Best practice (for any backup tool and not just SpiderOak One or Groups) is to create the group "backup" and add to that group (1) the non-root user that runs the backup application and (2) any files that the backup application would otherwise not have permission to access. Running any user application as root is hazardous and can almost always be avoided through appropriate permissions. For these reasons, running our software as root is discouraged and is not supported.
You can view the groups that files and directories belong to by adding the -l switch to the ls command, and change them with the chown command.
It is also relevant to note that the intended use case for the backup product is backing up a user's personal files, so file permissions should not be a problem. Backing up system files requires additional tools and special procedures.
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