Fix some issues with nag compiler, remove rtmhist_ndens==2 option

basetype wasn't declared and needed to be. Also add more "implicit none"
statements in. Remove the deletion of "rtm.input_data_list" file, as cime
now does this. Remove the option of setting single-precision
history output, as it sometimes has numerical conversion issues. The
real solution for it should be to keep a single-precision history
buffer that then outputs at the same precision as stored, rather than
converting just before. This would trigger issues with the conversion
earlier.