Update git ignore file.
Remove CMake modules (will be replaced with submodule in next commit).
Add CMake modules directory as submodule.
Update Doxygen config file.
Update CMakeLists.txt based on [Stomi](http://www.github.com/kartikkumar/stomi/Stomi/CMakeLists.txt) example.
Update entire codebase based on changes to main CMakeLists.txt.
Create new Config/ sub-directory for all configuration files.
Add dustsim executable.