I had not crafted in a few months and I went to MA yesterday and noticed that things have changed.
It seems though, that I am having to start over, with Mk II stuff (with one character but not with another). Is this an accurate perception or did I miss something?
I only discovered the changes when I played Vault for about the 10th time and I changed the way I talked with Obisek. Some data appeared that I had not seen before in the Vault and this new data (the orange data) caused me to go to Memory Alpha.
I saw a crowd at the crafting area, so I suspect people like the changes. I have seen ships with Borg stuff on them. Is this Borg stuff from crafting?
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As for the borg equipment, no. You obtain those pieces by completing the 3 Borg STFs (Infected, Cure & Khitomer Accord) and there is a console in the 'Assimilation' mission now.
You can craft the Aegis set though, which gives your ship a nice Tron makeoever, if you will.
You shouldn't have to start over. If you maxed all three branches out out in the previous system, you had 1500 in the new single-level system, which gives access to mk X. The scale goes up to 1600 and change for mk XI. Though if you only had General R&D maxed out in the old system and hadn't gone far down the three specialized branches you might not have ended up very far down the new scale.
Anyway, the orange data are scematics. You make schematics with the low level red samples, and then use them in place of the old vendor money sink items when making actual items.
There's a crowd there because there is some really good stuff to make - mk XI purple just about everythings, and many items have preferrable bonuses over emblem gear.
You should be able to make at least the Mark level you made before the changes. You will need to work it up to near maximum if you want to make the sets.