safe files put dir will include hidden files. As https://github.com/maidsafe/sn_api/blob/master/sn_cli/README.md#files-sync already refers to rsync, it would be very helpful if safe files add and safe files put supported rsync’s basic exclusion option.
–exclude=PATTERN exclude files matching PATTERN
safe files put --exclude='.*' dir would then solve the case of including unwanted hidden files.