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Nested stacks won't be possible, but if you want to sort a lot of stacks into a few groups, just put those stacks into simple directories like so:

ros_workspace (or any directory put into ROS_PACKAGE_PATH)
  | navigation
     | stack1 (with stack.xml)
        | package1 (with manifest.xml)
        | package2 (with manifest.xml)
     | stack2 (with stack.xml)
        | package3 (with manifest.xml)
        | package4 (with manifest.xml)
  | objectdetection
     | stack3 (with stack.xml)
        | package5 (with manifest.xml)
        | package6 (with manifest.xml)
     | stack4 (with stack.xml)
        | package7 (with manifest.xml)
        | package8 (with manifest.xml)