[WenMeng-NOAA]

Kate,
I conducted the UPP regression tests on Dell. The results look good for me. No changes were found.
We will have a UPP branch develop commit next week for RAP/HRRR implementation. I will schedule
your branch merging after it. You might manually pick up some changes from RAP/HRRR
implementation in RQSTFLD.F.

[fossell]

Wen,
Great news, thanks! We will look for RAP/HRRR merge and take those changes into our DTC_post branch when available.

[WenMeng-NOAA]

Conducted regression tests on Dell, Cray and Hera. No changed results were found. This pull request is ready for merging.