Add boundary conditions and refactor

Adds a header file containing functions for setting basic boundary
conditions along with a function interface.  Also changes a number of
basic parameter names to more Clawpackish names.

Note that as of this commit EVERYTHING BROKE!
Fixing some makefile stuff.
Fixing more makefile badness
Removing dynamic flags from executable compilation
Bug tracking commit for update and BCs
Add html output
Adding simplier example
Merge branch 'advection-example' of github.com:aterrel/ManyClaw into advection-example
Adding some more testing
fixing few small imports, adding indexer
Adding gtest test for indexers
Adding gtest files to contrib
Adding edge field indexer and test
add num_ghost to solver calls
Adding riemann problem test
Fixing advection riemann problem
Updating edge field indexer
Add clang++ as a supported compiler
Add num_ghost as parameter for Solver
Use indexers