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JGit is respecting the proxy settings provided to the JVM by -Dhttp.proxyHost and -Dhttp.proxyPort, but ignoring the proxy credentials provided by -Dhttp.proxyUser and -Dhttp.proxyPassword. Even though those attributes are not 100% java standard, they are used everywhere...
I think JGit is never reading explicitly the system properties http.proxyHost, http.proxyPort. It's a feature of the JDK as described here: https://docs.oracle.com/javase/8/docs/technotes/guides/net/proxies.html. When JGit opens http connections using the classes under java.net then these classes react on a system property http.proxyHost beeing set. Sadly I don't see support for user/password protected proxies. The discussion at http://stackoverflow.com/questions/1626549/authenticated-http-proxy-with-java shows some ideas what could be added to JGit in order to support such proxies. Other ideas?