Namelist appendix

Added appendix for namelist

Minor changes to ftuv bug fix appendix
Namelist appendix updates

Table width adjustment
split (h,v)_(mon|sca)_adv_order into two entries
Updated certain namelist descriptions
Hyperref compliance

Modified thesis.cls to allow 4th argument to \contentsline and thus
compliance with hyperref.

Also added hyperref package to root tex
Merge branch 'Appendix'