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