Squid, like all HTTP intermediaries these days doesn't really pipeline - its insecure and problematic. APT should open more connections rather than pipeline (this is mandated by the current HTTP WG recommendations - the '2 per server' connection limit is gone, replaced by a 'be sensible' exhortation instead.
Its possible squid has a bug here, in which case I'd expect wireshark analysis to help show it up. However, its very unlikely to simply be a concurrent request issue - squids regularly handle thousands of concurrent requests. -Rob
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