Nice to see something as huge as this to come up. Great work.
Still, I haven't seen my mod implemented. I'm probably the worst.
Check the changelog, you are indeed supported now.
EDIT: Downloaded, got all the latest versions of almost all the compatible mods, and am running into this bug directly after selecting the starting aptitude points for my character. The bug only occurs when I have prism freeport enabled, both with and without boss-ships enabled.
Spoiler
429425 [Thread-5] ERROR com.fs.starfarer.combat.D - java.lang.NoClassDefFoundError: Could not initialize class exerelin.campaign.submarkets.PrismMarket
java.lang.NoClassDefFoundError: Could not initialize class exerelin.campaign.submarkets.PrismMarket
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Unknown Source)
at com.fs.starfarer.loading.scripts.ScriptStore.Object(Unknown Source)
at com.fs.starfarer.loading.OoOo.getNewPluginInstance(Unknown Source)
at com.fs.starfarer.campaign.econ.Submarket.<init>(Unknown Source)
at com.fs.starfarer.campaign.econ.Market.addSubmarket(Unknown Source)
at exerelin.world.ExerelinSectorGen.addPrismMarket(ExerelinSectorGen.java:581)
at exerelin.world.ExerelinSectorGen.generate(ExerelinSectorGen.java:775)
at com.fs.starfarer.campaign.save.CampaignGameManager.o00000(Unknown Source)
at com.fs.starfarer.title.OoOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO.dialogDismissed(Unknown Source)
at com.fs.starfarer.ui.do.dismiss(Unknown Source)
at com.fs.starfarer.ui.impl.O0oO.dismiss(Unknown Source)
at com.fs.starfarer.campaign.save.O0oO.actionPerformed(Unknown Source)
at com.fs.starfarer.ui.thisnew.super(Unknown Source)
at com.fs.starfarer.ui.H.processInput(Unknown Source)
at com.fs.starfarer.ui.V.o00000(Unknown Source)
at com.fs.starfarer.new.Òôo000(Unknown Source)
at com.fs.oOOO.oOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO.Ò00000(Unknown Source)
at com.fs.starfarer.combat.D.o00000(Unknown Source)
at com.fs.starfarer.StarfarerLauncher$2.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
If the other settings are relevant I'm using max stars, planets, and stations along with the junk pirates as my starting faction and a non-randomized omnifactory. Faction respawn is on.
Oh, and independant ships seem to spawn from junk-pirate planets despite the pirates being hostile to the independents, though I'm not sure if this is actually a bug or not.