Ok, so, first problem I noticed was that I hadn't noticed the "Apply Changes" button in my previous test. Queue up one slap in the face for me.
Second problem, now that I had copied entity.manifest into the mod folder and found the Apply Changes button, applying said changes now makes Entrenchment lock up. I waited for a good while, then finally killed the process. Does it really take an ungodly amount of time to load up if some files aren't in binary or am I still doing something wrong?
If it might be my mod, here's what I'm doing: I've added no new entity files and all the work I've done is on the frigate, planet, and planet module rules already in the game. I've made it so that all frigates are CapitalShip entity types so they can be renamed, as well as making all gravity wells able to support ludicrous amounts of starbases and mines. All planet modules have their capacity costs removed and I'm thinking of making those rename-able, too, by giving them Starbase entity types. So, are there any issues with my mod or am I just implementing it wrong?