Swapping ctrl and cmd keys on a per-application basis

Mac OS lets you swap ctrl and cmd keys.
Is there a way to have them swapped on a per-application basis?

Basically I’m trying to run a terminal (via “Terminal” or X11 emulator or what not) and have the key mappings re-reversed. (System-wide, I need ctrl and cmd swapped, but that messes up my terminal, so I’d like to unswap them just when running that application)

You can use IronAHK with #IfWinActive.