What is the best way to keep black holes from spawning on random maps? I'm fine with all other star types, but continuous damage is a no go. I could just edit the continuous damage down to zero, but I'd prefer to remove them entirely.
GalaxyScenarioDef file handles random planet/star types. I'd start there.
What is the best way to prevent Magnetic Clouds and AntiMatter Fountains from spawning on random maps? Alternatively, what is the best way to allow abilities to be used in Magnetic Cloud wells and allow starbases to be constructed in AntiMatter Fountain wells?
A. Same as above. B. Look at the entity files for those "planets". Both abilities and max starbases are set there.
Is there a way to reintroduce automatic mine sweeping to scout ships? Early in beta testing for the original game you could leave a scout in a gravity well and they would automatically seek out mines to be swept even if they were not in range of the reveal mine ability. I don't want to remove mines entirely, and I'd prefer not to buff the detect mine ability to absurd range although that's looking like my best option right now.
Mods like my Enhanced 4X Mod already do this. You could grab the mine sweeping ability files from there.
What is the easiest way to increase level cap on capital ships?
You cannot. You are stuck at 10. You can increase the XP required and the buffs from leveling up on a capitalship by capitalship basis though. I.e. make each level up do more but take longer to get.
What all needs to be changed to allow an additional level of a capital ship ability?
You cannot have more than 4 levels. Otherwise just change the ability entity file and possibly related buff entity files.
When as much as possible of the above is done, where do I put the altered file so it will function as a mod?
Make a folder called "My Mod" in your mod folder (use the "Show Mod Path" button to see where that is from the main menu options). Put any files you mod with folders of the same name in your "My Mod" folder. E.g. "My Mod" -> "GameInfo" -> "GalaxyScenarioDef.GalaxyScenarioDef" for the black hole removal.