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Just to add a little more information. You can set the inital pose of the robot by publishing to the "initialpose" topic used by AMCL and documented here: http://www.ros.org/wiki/amcl#Subscribed_Topics. This is, in fact, what RVIZ does when you use the "2D Pose Estimate" button. You can always user "rostopic echo initialpose" to see exactly what it's sending.

Hope this helps.