I was thinking, is there any need using the ctrlr files anymore? Dumb question I know but what I mean is, will the new .cfg files get outdated over time? Seems to me with the xml format it shouldn't be so much of a problem as the old cfg files... I'm sure I'm wrong, or the mame devs would've removed ctrlr support altogether...
Currently, AFAIK:
cfg/cfg: All inputs used in the game needs to be listed. Also does inputs and other stuff (counters and mixers).
ctrlr/cfg: You can pick and choose what inputs you want to include (one button, all inputs, even not used input). Only reads the input part (not counters and mixers).
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cfg/cfg: Game and default.
ctrlr/cfg: Game, parent, driver ("neogeo"), and default.
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cfg/cfg: Can have problems if driver is changed (inputs, counters, and/or mixers)
ctrlr/cfg: Will ignore unused parts (designed to be "forward comptable").