Based on the comments here, I started checking how I could make sure that my Ant build
wouldn’t interfere with my Eclipse build.
I found an option in Eclipse that clears up the problem (and is possibly more efficient than
changing the 2 build system’s output folders).
Windows–>Preferences–>Java–>Compiler–>Building–>Output folder–>
”Rebuild class files modified by others”. This exists in Eclipse 3.5; I’m not sure about earlier versions.
Checking this seems to have fixed my problems