- Added stub functions required for model restart
- Added ElementCount to GridPatchGLL to describe number of finite
elements in each coordinate direction
- Added description of second derivatives in SE
- Removed some unneeded classes
- Added GridStamp to keep track of changing grids
- Moved patch construction outside of Initialize routine in Grid
- Removed InitializeBuffers from Connectivity.  Buffers are now
initialized when Neighbor is constructed.
- Only construct Neighbors on active patches
- Added preliminary ShallowWaterEddyTest
- Added initial functionality for restart file support
- Includes incomplete automatic Connectivity generation
Automatic connectivity generation

- On Initialization Grid now automatically generates exterior neighbor
connectivity
Added BuildJacobian function to VerticalDynamicsFEM

To facilitiate a direct solve
Merge remote-tracking branch 'origin/master' into CartesianJEG

Conflicts:
	.gitignore
	src/atm/GridCartesianGLL.cpp
	test/Makefile

Everything compiles, but I'm still getting NAN's in the cartesian test
that need to be resolved.