When doing an in-tree build, Makefile.gen.sh isn't ignoring any .java files generated from .javain files (it can see both), instead adding both to GEN_SOURCES. Makes for a very confused automake error.
Index: frysk-core/common/ChangeLog 2005-11-21 Andrew Cagney <cagney@redhat.com> * Makefile.rules (.java.classes): Delete rule. * Makefile.gen.sh: Do not generate .classes.o dependency. Do not add a .java file to GEN_SOURCES when there is a .javain.