As far as I can tell from this happening to me recently, you get this
when you have a text file with unix line-endings in your local working
directory. It is just warning you that it will convert to crlf line
endngs when it commits to the repository. If you force a checkout of
the file I suspect this will clear up automatically. If the file needs
to remain unix line endings then edit .gitattributes to include this
file path and -crlf to prevent automatic line ending conversion.
Looking cache.c it seems the warning is controlled by the checksafe
variable which can be one of SAFE_CRLF_FALSE, SAFE_CRLF_FAIL,
SAFE_CRLF_WARN
This appears to be set from core.safecrlf (in config.c).
So I reckon if you set core.safecrlf to false it will silence the warnings.
(I have not tried this yet).