This is almost certainly related to how the .classpath files are setup in the repo.
I've tried adding things to them that seem like they should be there:
Like adding some of the source in the project to the build path.
However that breaks thing horribly.
And then importing the created packages into eclipse. This doesn't appear to set things up correctly. i keeps seeing:
"Some classes are missing from the generated module archives, probably because of an error in the Java backend compilation."
for ceylon-compiler. When I look at the list of missing files, it appears to be all of them.