Konstantin Khomoutov writes on the fossil-users mailing list:

I'm just handwaving, but Git's code base recently received some
modifications to specifically deal with issues a native Mac OS X
filesystem have with regard to UTF-8.  AFAIK the deal was about that
filesystem pefrorming one of standard UTF-8 normalizations either when
writing or when reading (or both) so that when you create a directory
entry and then read it back, you might get an octet string different
from that you wrote.

See the extensive commit message in [1] and [2] in general.

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