Youtrack6/zip based installation - baseUrl does not work

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My youtrack6 installation is behind a reverse proxy:
ProxyPass/x/youtrack   http://localhost:8888/
ProxyPassReverse        /x/youtrack   http://localhost:8888/

ProxyPass/~socket.io/1/websocket ws://localhost:8888/~socket.io/1/websocket

I added both the jvm option:
-Djetbrains.youtrack.baseUrl=https://mydomain/x/youtrack

and internal/bundle.properties:
base-url=https\://mydomain/x/youtrack

They have no effect in the generated html. This was not a problem with tomcat installation. It popped out after 5 to 6 upgrade.
<!doctype html><!--[if lt IE 7]>
<html class="no-js lt-ie9 lt-ie8 lt-ie7"> <![endif]--><!--[if IE 7]>
<html class="no-js lt-ie9 lt-ie8"> <![endif]--><!--[if IE 8]>
<html class="no-js lt-ie9"> <![endif]--><!--[if gt IE 8]><!--><html class="no-js"><!--<![endif]--><head><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><title>YouTrack</title><base href="/"><meta name="description" content=""><meta name="viewport" content="width=device-width"><link rel="shortcut icon" href="favicon.ico"><link rel="stylesheet" href="bower_components/ring-ui/ring-lib.min.css"><link rel="stylesheet" href="styles/99409388.main.css"><body><!--[if lt IE 7]>
<p class="browsehappy">You are using an <strong>outdated</strong> browser. Please <a href="http://browsehappy.com/">upgrade
  your browser</a> to improve your experience.</p>

I guess href="favicon.ico" should have been href="/x/youtrack/favicon.ico".

When I type https://mydomain/x/youtrack/favicon.ico I can see the icon.

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I guess it is similar for upsource.

https://www.jetbrains.com/upsource/help/1.0/install_config.html

HTTP proxy
You can set up Upsource to work behind a reverse proxy server. There are two requirements that your environment should meet to make this possible:

  • Your proxy server must support WebSockets. For example, Nginx supports WebSockets since version 1.3.13.
  • Upsource should be hosted under root URL (/) on your virtual host.

If these requirements are met, start with configuring Upsource to use a base URL (the URL that end users will request for to access your Upsource installation):

<upsource_home>\bin\upsource.bat configure –listen-port 1111 –base-url https://upsource.mydomain.com
Now configure headers in your proxy server, and you’re done. Configuration guidelines for Nginx and Apache HTTP Server are provided below.
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