I did.
Working for the Kol Battleship, I wanted to add small point defense lasers, so I copied all of weapon-1 (10 weapon points) and added 10 the the NumPoints, (29-39), renaming my copied points weapon-3.
After a little test, I found that they can't have four weapons, so I added weapon-2s to weapon-0, and renamed all weapon-3s to weapon-2s. Adjusted the .entity file so that weapon-0 was the lasertech weapon, weapon-1 was the autocannon, and now weapon-2 was the point defense beam weapon.
Since I have a copy of the entire game elsewhere, I was altering the actual game's files. When I loaded the game, it worked. It showed the new weapon, and the animations were only a little off.
However, I replaced the modded files with the original again, and put the modded capital.entity and .mesh into a gameinfo folder in the mod folder. Now I get a minidump... If it worked in system, it should work in mod, right?
Edit: I was working with Diplomacy, so I made sure I had an Entrenchment folder, with the .entity inside a GameInfo folder, and outside the Entrenchment, I had a mesh folder, since Entrenchment didn't update most of the meshes, so I'm pretty positive I put them in the right places.