Atmosphere configurations have unnecessary files

[MartinDix]

The atmosphere directory has files (e.g. from the historical branch but all the ones I checked were the same)

CNTLALL   PPCNTL  UAFILES_A  errflag  ftxx.new   ihist          parexe          prefix.PRESM_A
CONTCNTL  SIZES   UAFLDS_A   exstat   ftxx.vars  input_atm.nml  prefix.CNTLATM  um_env.py
INITHIS   STASHC  cable.nml  ftxx     hnlist     namelists      prefix.CNTLGEN

Many of these are not used by the model and their presence is confusing because the same namelist variable may be set in multiple files. The minimal set required is

STASHC     UAFLDS_A   errflag  ihist          namelists       um_env.py
UAFILES_A  cable.nml  hnlist   input_atm.nml  prefix.PRESM_A

This also requires a change to payu to remove them from the list of required files.

[MartinDix]

Also some unnecessary entries in um_env.py.

Tested with pre-industrial run (and modified payu)
MartinDix@9425943