Quote:
Originally Posted by Quagmire1975
Yes, that's true, but I'm not using that as it alters other files like basic.cfg etc which I've edited myself to my own liking.
At least that's my experience anyway.
Is there something in the flotilla.cfg file that I can change instead? 
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I'm not sure what other files you may be editing but I'm also using a manually tweaked basic.cfg file and the latest version of Commander with no issues... I actually use Commander to tweak my basic.cfg even more for different date ranges. So far Commander hasn't interfered with anything I've modded or tweaked either manually or with JSGME. Depending on what edits you're making and to which files, it might be possible to use Commander without any conflicts or even use it to help with that process.