Add empty and non_existent field to backup manifests

Currently, non-existent repos are skipped during backup, the goal is to include them in the backup. For such repositories, the manifest file will consist of a new field, non_existent, set to true. Additionally, an empty field is encoded into the manifest indicating whether the repo is empty. This will help determine if any extra work is necessary(restoring from refs and bundles).

Closes #5787 (closed)