Do not fail certificate validation because some files in Jenkins Home are not actually certificates

- If there are any files in `$JENKINS_HOME/update-center-rootCAs` that are not ending in `.txt` and are
  not valid certificates, do not blow up the entire certificate checking (and hence the ability to see updates
  or tool installers) but rather ignore those files and warn the user that the file should not be there.
  The correct thing to do is only use as trusted certificates those certificates that parse.

- Also fix resource leak