After some searching, I found that Building Arduino - Steps for First Time Setup was good. It was tricky to find; most searches for 'Build Arduino' assume it's a project with an Arduino, rather than the IDE.
By building this way, I could change the source, then inside the build folder run ant run. So, no need to actually know where it goes.
I had a problem ...
You can't just "find and replace" that file.
Java isn't distributed as source code. It's compiled "bytecode" that isn't modifiable by a human.
You would need to download all the source code, make your changes to it, and then recompile it.
Or, simpler: just use a more capable serial terminal program, such as "Putty" or "...