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The Apple File System (APFS) is specifically designed to handle the requirements of modern storage technologies and enhances the integrity and security of macOS. One of its key features is the use of strong encryption, which can be applied to individual files and entire volumes. This encryption is particularly important for protecting sensitive data found in critical macOS directories.

APFS also includes features such as snapshots, which allow the system to create a point-in-time representation of the file system, making it possible to recover lost or changed data effectively. This is critical for system integrity and can protect against data loss during operations like system updates or unintentional deletions.

In contrast, HFS+ (the previous file system used in macOS) does not offer the same level of encryption and protection for files. FAT32 and ext4 are not native file systems for macOS and do not provide the same security features that APFS does. Therefore, APFS is the correct choice as it is built to secure and protect critical directories within macOS, ensuring that the system operates smoothly and securely.