Currently, when ever ISPConfig writes to a configuration file, it just makes a backup of the file by copying the file to "~". This not only clutters the system, it is also hard to keep track of changes and who did what (especially if you self are also making changes).
Etckeeper can fill this roll quite nicely, Falko already wrote a guide on how to use it so you guys are familiar with it (https://www.howtoforge.com/using-version-control-for-your-etc-directory-with-etckeeper-and-bazaar-on-debian-squeeze).
I would suggest the following: If etckeeper is installed, after updating or creating a configuration file in /etc, commit it Perhaps the commits can be batched up by using the ISPConfig cron script to commit changes, while always adding a file to git when written (this is done to keep the commit frequency down).
Thanks for your hard work!