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MoveIt! allows for adding objects to the workspace through either directly the URDF, through the planning scene, or to the octomap (from a camera).
Pick and place can be used to move the object once you have it added to your workspace.
Then you should be able to move the bottle with your manipulator.
I am not aware of being able to move the obstacle out of the way when planning for the bottle however. From what I understand (correct me if wrong), you would have to manually move the obstacle out of the way if planning to the bottle is unsuccessful (from the obstacle stopping you from reaching the bottle). You could code this using Python/C++ though without too much effort I think.
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