I'm afraid I don't know enough about the emulator - probably one for @gfwilliams

This is essentially a workaround like #4160 . It is a bit less complex by just doing a complete new initialization of the whole emulator instead of adding logic for waiting for finished commands. I think that should be fixed in the emulators reset methods to prevent internal state surviving.
For now I have removed the testindex stuff from this PR to make this easy to revert when the emulator has been fixed. At least it gets the CI tests working again.

Yes - I guess ideally we'd fix factoryReset. I think the issue is that while sending "reset()" the emulator is still running the old code while characters are sent and interpreted, right until the point the command is run. I think ideally we'd export the jswrap_interface_reset function from the emulator, but until then if this solution works then great - after all it's just for tests so it's not goingto effect the end user