I am thinking about putting my whole linux server under version control using git. The reason behind it being that that might be the easiest way to detect malicious modifications/rootkits. All I would naively think is necessary to check the integrity of the system: Mount the linux partition every week or so using a rescue system, check if the git repository is still untempered and then issue a git status to detect any changes made to the system.

Apart from the obvious waste in disk space, are there any other negative side-effects?

Is it a totally crazy idea?

Is it even a secure way to check against rootkits since I most likely would have to at least exclude /dev and /proc ?