Confusing variable naming in magnet misalignment

[cr-xu]

The calculation is correct but code/ variable naming is misleading.

$R_\text{entry}$ should be acted on the incoming beam first, and shift the incoming beam to -misalignments w.r.t. the quads-frame.

Suggestion: The names and definitions of R_entry and R_exit should be switched so that the transfer matrix multiplication makes more sense:

$$ \begin{split} p\text{out} &= R\text{TM} p\text{in} \ &= R\text{exit} R\text{Q} R\text{entry} p_\text{in} \end{split}$$

c.f. line270-298