Follow-up Comment #4, bug #41331 (project wget):

Having a file that is not a certificate is not something broken. The message
is distracting and can make more useful messages less visible.

Also, wget is not the right tool to see if something is broken in the
certificate directory. Even if something is broken, when I run wget, I don't
want to be distracted by any error that doesn't affect the current download.

I have a script (which is run by cron every night, but can also be run
manually, e.g. after updating the certificates) that does a

  openssl verify -CApath . *.{crt,pem}

so that I can see whether something is wrong, such as an expired certificate.
BTW, that's this script (and another one) that makes wget complain. I've put
it in the directory so that everything related is at the same place (and if I
move or rename the directory, I don't have to update the script).

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  <http://savannah.gnu.org/bugs/?41331>

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