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
distributing src/nmProcessSpec.f
Merged in Peter's edits