tripwire is getting a bit long in the tooth, but still works well and does the job it supposed to (send you emails warning of any and all changes to monitored files - e.g. set it to monitor all files by default and exclude files/dirs you don't care about).
Available pre-packaged for most, if not all linux distros (as well as *bsd). Here's the description from the debian tripwire package:
Description-en: file and directory integrity checker
Tripwire is a tool that aids system administrators and users in
monitoring a designated set of files for any changes. Used with
system files on a regular (e.g., daily) basis, Tripwire can notify
system administrators of corrupted or tampered files, so damage
control measures can be taken in a timely manner.
I also recommend using
git for version control of all important files (and
git push to push changes to a remote repository as a backup to protect against corruption and accidental or deliberate deletion).
And, of course,
etckeeper for automating revision control (
git by default) on
Description-en: store /etc in git, mercurial, bzr or darcs
The etckeeper program is a tool to let /etc be stored in a git, mercurial,
bzr or darcs repository. It hooks into APT to automatically commit changes
made to /etc during package upgrades. It tracks file metadata that version
control systems do not normally support, but that is important for /etc, such
as the permissions of /etc/shadow. It's quite modular and configurable, while
also being simple to use if you understand the basics of working with version