Could you please update the Bundle-Classpath (used by OSGi) in trunk/src/java/Manifest.mf when you update jars in lib/core or lib/endorsed. I did it for your update, but I might miss updates so it is good if more people remember it. This is only a temporary situation, the jars should be separate bundles instead of being packaged in the Cocoon core bundle, also I didn't felt to write something more automatic until we have finished changning build system to Maven2.
What about generating this file?
Joerg
