ENH: Organize Binary directory

Redo the configuration commands for the Setup python files and the
GetFilemanSchema test of the Dox generation to follow the structure of the
source directory.

Move the Setup generation code into a CmakeLists.txt file in the setup
directory.
Update all the necessary references to those files.

OSEHRA-Id: http://issues.osehra.org/browse/OAT-49
Change-Id: I81f0d5a0bdffdafa8cdd5fb61c49efa755e260dc
Merge "ENH: Organize Binary directory"