moved expression.py to controller.py

More functionality added to controller.py

The following is implemented:
* a single Controller
* built in embedded flag checker - returns set of flags
* removed unecessary calls to unicode
Updating for use with refactored controller

Added calls to the controller and included it in pree.py

I also fixed error with compile_obj being accidentially deleted.

Reworking Process_embedded_flags to be much more clean and set it up to
be ready to use the controller.
Updated gitignore to ignore rope files
updated embedded flags

Various changes to embedded flag function to be more readable

changes
* function now returns bool on if flags changed (this may be unecessary)
* function now uses the controller
* passes the set checked a bool instead of an int to clarify purpose
better