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After futher thinking and digging, I think the root cause is that CompressionFilter was using setHeader("Content-Encoding","gzip") as a trigger to automatically insert transparent gzip compression.
This just doesn't work with servlets that handle gzip content encoding on its own, such as jgit.
In https://github.com/stapler/stapler/compare/08d582d...5b6496c9 I made a fix to change the way the transparent content compression kicks in.
Because this is a core change, git-server plugin should work around this in the mean time by hiding "Accept-Encoding" from the request.