When I do eclipse clean on an android project, it no longer is able to generate the GEN files for the project (gen folder becomes empty). The project was previously imported and ran FINE on my phone UNTIL I did clean and could no longer compile because of R.java not found. I could not find any project property changes as a result of the clean that could have been gotton messed up. So I don't know what the cause is of the corruption!
My version:
Eclipse IDE for Java Developers
Version: Juno Service Release 2
Build id: 20130225-0426
I never before had the problem that clean made a non-working project from a perfectly fine working project.
Check my answer: Error in all the classes files: R cannot be resolved
The fact is that probably you're missing the Android Build tools. Or you just need to update them.