I have created a Ceylon project in Eclipse Oxygen.
There are Ceylon source code files in the folder C:\Users\Jon\Aukitekt\milling\source\designs, but these are not shown inside Eclipse, as can be seen in this screenshot:
EDIT:
Making a single run, to 'kickstart' Eclipse, seems not possible. In run configuration I cannot click 'Run', for some reason.
Refreshing the Project Structure Window (right click -> refresh) revealed two files in the root:
ceylonbceylonb.batbut no files in the
sourcedirectory was revealed.The problem might boil down to Eclipse not recognizing this as a proper Ceylon project, as suggested by Vitaly Banchenko.

The problem was that the project was not created as a proper Ceylon project.
When creating the project, choose
File -> New -> Ceylon projectrather than
File -> New -> Project