Several solutions come to mind.

On linux, use a journaling file system.  You'll need to dive into the details,
but essentially you checkpoint the directory then update.  I'm not so uptodate
on this method but you should be able to set up BTRFS and do this.

In a similar vein, on MAC, time machine.

On windows set up a checkpoint.  About 4 methods come to mind for windows.  1/
Volume shadow but is a little flakier but in NTFS for a long time.  You can
take checkpoints on a directory, then search on a particular dates.

Right click on a directory then properties.  On the tabs is previous version. 
It has restore points as one option and file history.  In control panel you
can set up a system for backing up, either on a different disk or computer so
that it monitors changes.

Another method is using virtual machines.  These allow snapshots using
differencing.  Index a site then take a snapshot.  You can run multiple VMs
concurrently and browse, or even mount the virtual disks outside of the
virtual machine and easily see a particular version.  Neat thing here is you
can instantly see the size of what has changed.