You probably noticed from the chat log that I was contemplating taking the terran but hesitated. Fatal mistake, turned out.
The fatal mistake was going back for that ice, as it turns out. What you need to do is scout, you need to know where your opponent is and how far away he is. If you'd have sent a scout over there, you'd have known he had just taken the planet. You could have literally walked in and started bombarding before he got any defenses up, and because your fleet was already on the field he'd have been forced to retreat and leave you the planet.
His economy was primarily neutral-extractor. There were multiple uncolonizable gravity wells near his start position that were littered with extractors, and these are big money. If you could have taken the terran, you could have gone one step further and started grabbing his neutrals, which would have absolutely devastated his income.
I did get the starbase up and running at the desert planet but he essentially ran around it and pressed towards the roid next to it.
That's the normal response. You have to be prepared for that, but on the upside he loses all antimatter and 20% of his remaining hull points by bypassing a starbase. This is a huge blow to his fleet and leaves him very vulnerable to counter-attack. You have to be ready to deliver that counter-attack, or the antimatter and health will just come right back.
How do I keep ships that are built in a contested well from leaving the factory and heading straight into battle via auto-attack mode?
After every ship is built you have to manually switch it to "hold position" behavior. It's annoying, but you have to do it.
