Cleanup cmd() strings

[GiovanniBussi]

I would like to clean up a bit the interpreted for the cmd strings.

1. Simplify the addition of new cmd strings - perhaps the word_map can be generated automatically in the Makefile with some script
2. Work it out so that the commands are documented in the PlumedMain.cpp file

[carlocamilloni]

@GiovanniBussi is this closed?

[GiovanniBussi]

@carlocamilloni actually I would like to add something so that cmd are automatically added to the manual. Something like case() /// HERE GOES THE DOCUMENTATION cmd_setNAToms:

I don't know when I will have time to do it..