X-1.0rc2: Linux: App.window() returns null/none --- class App not fully available for Linux

Running: Red Hat Linux 6.0 64bit

I've tried using Sikuli 1.0rc2 as well as the latest continuous build.

Using the latest continuous build, I've been able to get Firefox to print out 3 different regions, using App.window(), but if I have a calculator opened, for instance, I can focus it but get null when I try using App.window(). Also, if I switch to the correct firefox region and try to hover/find an image it will fail. It works when I use Screen to find the image.

When using App.focusedWindow() :
   xdotool Error:java.io.IOException: Cannot run program "xdotool": java.io.IOException: error=2, No such file or directory