Presumably the folders Mark refers to represent phases of the design. So for the most part files in past phases are actually archives, not working files. TW2 and the BIM Server greatly expand our opportunities during the working phase but in it's current incarnation do not offer new archiving options. So I would suggest simply saving out a copy as PLA into your usual folders at your chosen milestones.
Related are the issues of design options, construction phasing and revisions. Again AC13 offers nothing new here, yet since they are all part of every project they are clearly areas that deserve attention.
Regards,
Geoff Briggs
I & I Design, Seattle, USA
AC7-28, M1 Mac, OS 15.x
Graphisoft Insider's Panel, Beta Tester