Cleanup of .tex files (training @ UAntwerpen, October 13, 2014)

 - e.g., i.e., ...: always followed by comma
 - consistent use of capitals: TORQUE, Moab, PBS, Perl, Python, Fortran, MATLAB, Intel, ...
 - consistent use of I/O, MB, GB, kB, ...
 - replaced " by `` ''
 - replaced single quotes (both ` and ') by `` ''
 - removed spaces before punctuation
 - added space after punctuation
 - removed $ from \footnote
 - replaced 's by s (plural)
 - replaced commando by command
 - removed space before },) and after {,(
 - added space before {,( and after },)

 - introduced menukeys package and \keys and \menu macros
 - introduced tip environment
 - introduced \ref, \nameref and \autoref

 - first update of UA related items