There are two different versions of make_fragments.pl, several copies under demos/ (all similar except pathes) and one under tools/fragment_tools/.
Latter seems to be more recent, as it refers to the more recent vall.jul19.2011 (which is also included in this release).
But the flexpepdock tutorial points to the version in demos/
Which to use? (Sorry, if that is a very silly question)
The "official" version of make_fragments.pl is the one at Rosetta/tools/fragment_tools/make_fragments.pl
The issue with make_fragments.pl is that it needs to be edited to tell it where to find all the other applications and databases it uses. So people often copy the file to make changes to it. That's the case with the variation in the demos directory -- the differences are just differences from where different authors adjusted the script for their different environment. (And if you use it on your machine, you'll likely have to change things around, as well.)
The other issue is that the demos/ versions are copied from an older version of make_fragments.pl -- I don't know if there's modifications in them for use specifically with peptides (versus longer proteins).
You can try to use the one in tools/, but if you run into issue with peptides, you may want to try using the one with the peptide demos.
All make_fragments.pl, which are in the demos folder are version 1.3, while the one in tools is 3.10.
Latter is significantly easier to install from scratch. However, they differ in their output format. Luckily, there is a '-old_name_format', which allows to use 3.10 for those applications that require fragments in the old format.