Currently header files (jni.h, jawt.h, etc) get installed to $prefix/include. On Debian systems this means the header files are installed to /usr/include. To not clutter this directory and to no conflict with possible other implementations please move the header files to $prefix/include/classpath. This would move the files to /usr/include/classpath on Debian systems.
Personally I don't think this is a bug. Shouldn't Debain use --includedir=/usr/include/classpath to be what they want?
Its not a bug, more a wish. And I think this should be consistent to all installs, not make Debian a second class citizen on this. I think this is a problem elsewhere too. And people just doing "./configure ; make ; make install" just dont recognize it as they just overwrite jni.h with another version...