What steps will reproduce the problem?

Adding a e.g box.com repository from behind a http proxy via webapp.

What is the expected output? What do you see instead?

Connection should be made. But there is an error message:

"Internal Server Error
connect: does not exist (Connection refused): user error"

What version of git-annex are you using? On what operating system?

3.20121127 on Archlinux

Please provide any additional information below.

I don't use networkmanager if proxy information is obtained from it. There should be a fallback to environment variables.
