Remove setting of STOP options in user-mod directories

In ctsm5.1.dev129 we are bringing in a setting of STOP_OPTION and STOP_N in the NEON user-mod directories. This is problematic because the user may want to run for a different length than given, they may use end-date or run-length options in run_neon.py, or this may be in the context of a CESM test.

For tests I've added an if statement to ignore it for tests, but the other issues still apply.

There is still a need to have the run-length have default values that is specific to the site and the type of simulation. I think what we want is for this to be the default setting, but for the user to be able to modify it to what they want.

There is some discussion on this here:

https://github.com/ESCOMP/CTSM/pull/2015#pullrequestreview-1491663809