Basic implementation of module workflow started (see issue #3)
i) Modified implementation and interface for referencing module directories
ii) Started working at "full modular" system that uses full namespaces as names such as a|b|c|d instead that a|d

TODO
i) migrate variables to the format in (ii)
ii) make the list of module directories contain the parents of the modules so that in .c and .h files we can:
\#include "mymodule/foo.h"
Finished implementation for modular workflow

TODO
update tests to match new variable style
i) Almost finished #3 along with tests
ii) Closes #4 flat workflow (classic)

TODO
i) in order to finish #3 need to modify the inclusion list return to
give the parent of each module instead of the module path itself so that in
the C/C++ (or source) files one can include as #include "<module>/<file>.h"
i) Closes #3 now the include path shortcut for modular workflow returns the modules parent
i) This closes #11 now the path traversal during module inclusion is enforced to be breadth first
i) cleaned temporary files