Add bottom layer in the CVMix module and clean up the Stokes drift mo…

…dule (#48)

* Add option for bottom layer KPP

* Working on bbl in cvmix

* Pass u_taub to cvmix

* A first implementation of bottom layer in CVMix

* Update CVMix namelist and YAML configuration for bottom layer

* Set surface Stokes drift in theory wave

* Independent surface Stokes drift input

* Clean up Stokes drift

* Fix a bug in the range of indices when computing Langmuir number

* Fix a bug in CVMix and Stokes drift for non-zero zi(nlev)

* Use potential density in CVMix -- bug introduced in 459c09b

* Clean up Stokes drift in theory-wave