Bugs Fixes for Commands

• For the twiss_output command, the previous version gave incorrect results for the couplingIntegral and emittanceRatio values. In addition, solenoid elements were ignored, but are now included.
• Fixed a bug in the lattice parser that resulted in a crash when a value was missing for a parameter.
• Previously, the momentum_aperture command would not work correctly for runs with multiple steps. This bug was discovered by H. Shang (APS) and has been fixed.
• Fixed a bug in chromaticity correction when link_elements was used. The chromaticity correction matrix was sometimes wrong and the correction would not converge. This bug was discovered by A. Xiao (APS).
• Fixed a bug in Twiss parameter output when link_elements was used to change element lengths. The s values in the file were sometimes wrong.