Merge Storm Surge Code Into Main Code

In an effort to cut down on the upkeep of the storm surge code I decided to try and merge the storm surge specific code back into the general "shallow" code.  With a few modifications of what was being done with the storm surge code, the modifications were actually pretty minimal.  The primary bother for existing applications will be adding the required storm surge modules to the Makefiles.  Crude speed tests are below  but at least for the examples in GeoClaw do not show and performance degradation.

### Timings
`FC=gfortran (v4.8.2)`
`FFLAGS=-O3 -funroll-loops -finline-functions -fopenmp`
Results were averaged over 3 runs

Example   | Old Time | New Time
-------------|--------------|----------------
Chile2010   | 16.16900000 s | 14.64300000 s
bowl-slosh  | 3.18000000 s  | 3.00400000 s
bowl-radial | 10.74600000 s | 10.00000000 s
Ike         | 61.82000000 s | 60.14500000 s