Follow-up Comment #1, bug #43363 (project make):
It's fantastic that you've provided reproducible cases (although please attach
the sample files directly to the bug in the future rather than using
pastebin).
However for errors this complex it would be really, really helpful if for each
example you could point to exactly which part of the output you felt was
incorrect and what you think the correct output should be... without that
information it takes a lot of effort to examine every line and determine
whether it makes sense or not.
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