The /etc/apt/apt.conf file is still read if it exists. The apt configuration provided by packages is installed as separate files in /etc/apt/apt.conf.d/ so that it can be added and updated independent of any local changes you make in the main configuration file.
So if you have local configuration changes, just create the file.
Based on my past experience, overall Ubuntu (GNOME) doesn't work very well with PAC (Automatic Config). Pac (Proxy Auto-config) is basically JavaScript logic to determine the closest or most appropriate proxy for you, I strongly recommend using the proxy servers directly (in your case Network - Network Proxy).
A few things to check
Check your /etc/apt/apt.conf
Network -Network Proxy GUI will update /etc/apt/apt.conf and set the proxy info there.
Find out the proxy server info from pac
You can find the details by reading the proxy.pac file anyway.
So the /etc/apt/apt.conf should look like below (suppose the proxy server is => proxy.company.com port 80), do NOT use pac URL.
Acquire::http::proxy "http://proxy.company.com:80/";
Acquire::https::proxy "https://proxy.company.com:80/";
Acquire::ftp::proxy "ftp://proxy.company.com:80/";
NOTE: If no proxy is specified in the apt config files, apt-get will fall back to http_proxy environment variable.
From apt.conf man page, respond to the comment from @Braiam
http
HTTP URIs; http::Proxy is the default http proxy to use. It is in
the standard form of http://[[user][:pass]@]host[:port]/. Per host
proxies can also be specified by using the form http::Proxy::<host>
with the special keyword DIRECT meaning to use no proxies. If no
one of the above settings is specified, http_proxy environment
variable will be used.
Check proxy environment variables
You can check proxy settings by running the following in terminal
echo $http_proxy
echo $https_proxy
echo $ftp_proxy
If you set env variables correctly, you should be should be able to update in CLI.
Prefer IPv4
I noticed apt-get was trying to connect to the update servers using their ipv6 address. This could cause problems (sometimes the IPV6 addresses expire or change).
You can edit /etc/gai.conf and add precedence ::ffff:0:0/96 100 to prefer ipv4 over ipv6.
More details
Best Answer
In Ubuntu 12.04 LTS:
When you come home, try not applying
no-proxysystem-wide. This doesn't edit theapt.conffile, yet software center uses no proxy. Works for me, dunno how.