Feature swaptiles

[diaza]

A final incomplete PR, I'll leave the rest to you all.

This PR should allow tile swaps for 2x2. This should be pulled in conjunction with the PR in larnd-sim.

The only validation I've done is look at the outputs of calib_prompt_hits, and the outputs are identical to develop if I only look at the fields ['id', 'x', 'y' 'z', 't_drift', 'ts_pps', 'io_group', 'Q_raw', 'Q', 'E'].

calib_final_hits, on the other hand, is not matching with develop. I corrected develop by adding channel_threshold_file: 'data/proto_nd_flow/thresholds_2x2.swapped.json' ( I believe it was defaulting to the unswapped version before) to yamls/proto_nd_flow/resources/RunDataMC.yaml, but that didn't seem to help. I'll leave that to you...

The remaining input files to update are the disabled channels/chips. I don't have the unswapped versions available. @jaafar-chakrani?

The file 2x2.yaml in this repo, the one copied in scripts/proto_nd_scripts/get_proto_nd_input.sh, and the one in the develop branch in larnd-sim, have all diverged a bit. I've kept the 2x2.yaml curled in scripts/proto_nd_scripts/get_proto_nd_input.sh, updated it to include the updated tile_map, and removed the curling from scripts/proto_nd_scripts/get_proto_nd_input.sh.

The update in src/proto_nd_flow/resources/geometry.py takes into account that tile_map now has an entry for each module, instead of only one.

I also noticed that the layouts used in yamls/proto_nd_flow/resources/GeometryData.yaml for data were slightly outdated, so I also updated those.