Add flags for alignment in reconstruction

This MR modifies the make_PrKalmanFilter_X wrappers to allow FillFitResult and ClassicSmoothing to be accessed in Moore without bind statements on the PrKalmanFilter. This allows a forAlignment flag to be added to the relevant reconstructions, which should be more future-proof if changes are made to the central reconstruction sequences.

Goes with Alignment!359 (closed)