Just went through both the Alpha Kit and the Expansion Modules and found a couple of issues, one breaking the AE toggle (Doesn't matter for CR), another being an issue that occurred as a result of Kestrel B's new cloak, and the latter being inconsistent with the Alpha kit.
[Alpha kit only] There are AE systems on the Flagship Construction without a vanilla version for when AE is disabled.
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<shipBlueprint name="BOSS_SPECIAL" layout="boss_con" img="boss_con">
<class>Rebel Flagship Construction</class>
<systemList>
<pilot power="3" room="0"/>
<shields power="4" max="8" room="1"/>
<teleporter power="1" max="2" room="3" start="false"/>
<medbay power="1" max="2" room="5"/>
<engines power="2" max = "6" room="8"/>
<oxygen power="1" max="2" room="7"/>
<hacking power="1" max="2" room="2" start="false"/>
<mind power="1" max="2" room="4" start="false"/>
<artillery power="2" max="3" room="9" weapon="ARTILLERY_BOSS_1"/>
<artillery power="2" max="3" room="10" weapon="ARTILLERY_BOSS_2"/>
</systemList>
<weaponList count="0" missiles="20"/>
<health amount="15"/>
<maxPower amount ="14"/>
<boardingAI>sabotage</boardingAI>
<crewCount amount= "5" max="8" class="human"/>
</shipBlueprint>
This will lead to the Incomplete Flagship having either Hacking or Mind Control regardless of the AE Toggle. I've address this for my fixes module by removing the AE systems from the shipBlueprint (But adding a combat-based drone control system to make up for the difficulty), and making an Override version with the standard systems (with the chance of the same Drone Control System for good measure).
I'll lend you my own fixes to save some time. (Just don't fix the issue while you're half asleep)
Replaces "BOSS_SPECIAL" in "blueprints.xml"
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<shipBlueprint name="BOSS_SPECIAL" layout="boss_con" img="boss_con">
<class>Rebel Flagship Construction</class>
<systemList>
<pilot power="3" room="0"/>
<shields power="4" max="8" room="1"/>
<teleporter power="1" max="2" room="3" start="false"/>
<medbay power="1" max="2" room="5"/>
<engines power="2" max ="6" room="8"/>
<oxygen power="1" max="2" room="7"/>
<drones power="4" max="6" room="6" start="false"/> <!-- You can change or remove this if your want to -->
<artillery power="2" max="3" room="9" weapon="ARTILLERY_BOSS_1"/>
<artillery power="2" max="3" room="10" weapon="ARTILLERY_BOSS_2"/>
</systemList>
<weaponList count="0" missiles="20"/>
<droneList drones="10" load="DRONES_COMBAT"/> <!-- You can change or remove this if your want to -->
<health amount="15"/>
<maxPower amount ="14"/>
<boardingAI>sabotage</boardingAI>
<crewCount amount= "5" max="8" class="human"/>
</shipBlueprint>
Insert into "dlcBlueprintsOverwrite.xml" (Should take place of "BOSS_SPECIAL" when AE is enabled)
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<shipBlueprint name="OVERRIDE_BOSS_SPECIAL" layout="boss_con" img="boss_con">
<class>Rebel Flagship Construction</class>
<systemList>
<pilot power="3" room="0"/>
<shields power="4" max="8" room="1"/>
<teleporter power="1" max="2" room="3" start="false"/>
<medbay power="1" max="2" room="5"/>
<engines power="2" max = "6" room="8"/>
<oxygen power="1" max="2" room="7"/>
<hacking power="1" max="2" room="2" start="false"/>
<mind power="1" max="2" room="4" start="false"/>
<drones power="4" max="6" room="6" start="false"/> <!-- You can change or remove this if your want to -->
<artillery power="2" max="3" room="9" weapon="ARTILLERY_BOSS_1"/>
<artillery power="2" max="3" room="10" weapon="ARTILLERY_BOSS_2"/>
</systemList>
<weaponList count="0" missiles="20"/>
<droneList drones="10" load="DRONES_COMBAT"/> <!-- You can change or remove this if your want to -->
<health amount="15"/>
<maxPower amount ="14"/>
<boardingAI>sabotage</boardingAI>
<crewCount amount= "5" max="8" class="human"/>
</shipBlueprint>
The second issue is related to the Kestrel B's cloaking image. When you were importing my version of the Cloaking image, you forgot to change the cloak coordinates to x="0" and y=0", this would result in a misplaced cloak when the Kestrel B ever activates the Cloaking Device.
[Applies to both Expansions] The third issue is that the misc.rawclobber files in both
Insurrection or
Captain's Remix are inconsistent with the Alpha kit's misc file, leading to different Stat names, system descriptions, and warning notes when installing a system during an event. Before you go and address all of these inconsistencies, I would also like to warn the half-awake version of yourself that
some of text's changed in both expansions are probably intentional (CR's Non-AE warning, Hiding "Augment:" in the rewards box, Changed cargo tip for lore stuff, Additional Credits, and all lore descriptions) and shouldn't be changed/removed for obvious reasons. (So you don't "shoot yourself in the foot" while fixing the issue.)
[Insurrection Suggestion] I would also like to make a change to the Beacon Access Kit in Insurrection, let it automatically gain map data only for the Start of the game. This would allow the Insurrection variant of Stealth C to gain map data and not risk an early game disadvantage/instant restart. (You can make the Beacon Access Kit link to the same AUTOMAP event as Adv. FTL Navigation and it will still allow you to hack the beacon for other stuff, or trigger the alarm and let the Fleet get you.)
