Sorry WAC, I'm not at all sure what your asking, at first I thought you were asking about the releases list, which is what I mentioned, now for the first time I see the word 'folder', so I'm guessing you're asking about the \modules folder layout, or both - I'm confused. Examples of 'old' and 'new' would be nice
My opinion is meaningless, I haven't used AutoPatcher for so long I don't even know what you guys are doing anymore, and the few people I had been helping are using my friends app exclusively.
My opinion still stands - keep it simple, use their respective names, put it on paper first, see how it looks, is it logical, do-able. Maybe,
\modules
................ \xp_x86_enu
................ \xp_x86_ita
................ \7_x64_any
................ \adobe
........................ \reader
........................ \air
................ \directx
................ \extras
................ \dotnet
........................ \x64
........................ \x86
or according to language, something like,
\modules
................ \enu
........................ \xp_sp3_x86
........................ \xp_sp2_x64
........................ \office_xp
................ \ita
........................ \2k_sp4_x86
........................ \xp_sp3_x86
........................ \adobe_reader
................ \any
........................ \7_sp1_x64
........................ \vista_sp2_x86
........................ \directx