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There are two packages containing a bunch of trajectory filters that you could use: spline_smoother and constraint_aware_spline_smoother. If you look in spline_smoother/default_plugins.xml, you can find a list of plugins that will just fill in timing information without doing any short-cutting. I don't recall the full details of each filter (there are many), but for a start you could try replacing your filter with this one: spline_smoother/CubicSplineVelocityScalerFilterJointTrajectoryWithConstraints.