In all but the largest of organisations, transparent proxies are rare in
my (admittedly limited) experience.  Transparent proxies are pretty damn
expensive because in order to be transparent, they must be a hop on the
way to your internet connection - therefore, they see ALL traffic, not
just web.  Therefore, they must be exceedingly powerful, at least
compared to explicit proxies.  Plus, if a non-cluster transparent proxy
fails, you lose everything until the hardware is fixed, or bypassed.
With explicit proxies, you can usually just push a group policy change
(in an AD environment anyway) to tell the browsers to go direct (and
open your firewall accordingly).  Anyway, implementation aside, this is
still an issue for anyone using Ubuntu in an environment where port 80
is closed and explicit proxies are your only route to the internet.

And yep - volunteer led.  I get it.  That's why I'm filing against this
report.  However, I don't know the first thing about how to recode
Synaptic to make use of Gnome-led initiatives such as
preferences/Network Proxy when using wget.  In fact, I don't program at
all - I'm a network and security analyst and Ubuntu enthusiast.  If any
of my talents become applicable to resolving a bug in Ubuntu, I'll do my
best to help.

For now, I'm just happy that I've managed to introduce Ubuntu to my
corporatation (albeit in a small way) and if this bug is nailed, it's
got more chance of taking off.

-- 
Synaptic does not use proxy in some cases
https://bugs.launchpad.net/bugs/232469
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