Reset output alarms on initialization

Since all alarms are ringing upon initialization, output alarms need to
be reset to prevent writing output on the initial time step when we
don't want output written.
Update common_level_eos to Jacobian_from_TS.
Fix unitialized pointer bug.

Before, highFreqThicknessNew would be passed into
ocn_vert_transport_velocity_top even when it was an
unitialized pointer.  Change highFreqThicknessNew to be
an optional variable.  Otherwise, the pgi compiler always
errors out on this line in debug mode.
Updating version number to 3.2
Merge branch 'v3.1_fix/ocean/initial_output_fix' into hotfix_v3.2

This merge introduces a fix where the ocean model would incorrectly
write output on the first time step even if no alarm was ringing.

* v3.1_fix/ocean/initial_output_fix:
  Reset output alarms on initialization

Conflicts:
	src/core_ocean/mode_forward/mpas_ocn_mpas_core.F
Merge branch 'ocean/fix_Jacobian_from_TS' into hotfix_v3.2

This merge introduces a fix for an issue where an invalid config option
was reference in the model, causing a valid config option to be ignored.

* ocean/fix_Jacobian_from_TS:
  Update common_level_eos to Jacobian_from_TS.
Merge branch 'ocean/unitialized_pointer_bug' into hotfix_v3.2

This merge introduces a fix that caused the PGI compiler to complain
about null pointers when build in debug mode.

* ocean/unitialized_pointer_bug:
  Fix unitialized pointer bug.

Conflicts:
	src/core_ocean/mode_forward/mpas_ocn_time_integration_rk4.F
	src/core_ocean/mode_forward/mpas_ocn_time_integration_split.F
	src/core_ocean/shared/mpas_ocn_diagnostics.F
Merge branch 'hotfix_v3.2'

This merge introduces three fixes for the ocean core, which are listed
below.

* hotfix_v3.2:
  Updating version number to 3.2
  Fix unitialized pointer bug.
  Update common_level_eos to Jacobian_from_TS.
  Reset output alarms on initialization