That dependency checking script sounds like a really good idea. I agree that PD embedding everything without asking would be wasteful and a bit rude. I think that having the option of Embedding abstractions would be a useful one. Either that or giving subpatches some of the same advantages that abstractions have.
I have been thinking a bit about the problem of Embedding (via voice has decided to spell Embedding with a capital E today, don't be alarmed; - ) abstractions and then keeping them automatically updated (from the original file) I think that some kind of script similar to the one you have described might be useful in this case, so that when Apaches (ViaVoice again, I mean " a patch is" ) loaded, the embedded abstractions are checked against the original file in the same directory and the user is given the option to update them.
Keeping all the project files in their own directory seems like a very good solution as well..
Best wishes
Adam
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