Checkout script fixes and mk_paths fixes

[laurenchilutti]

Describe the bug

In CHECKOUT_code, we set the release to "main" and the latest main branch code is always checked out. It would be safest to set the release to the latest release (currently 202305) and users can manually modify this when they would like to checkout the latest main branch.

When compiling SHiELD, there is a warning in the build output file:

find: ‘GFDL_atmos_cubed_sphere/model/gfdl_cld_mp.F90’: No such file or directory
find: ‘GFDL_atmos_cubed_sphere/model/cld_eff_rad.F90’: No such file or directory
find: ‘GFDL_atmos_cubed_sphere/GFDL_tools/fv_diag_column.F90’: No such file or directory

These files were removed in FV3202210 release. gfdl_cld_mp.F90 and cld_eff_rad.F90 were replaced with SHiELD_physics/gsmphys/gfdl_cld_mp.F90

To Reproduce
Checkout the code via the CHECKOUT_code script and build via ./COMPILE (defualt is a SHiELD configuration - a SHiELD configuration gives the no such file warnings)

Expected behavior
No warnings, checkout latest release.

System Environment
N/A

Additional context