Regressions related to no longer setting user.dir

JDK-8226904 changed the applauncher to no longer set the current directory before launching java.
The launch of java depended on several entries in the cfg file (main-jar, app.runtime, app.classpath, and --module-path).
Each of these previously depended on the current directory being set to the app dir.

app.runtime has always been $APPDIR/runtime.

Now the --module path, the main-jar, and each entry in the classpath must also be based on $APPDIR