Fix the creation of project file based on dub project
There was an issue where it was importing every dependency folder into the project, rather than just the includes, severely polluting the project space. It also failed to include the main project folder (instead including only source)

Changed the dub create script to include only the base dependencies folders rather than the entire flattened folder tree. Also set up the project to be updated and saved through sublime instead of outside of it. This should help keep things synchronized for the user, as well as allowing in the future to update the project automatically as dub changes.

updated check against overwriting existing projects

Reorganize code to group functionality in the command (could probably move them into functions). Switched to using dub package import paths instead of a bunch of individual directories. Fixed bug when the only thing open is a file and Window.get_project_data() gives back None.