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MoveIt is not specific to arm planning. As I understand what you are trying to do, all you will need to do is specify that your robot is free flying (aka, a 'floating' joint connection between the world and the robot). This you can do when creating the moveit configuration package for your robot. At that point you should be able to do motion planning with collision avoidance. octomap is used internally, but octomap_server is not (the pipeline for processing sensor data in moveit is significantly more efficient).