/usr/lib/jvm/java-1.5.0-gcj-4.6/include/linux/jni_md.h is in gcj-4.6-jdk 4.6.3-1.
This file is owned by root:root, with mode 0o777.
It is a symlink to /usr/lib/jvm/java-1.5.0-gcj-4.6/include/linux/../../../../gcc/x86_64-linux-gnu/4.6/include/jni_md.h