clarified directory structure;

maintain classpath in more elementary manner: turn ISABELLE_CLASSPATH into -classpath option, so that all jars are covered by sun.misc.Launcher.AppClassLoader (e.g. relevant for loading add-on resources); ignore $ISABELLE_JAVA_EXT -- do not change java.ext.dirs;

more official initial class path according to sun.misc.Launcher;

provide main classpath again, notably for cold-start;

cold-start of main application even on Linux;

tuned proofs;