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For research purposes I'd like to implement my modified version of the Tor source code in the Shadow simulation network, but I am not exactly sure how to do that. Shadow uses a plug-in called Scallion that is a wrapper for the Tor source code. This solved question (How to implement the modified source code of Tor?) merely mentions the idea, but could someone please explain to me clearly the steps of doing modifications in Shadow?

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The method is the same as modifying the Tor source code without using Shadow: simply modify the .torrc files. An explanation of this is available: Editing .torrc in Tor Browser Bundle

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