Yep, anything I can put in as a mod, I do. That way, in case there's a patch that doesn't affect that file, all I have to do is reenable it after patching and I don't forget to redo it.
I keep all my command stuff in my "uber mod". It's got almost all the stuff that works on the same files (including commands.cfg). Now with JimiMadrid's excellent ini merger I may have to rethink that whole thing though (I hate to rethink, but sometimes it's the best thing to do).
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