Suggestion: add a checkbox to each ability on each building, to set whether the readiness state of that ability turns the building button white or not. For example: I don't care if Temple of the Star has Meditate ready to use, but very much DO care if Battle Regulators is ready.
Your game is coming along quite well. As a fellow dev, let me know if there's anything with which you might like assistance or just a second set of eyes.
Yeah, altering the AI so that enemy ships prefer to clear all of your ships out before attacking the reactor would make getting past level 6 possible on a regular basis.
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