Comment 13 for bug 67589

The Ubuntu package "etckeeper" uses a similar hack to version the /etc directory. It stores all non-standard file ownerships (that is, user/group != root) and non-standard permissions (mode != umask) in a versioned file /etc/.etckeeper. This file is formatted like a shellscript, which when executed will reset all ownerships and permissions to the values stored within.

This approach has the merit that it's compatible among all VCS' supported by etckeeper (bzr, git, mercurial), though it effectively keeps file metadata detached from the file it belongs to and doesn't understand keeping ancestry on renames. etckeeper has worked nicely for my machines so far, though I can imagine its permission approach could cause trouble later on.