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move_base exposes two APIs: a simple topic for recieving goals ( move_base_simple/goal ) and an actionlib server ( move_base/goal, move_base/cancel, etc).

The actionlib server supports queuing and canceling goals, so it does in fact support canceling a goal while it is in progress.

This tutorial describes how to set up an actionlib client to send goals to the navigation stack, and the actionlib API documentation documents the various cancel functions that are available.

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