There is a really stupid workaround,
Download the Library (in this case jQuery) from inside the IDE itself.
- Open up settings (Ctrl + Alt + S on Linux)
- Navigate to Languages & Frameworks -> Javascript -> Libraries
- Click Download and choose jQuery
Hopefully the errors will vanish
EDIT:
After running the IDE through Fiddler, I realised this only solves the problem because of the version the IDE downloads.
So, the correct workaround is to Add older, non-AMD jQuery versions as a Global scoped Library and add the latest one as a Project scope library.
The latest non-AMD versions are:
1.10.2 for 1.x series. And, 2.0.0 for 2.x series.