There's definitely a need for a tutorial on turning paper pep to foam and vice versa.
The first step for changing a paper pep file into a foam pep file starts right here, at removing the flaps
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Uncheck "show flaps" and you immediately have a foam pep file.
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But you don't get a 124 page thread by leaving the file as is. Most foam unfolders like to have the duplicate mirror pieces removed and only have one side of a model to print out. When tracing onto foam, you just flip the template over to trace out pieces for the opposite side, of course. So you'll want to move all the pieces from one half of the model off the paper entirely.
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Or like some unfolders do...
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The next step for optimizing your foam pep (like JFcustoms has become awesome at) is joining the pieces together. You normally have a ton of smaller pieces for paper pep so that single pieces will fit on a single sheet of paper. With foam, you can tape multiple sheets of paper together and it just has to fit on a roll of foam. So you join the pieces together into shapes that make sense. This was done quickly and I'll admit could have been done better.
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Less pieces mean less gluing and faster building.
Lastly, you can pretty up the template by removing fold and cut lines that aren't needed. You can affect the whole model at once by lowering the angle threshold for showing edges, but if you want to be specific about where your mountain and valley folds are on the template, then you can use the Set Edge Color tool.
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I ignored this tool for a while because who cares about edge color? But it actually has a better use. When unfolding you'll have these cut lines where the faces of the model don't line up perfectly, but aren't significant enough when working with foam. Foam is forgiving enough that you don't need millimeter cuts and stuff.
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So you'll want to take a look at the "Hide Clicked Edge" tool. From here, you can just get lost for hours clicking and clicking to your heart's content.
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This makes it so you don't accidentally create a valley or mountain where you just wanted a nice smooth bend, or cut into the foam where it should just be nice and flat.
So there you go. Hopefully that answers your question, and other people's as well.