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You would have to disambiguate every time you are in an ambiguous situation. What causes ambiguity is having multiple '.rosinstall' files lying around.

You could rename or delete the one in /home/sam/my_workspace/android_core.

Is there a particular reason you want a .rosinstall there as well, as opposed to having the file named e.g. android_core.rosinstall?

rosws could have a switch that says it should use ROS_WORKSPACE in case of ambiguity, like --env or so. But for now I believe it is better to warn people that they have multiple .rosinstall files lying around.