Remove unused configuration files from atmosphere directory

[blimlim]

The atmosphere control directory contains several overlapping configuration files:

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

As noted here, 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

The extra files have been removed from the required configuration files in payu (payu-org/payu#455) and can be removed from the configurations once those changes make their way into the latest version of payu.

[blimlim]

Closing as this was addressed in #42 and #43