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It seems that with every major untethered Jailbreak Cydia’s servers, as well as many other big repositories will be extremely sluggish or in some cases go offline due to the mass influx of traffic. As such, a general rule of thumb used to be Jailbreak your device and then wait a couple days before you can reliably use Cydia. It looks like this will be less of a problem for the release of the iOS 6.1 Untethered Jailbreak however, as Saurik has chimed in on a Reddit thread that a “pre-primed Cydia” version of Cydia will be deployed upon Jailbreak your device.
This pre-primed version of Cydia will already have a package catalog from all of the default repositories, this means that it does not need to do a full refresh cycle (which is what really pummels the repositories during new jailbreaks). You can read the official explanation from Saurik himself below…
This will not be as serious of an issue this time around; in addition to how every jailbreak this problem is less problematic, planetbeing said he would finally deploy my “pre-primed Cydia” proposal, so when you open Cydia immediately after the jailbreak it will already have a package catalog from all of the default repositories, and will not need to do a full refresh cycle (which is what really pummels the repositories during new jailbreaks): it will only need to grab the diffs. (That’s the one thing I thought random people seeing this conversation may actually want to know; beetling and 0ptimo otherwise correctly covered this suggestion itself.)
There you have it folks! Hopefully Cydia will actually be usable on Sunday when the iOS 6.1 Untethered Jailbreak is expected to be released.