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What's a filesystem?

The file system is perhaps the most important piece of software on your Mac. It’s also one of the most transparent, at least when it’s working correctly. Every user and every application uses the file system. The file system keeps track of and organizes all of the files on the hard drive, and also determines which users and applications have access to those files. The file system also keeps track of how many files you have and how much space they consume. Every time you look for a file, open a file, move a file, save a file or delete a file, it's the filesystem that is fulfilling that action.

Does CCC support encrypted APFS volumes?

Yes, CCC can backup to and from encrypted APFS volumes (aka FileVault encryption). Note that CCC doesn't play any role in the encryption process – encryption is a function of the volume, not of the tool that's writing a file. If you enable FileVault on your startup disk, then the files on your startup disk will be encrypted. Those files are decrypted on-the-fly by the filesystem when they're opened by an application. Likewise, if you enable FileVault on the destination volume (e.g. via the Security Preference Pane while booted from the backup), then the files on the destination will be encrypted. CCC doesn't have to encrypt those files, they're encrypted on-the-fly by the filesystem as the bits are written to disk.

I heard that APFS has a "cloning" feature. Is that the same as what CCC is doing?

No, the cloning functionality within APFS is completely unrelated to the copying that CCC performs, although in some cases CCC does leverage the APFS file cloning functionality.

APFS cloning allows the user to instantly create copies of files on the same volume without consuming extra storage space. When cloning a file, the file system doesn’t create copies of the data, rather it creates a second reference to the file that can be modified independently of the first file. The two files will share storage on the disk for portions of the files that remain identical, but changes to either file will be written to different parts of the disk. APFS file cloning only works when you make copies of a file on the same volume (e.g. duplicate a file or folder in the Finder). CCC is typically copying files between volumes, so APFS cloning isn't applicable for that kind of task. In some cases CCC may clone a file on the destination prior to updating its contents.

The important take-away is that APFS file cloning can save you space on your startup disk, but CCC backups can save your data if your source disk fails. They serve completely different purposes; APFS file cloning is not at all related to making backups.

Why doesn't the disk usage on my backup disk match the disk usage on the source disk?

CCC's global exclusions as well as the SafetyNet feature have traditionally led to legitimate differences in disk usage in the past. The aforementioned APFS file cloning feature, however, adds a new dimension to this concern. While APFS file cloning saves space on your source volume, those space savings can't be consistently applied when copying your files to another volume. Making matters worse, Finder does not accurately represent the true disk usage of your files. Finder doesn't take into consideration whether one file is a clone of another, rather it sums up the total size of each file and folder, presenting a total value that is possibly astronomically higher than the capacity of the disk.

The disk usage on your source and destination may never add up, and therefore may not be a reliable measure for comparing the source and destination.

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