Standardize CIME submodule conventions

The CIME submodule can be placed anywhere as long as there's a `config_files.xml` in the CIME repo. This is a major coupling between the model and CIME, which without CIME would not be able to find the models config.

The proposal is the standardize the CIME config directory name and placement within the model repo. With this we can remove this couple as CIME whenever used a submodule will be able to detect the models `$SRCROOT`.

Related https://github.com/ESMCI/cime/issues/3923