Added Perlpod documentation for assembleByProtv2
Added perlpod for callVelvetAssemblies

Also added sample name to error reporting for assembleByProtv2 and
callVelvetAssemblies and standardised shell script header comments.
Added perlpod up to best2refs.pl

Documented catcontigs, bestcontig_distrib, best2refs.
Added perldoc to remaining scripts

Tidied up formatting also.