У меня возникло бы желание сказать copyfs:
NAME
CopyFS - Versioning File System for FUSE
DESCRIPTION
CopyFS is a copy-on-write, versioning file system for FUSE. CopyFS can
be used to maintain the revision history of a directory containing
files for which you want to track changes, and be able to revert to any
older version. CopyFS lets you do that by transparently making backups
of each file that you modify so that you can review and revert to any
previous revision.
, но вряд ли это можно было бы использовать для всего корневого каталога или для какой-либо системы (не для пользователя).