Verified all documentation deleted with this issue resides on
our wiki. Nothing is lost. Modified the doxygen makefile and
main page to point to the wiki where the user's guide used to be.
TODO: Need to move the requirements and design doxygen files.
Updated the directory names in the doxygen files to match the new directory locations
of our source code files. The documentation builds now. But we still need to
remove the duplicate documentation that is now in the wiki, because the wiki is
more up to date.
refs #158
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.
