Renamed configure.ac.
Switch to using check_java_home and jni_include_dir
Also added check/setup for $JAVA.
Added SPEC_VERSION out of desperation from dealing with Makefile.am troubles.
Switched to using tab separators .
Explicitly put the App & EmbeddedLIbraryTools in to the jar.
Added a proper Manifest to the jar.
Added the native libraries in to the build.
Fixed bug where javah didn't have -force, causing multiple invocations.
Ignoring only some files in config directory now.