Initial import
Initial readme with build instructions
Beginnings of mesh reader
More work on mesh reader
write exodusII mesh files
Added ifdefs for debug output
More work on debug output
Added STK mesh

At this point, the ExodusII data is read from file and STK parts,
elements, etc are created and populated with a coordinates field.

The ExodusII output file writer still needs to be updated to draw
its data from STK mesh, for now it just has bogus arrays used for
testing
add missing includes, remove absolute paths
update example cmake configure script
add example cmake configure script for Trilinos
make include/ a known include path
Forgot the STK_mesh file...
Merge branch 'master' of https://github.com/patnotz/cj

Conflicts:
	src/cj_main.cpp
	src/mesh_manager.cpp
add stk and shards as target link libraries
move include files into src directory

There's really no benefit to having the separate include directory and
this simplifies some build configuration.
move application code to a function

This will allow us to have different main functions (command line and
gui) without duplicated code.
cleanup some headers

 - move includes inside the include guards
 - don't use 'using namespace' in headers
 - minor formatting
begin logging stream abstraction

In order to support a GUI we'll pass around ostream objects for
logging output. This is just the first step.
add libz to the link flags