See something missing here? I sure do. You don't see it? Does the word "Junction" ring a bell? Not anymore, because Junctions no longer exist as a system. Dreams really can come true~
Implications: If you have an SP with a Junction ability, get rid of it. That includes the 5 levels that the Junction abilities granted. If you still want to equip or wear your SP in some capacity, that's fine. It's all fluff now, so the only thing stopping that is whether or not you want to. Considering how Junctions functioned before, some of you might have really designed your SP's build around it. A common example is a Weapon Junction SP with no HP upgrades. Now... That's not such a good idea. As such, everyone with a Junction-owning SP (and only those people) can rebuild said SP. That means get refunded the Bugfrags that you have spent on that SP, and re-spend those same Bugfrags on the same SP. Removing the Junction ability from your SP is mandatory, but the refund and rebuild are voluntary.
And yes, going from such a clear-cut system to what's basically nothing at all is going to generate a lot of questions, as it's rather hard to read up on the rules of nothing. All those questions will be addressed as they come up.