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It depends on what interface you are using to make the planning request. If you are making the service call yourself, it is trivial to set the max_velocity_scaling_factor and max_acceleration_scaling_factor manually.

When using the the move_group C++ API, you have a function for the velocity and for the acceleration. These updates factors will then be used for the next planning request.

the moveit_commander move_group interface also has these functions (velocity and acceleration)

Setting the acceleration is quite recent for moveit_commander but I'm pretty sure it is in 0.7.6.