Filesystem-level encryption
Filesystem-level encryption, often called file or folder encryption, is a form of disk encryption where individual files or directories are encrypted by the file system itself. This is in contrast to full disk encryption where the entire partition or disk, in which the file system resides, is encrypted.
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General-purpose file systems with encryption
Unlike cryptographic file systems or full disk encryption, general-purpose file systems that include filesystem-level encryption do not typically encrypt file system metadata, such as the directory structure, file names, sizes or modification timestamps. This can be problematic if the metadata itself needs to be kept confidential. In other words, if files are stored with identifying file names, anyone who has access to the physical disk can know which documents are stored on the disk, although not the contents of the documents.
Cryptographic file systems
Cryptographic file systems are specialized (not general-purpose) file systems that are specifically designed with encryption and security in mind. They usually encrypt all the data they contain R**; including metadata. Instead of implementing an on-disk format and their own block allocation, these file systems are often layered on top of existing file systems e.g. residing in a directory on a host file system. Many such file systems also offer advanced features, such as deniable encryption, cryptographically secure read-only file system permissions and different views of the directory structure depending on the key or user.
Filesystem level encryption
Though James points out that random files in home directories including backups were deleted because of some file system error. Thanks for that. Though how am I able to find out if my filesystem has any errors/mistakes or corruptivity?