Initial incorporation of multilayer SWE into 5.0
First pass through reworking multilayer code to 5.0

Commit includes updates to a lot of the core multilayer routines for
compatibility with Clawpack 5.0 release.  Includes sectioning of much
of the actual data parameters to their own modules or data structures
and the reintroduction of some older codes.  Also makes some
modifications to existing surge code so that data structures play
nicely together including some changes to default values.  This also
corresponds to a change to the rundata object in clawutil in order
to be able to replace the default Qinit with the multilayer specfic
one.
Update src2 function to 5.0 and correct some bugs
Convert getmaxspeed to check all layers
Continuing updates, Riemann solvers now changed over

This commit does not work unfortunately yet, getting a FPE currently.
Add MKL specfic flags to makefile
Plane wave base test now works
Revert to ascii output, binary not supported
Add test cases, only quantitative at this point
Add bubble tests to plane wave multilayer example
Remove author line
Plane wave tests working, not bubble
Update multi-layer code to new dtopo code
Add bathy intialization to setrun and tweak plots
Add new dtopo handling to multilayer setaux
Remove extraneous use imports
Reduce computational load of example
Add ghost cell fix
Merge pull request #69 from mandli/multi-layer

Add simple multi-layer example and update code to 5.1