Well, for one thing, you are going to have to move the maps and quests folders into your server directory and rename them to "maps" and "quests" respectively. Make sure that the maps are directly inside that maps folder and not inside another folder within it. Also, quests should be in folders named after the shortname of each zone directly inside the quests folder.
You will also need to move your quests/plugins folder to your server folder.
Really, most of the debian install guide should still be useful information for getting setup. I think the only thing that has really changed is how you get the source code and database, as they both come from google svn now. Unfortunately, I don't have instructions on how to do that on Linux yet, but there may be some directions around the forums/wiki somewhere for it.
Once you get the EQEmuServer source code downloaded, you can just go into that folder and type "make" and if you have followed all of the other steps, it should compile properly.
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