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I have made a local apt repository, but my IT-department caches LAN traffic on the proxy server. Is there a way I could work around this to disable the proxy settings for this local apt repository? in apt.conf or simular?

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Just declare in a /etc/apt/apt.conf.d/99proxy file something like this :

Acquire::http::Proxy {
    your.local.first.repository DIRECT;
    your.second.first.repository DIRECT;

DIRECT tells apt to use a direct connection to connect to the repository.

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