MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.

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I don't really understand why you should need this?
I use the E3Dv6 hot end drop in cartridge all the time without a flag extender. There is even enough room to have a glass plate on top of the bed without any problem.