[WIP] Refactoring of neon_site into tower_site, and neon_site

[TeaganKing]

Description of changes

This PR will create a BaseSite class which defines common structures that are in both NeonSite and Plumber2Site classes. The TowerSite class (child of BaseSite) will define common
functionalities that are in both NeonSite and Plumber2Site classes. With this structure, we will be able to implement a Plumber2Site class parallel to the NeonSite class that utilizes structure and functionalities in the parent classes.

Contributors other than yourself, if any:
@ekluzek
@adrifoster

CTSM Issues Fixed (include github issue #):
This will address part of #1487

Are answers expected to change (and if so in what way)?
No, this PR should be BFB.

Any User Interface Changes (namelist or namelist defaults changes)?
No

[TeaganKing]

In a discussion with @ekluzek we decided to keep BaseSite and TowerSite classes combined in order to avoid scope creep.

TowerSite will include build_base_case, get_batch_query, and set_ref_case. A basic modify_user_nl function will be included in TowerSite, with extensions for NEON (and eventually PLUMBER) located in NeonSite (and eventually Plumber2Site). Some functionality from run_case will be brought out into TowerSite as well, while details specific to NEON will be in NeonSite.

[TeaganKing]

Closing and using #2363 instead...