Clean up redundant code, Registry checks + improvements, and simplification of certain defines

[islas]

TYPE: bug fix

KEYWORDS: make, cleanup, duplicates

SOURCE: internal

DESCRIPTION OF CHANGES:
Problem:
Fixes to various issues found while redesigning build system that are independent of new build system features. These bug fixes include removal of duplicate files, wrong #ifdefs, simplified ifdefs (no impact), poor Fortran syntax requiring sed or standard.exe for fixes, relying on autogen in-situ code where alternative coding practice suffices. No or few checks in Registry where checks would be incredibly useful for debugging purposes.

Solution:
Removal of dead/duplicate/obfuscating code and consolidating logic & makefiles to make use of changes. Slight rework of # defines. Checks on Registry generation with ability to run generation of files outside of repository.

LIST OF MODIFIED FILES:
M .gitignore
M dyn_em/module_advect_em.F
M dyn_em/module_first_rk_step_part1.F
M external/atm_ocn/cmpcomm.F
M external/io_adios2/wrf_io.F90
M external/io_grib1/Makefile
D external/io_grib1/wrf_status_codes.h
M external/io_grib2/g2lib/dec_png.c
M external/io_grib2/g2lib/enc_png.c
M external/io_grib_share/Makefile
D external/io_grib_share/wrf_io_flags.h
D external/io_grib_share/wrf_status_codes.h
M external/io_int/io_int.F90
M external/io_int/io_int_idx.c
M external/io_int/makefile
M external/io_netcdf/wrf_io.F90
M external/io_netcdfpar/wrf_io.F90
M external/io_pnetcdf/wrf_io.F90
M external/ioapi_share/wrf_status_codes.h
M frame/module_configure.F
M frame/module_internal_header_util.F
M frame/module_io_quilt_old.F
M inc/intio_tags.h
M phys/module_mp_SBM_polar_radar.F
M phys/module_mp_fast_sbm.F
M tools/gen_allocs.c
M tools/gen_streams.c
M tools/reg_parse.c
M tools/registry.c

TESTS CONDUCTED:

1. No impact to compiled binaries, changes at most affect auto-gen code resulting in same effect; improvements are moving towards better coding practices

RELEASE NOTE:
Various bug fixes & small improvements in code maintenance such as runtime checks on Registry generation, simplified # defines, removal of redundant code

[islas]

@weiwangncar @dudhia Here are the separated changes from #1896 that modify existing files that have no dependency on new system and can ultimately be categorized as improvement/bug fixes rather than new feature.

[weiwangncar]

The regression test results:

Test Type              | Expected  | Received |  Failed
= = = = = = = = = = = = = = = = = = = = = = = =  = = = =
Number of Tests        : 23           24
Number of Builds       : 60           57
Number of Simulations  : 158           150        0
Number of Comparisons  : 95           86        0

Failed Simulations are: 
None
Which comparisons are not bit-for-bit: 
None