Since release 0.11, -R option has been removed and now all directories are scanned recursively.
This means most of the commands can be shorter. E.g. searching for duplicates in the current folder is now just fclones .
You can force non-recursive scans by adding --depth 0.
Additionally fclones validates input paths before running. If any of the input files is not readable, fclones will terminate with an error.