Hi Maarten,
What is the full path to this project? Are there any characters in
the path that could be revealing bugs in the plugin?
Also, which View are using to look at the source folder? Can you
check to see if the Navigator view (Window > Show view > Navigator)
shows the files?
After the web app project is created, can you right-click on the
source folder and add a new class? Does that show up? Can you make
sure the View is not filtered? (You can do this by clicking the
down-facing arrow in the upper-right corner of the View, and selecting
"Filters".)
Do other projects work ok? (e.g. A regular Java project)
Thanks,
jason