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After a painful debugging, I found out that jgit recognizes "Accept-Encoding" header and performs gzip compression on its own in SmartOutputStream. It also uses the ServletResponse.setContentLength().
But at least on mvn hpi:run, this results in double content encoding via gzip, because either the servlet engine or some intermediate filter is also responding to the "Accept-Encoding" header and inserting GZIPOutputStream. Yet the Content-Length header value remains intact, and therefore curl that invokes the command gets the truncated output.
There are two issues here. Whoever inserting GZIPOutputStream needs to mangle the Content-Length}} header (or at least voids that), and second, I need to think about ways to avoid double gzip encoding.