You have a few inconsistencies with capitalization, which causes the game to refuse to load on Linux until a few file names are changed. I had to make the following changes to get it to load:
Already taken care of, but thanks, I shall pay more attention from now on!
In addition, your systems do not show up. I have made the changes you outlined, and I wonder if it comes to other capitalization issues. The mod is loaded (I can see your ships in the codex).
If you see only the Acheron system, it's working as intended: the Scy system is hidden, and you'll have to investigate to find it! (I gave a hint a few messages earlier)
finally found the system your SCI is in, sadly there are no pirates. And the game crashes every time I click intel ...
The intel bug is a vanilla bug because the game try to show the player position on the hyperspace map, witch it can't because the system is hidden. Alex already corrected it in the coming hotfix. In the meantime, don't open intel while in Tartarus.
As for pirates, I don't intend to put some, it wouldn't make any sense with their lore. I'm still thinking about how to deal with the reputation problem, and their double faced nature (half pirates, half smugglers)... I may create a subfaction, it would use vanilla ships and be the only ally of Scy. If you manage to get friendly with them, they would negotiate the open passage to Tartarus and access to their gear. Anyway, no promises as we modders are still familiarizing ourselves with the API to find what's possible and what isn't.