I've just downloaded Pd-0.41.4-extended in which the bug in the previous version that prevents makeapp function work properly has been fixed, so you can successfully create applications from a folder or a patch. One thing I can't really understand though: although the application you create works as a stand-alone one, unlike it's in Max, you can still edit the patch as if you opened it with Pd. I was wondering if anyone has an idea of what's the purpose of creating an application while it still works like a regular patch?

Good question!
and why theese patches are so big (tons of Mb)?

as far as i've seen, it just creates a copy of the entire pd-extended distribution, and then sets the startup flags to open your patch. pd doesn't have a 'REAL' makeapp function.