Enhancement: Improve handling of directories with duplicate entries

If for some reason a directory contains a duplicate entry, this caused the
backup command to fail with a `node "path/to/file" already present` or `nodes
are not ordered got "path/to/file", last "path/to/file"` error.

The error handling has been changed to only report a warning in this case. Make
sure to check that the filesystem in question is not damaged!

https://github.com/restic/restic/issues/1866
https://github.com/restic/restic/issues/3937
https://github.com/restic/restic/pull/3880
