Quoteit sounds like that launcher isn't removing 0kb files and it should be.
I wish I'd checked back again sooner because you're right. I finally came back and tried again and deleted empty files and it ran just fine. Well mostly. The one issue I'm having is a lack of light on many indoor maps. I'm running under wine on Linux but I'm able to do this with other CoH servers in the same wine prefix without this problem, so it doesn't seem to be a problem with wine generally.
If anyone has any ideas for things I could try I'd appreciate it. I'm 99.9% of the way there but not being able to see on indoor maps is likely going to be a showstopper for me here. I tried sort of randomly playing with graphics settings in the hope that maybe the problem was specific to one setting at one value but nothing I tried made a difference there.
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