fix writing intermediate restart files for fv3 two phase run sequence

[junwang-noaa]

Description

This is to fix the restart file issue when fv3 is running with two phases. It removes the dependency on the number of time step obtained from the advanceCount in ESMF clockget call. farray now only contains the intermediate restart writing time. The logical variable restart_endfcst is to control if writing restart files at the end of forecast. There is also minor cleanup.

The code has been tested with both two phases and one phase atm run and with different configurations of restart_interval.

Issue(s) addressed

Link the issues to be closed with this PR, whether in this repository, or in another repository.
(Remember, issues should always be created before starting work on a PR branch!)

• fixes Restart files are incorrectly generated when using multiple run phases NOAA-EMC/fv3atm#488

Testing

How were these changes tested?
Tested on orion with two phases restart test.

What compilers / HPCs was it tested with?
Are the changes covered by regression tests? (If not, why? Do new tests need to be added?)
Have the ufs-weather-model regression test been run? On what platform?

• Will the code updates change regression test baseline? If yes, why? Please show the baseline directory below.
• Please commit the regression test log files in your ufs-weather-model branch

Dependencies

If testing this branch requires non-default branches in other repositories, list them.
Those branches should have matching names (ideally)

Do PRs in upstream repositories need to be merged first?
If so add the "waiting for other repos" label and list the upstream PRs

• waiting on noaa-emc/nems/pull/<pr_number>
• waiting on noaa-emc/fv3atm/pull/<pr_number>