Clarify the effect of errors on the reference trajectory

[cemitch99]

In elements with alignment shifts or rotations, the alignment shifts and rotations do not affect the push of the reference particle. (These are treated as errors, while the reference orbit is treated as nominal).

It would be good to add a flag that allows the user to specify whether the shift/rotation provided for an element is to be treated as an error (no modification to the reference orbit) or as a design feature (with modification of the reference orbit).