That is fairly pointless... SE4 is designed to handle having dozens of mods installed at once, each in it's own mod folder.
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How did Atrocities combine it with his ST mod?
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In much the same way as the instructions in the help file tell you.
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Any suggestions on combining the FQM mod and Bab 5 mod?
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B5 Mod has a lot of custom items in it, such as Hyperspace systems. You might want to add those in to the FQM files as you add the FQM files to B5 Mod. Actually the Hyperspace systems might be all that B5 Mod adds... I am not sure.