Add option to flip A and B on-the-fly within the config.txt

[serbinsh]

@amcmahonBNL I was thinking it might be a good idea to allow for this since we may have data collected with the channels flipped and then not flipped. This way we avoid hard-coding this and instead allow for flipping if we need to. I suspect we could enable this in the config? Maybe having a section where you input what channel is A and which is B?