After about 6 unsuccessful builds I decided to run the unit tests
before checking in these files. I fixed the integrator unit
test that was failing from a previous issue along with problems
with the sims.
refs #86
Adjusted all of the source code to point to the header files in their new
locations. Adjusted the makefiles for the header locations as well.
Added .gitignore files in the test directories to ignore test object code.
Changed all header file once include variables to follow the same naming
convention and not start with any underscores. Also deleted old
incorrect copyright notices. Also removed $Id: tags from all files.
Fixes#14. Fixes#22.
