Use of package.yaml can be confusing when the user doesn't expect it - see #3380 . I think this case should somehow be detected and a noisy warning emitted.
One way to do this might be to output a copy of the *.cabal on hpack generation. Then, when later re-generating, check if the cabal file changed since the last hpack generation. If so, then the user modified it and a noisy warning should be displayed.
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