Major refactor of modules and associated files

Removed submodules from the repo:  they cause problems, they clutter the _static directory with unnecessary files, Generally they are harder to use than they should be and require and extra step when setting up and building a repository.
update to latest skulpt
update conf.py files for no submodules
use new location for js/css files used by extensions
Add README(s) with some directions about css and js files
Update to latest pytutor.js
Update conf.py to use the latest locations for third party modules (skulpt, OPT, and js-parsons)