Bug Fix with MSL2SWL

[luwang00]

This pull request fixes the issue identified and does not affect existing test results. However, it would be beneficial to check whether there are other bugs associated with MSL2SWL!=0.

Feature or improvement description
This is a bug fix to address the following issues:

• HydroDyn not correctly processing members crossing the seabed when MSL2SWL!=0.
• SeaState wave grid with default Z_Depth causing an error when MSL2SWL<0.
• Water depth with the contribution from MSL2SWL included (measured from SWL instead of MSL) being passed to the other modules (HydroDyn, SubDyn, MAP++, and MoorDyn).

Impacted areas of the software
SeaState, HydroDyn, glue code with changes to the water depth input to SubDyn, MAP++, and MoorDyn.

Additional supporting information

• SeaState overwrites WtrDpth with WtrDpth+MSL2SWL in SeaState InitOut, affecting other modules downstream using it as an input.
• This pull request changes WtrDpth in SeaState InitOut back to the original water depth from the user input files without the contribution from MSL2SWL. A new variable called EffWtrDpth with the contribution from MSL2SWL is added to SeaState InitOut to avoid confusion.
• Right now, WtrDpth of the various submodules of SeaState and HydroDyn is actually the effective water depth, i.e., WtrDpth+MSL2SWL. This gives the correct behavior, but it might be beneficial to change the variable name to EffWtrDpth for clarity, like in the new SeaSt_WaveField module.
• HydroDyn was not consistent when checking for joints below the seabed when evaluating joint-based hydrodynamic loads. This is now fixed.
• The default value of Z_Grid did not account for nonzero MSL2SWL, causing an error. This is now fixed.

Test results, if applicable
Does not affect existing test results. Only impacts the results when MSL2SWL!=0.