Just to be clear, my point is not to blame anyone or anything. Navigating through a pd patch fun, didactic, and is often hard unless there is a clear structure. That structure becomes clearer when it evidences itself firstly in the patch directory IMO.
I think, however, one of the nicest things of pd is that the way you structure is linked to how you organize stuff in your mind and not in a pre-established way.
And this intensifies with use, making your structures very personal to the way you think. (Mixing a bit of what other users teach you by going through their libs, patches, making this pd-mind a more interesting topic)
What i'm thinking here is a given structure, that is only there as a last step, not during the patching. And is only meant for the user to send to a non-pd user.
Dan mentioned there was a build feature in extended, and now i think that there is no real need for this since that build feature has been left out apparently. But, i'd still mess around with a script or two to automate this if i can manage.
Sorry to go so off-topic on this, thanks for your thoughts so far!!