Use slashes instead of backslashes, and a colon instead of a colon:
javah -classpath .:/home/thomas/Documents/LinuxProgramming/EclipseWorkspace/myJNI/bin/org/me/jni DoJNI
, , org/me/jni , bin, org.me.jni.DoJNI:
javah -classpath .:/home/thomas/Documents/LinuxProgramming/EclipseWorkspace/myJNI/bin org.me.jni.DoJNI