I'm seeing the same thing in my new game (1.55377081).

https://www.dropbox.com/s/qf6olgalogewj4d/Supernova%20Insider%201.55.377081.8025.GC4Sav?dl=0

Of course maybe the error is just in the name "Precursor Origins" and one of the other Precursor Techs will unlock the ships.  Still needs to be fixed.

Thank you all for verifying this report, Ill share it with the team, I believe there was a similar issue in the base game that was resolved, so its odd to see it pop back up

The Precursor Origins tech requires the Ministry of Justice tech.  The changes to the tech tree in 1.55 removed the Ministry of Justice tech, so the Precursor Origins tech can't appear, so the tier 3 commander ships don't appear for anybody.

The best way to fix this is to change the Precursor Origins tech to require a tech that does exist in the current tech tree.  The tech that seems to be most appropriate is the Colonial Law and Policy tech.

Doing this will repeat a problem that occurred in the base game.  The Colonial Law and Policy tech decreases crime, just like the Ministry of Justice tech.  In the base game, the Ministry of Justice tech had a preclusion added that didn't allow it to appear for races with the Crimelord ability, namely the Xeloxi.  As a result, they could no longer get their tier 3 commander ships.  In the current 1.55 game, there already is a preclusion in the Colonial Law and Policy tech, so the Xeloxi can't get it, so they still won't be able to get their tier 3 commander ships with this fix.

In the base game, the "fix" was "unfixed" by removing the preclusion.  The Xeloxi could now get their tier 3 commander ships, but they also regained access to the Ministry of Justice, which goes against their beliefs and way of life.

The best solution requires a little work.  Before the problem in the base game was "unfixed", I made a mod that "fixed" the problem in a different way.  Here is a brief description of what I did, but updated to use the current tech names.

1. Change the Precursor Origins tech to require the Colonial Law and Policy tech, and add a preclusion so that Crimelords can't get it.  All other races can now get their tier 3 commander ships.
2. Create a new tech that is like the Precursor Origins tech except
   • It has a different InternalName.  I used Crimelords in the name.  I left all other names the same so that the correct text would appear in the new tech.
   • It requires the Political Capital tech, which is the last one Crimelords can get in 1.55.
   • It has a prerequisite so that only Crimelords can get it.
3. Change the blueprints of the two Xeloxi tier 3 commander ships to require the new tech in Step 2.  This is in StaticShipBlueprintDefs.xml.

I think the above are correct and all the steps I did.  I think this fixes everything, but I'm not sure about custom races with the Crimelord Ability.  I didn't use this mod for very long before the original "fix" was "unfixed".

The more knowledgeable people at Stardock would need verify everything or maybe come up with a better solution.

As far as I know, custom races can choose any shipset, thus a civ without the Crimelord ability could choose the Xeloxi shipset, again rendering the top two ships unavailable. Is it possible for the XML to specify that those ships require Precursor Origins OR the new Crimelords tech?

Now that you asked and I have thought about it, I'm sure it can be done.  If so, that would be a more elegant solution that what I mentioned above.

Here is the code that determines what tech is required.

<Prerequ>
<Techs>
<Option>Tech_PrecursorOrigins</Option>
</Techs>
</Prerequ>

I have this vague memory of some other case where I made a mod and added a second option thinking it would require both to exist before it would work.  Instead, it worked if either existed.  I would need to verify all this, but the right people at Stardock should already know which is right.

Since modding in Supernova is so hard now, I may not do anything about verifying any of this.

What has been changed in regards to mods?  I've been trying to figure out why my changes to DEF files aren't sticking.