nmssmManual: added references to paper.
nmssmManual: edited Acknowledgements to include AEC grant and fixed style

(removed phrase *we would like to thank*).
nmssmManual:  fixed ordering of references, two typos, consistent use of SM
and SUSY acronym, dashed line in Fig. 1, all codes in typewriter font
Merged in Peter's edits
Merge branch 'master' into officialTag