Thats another thing i’ve been wondering about: why work inside the VM like that? With tech like docker (which I personally use extensively, even inside PHPstorm) i have the very best of performance and still have a clean development machine.
(i.e. no PHP install on my dev, but I’ve mapped my PHP executable in PHPstorm to a docker run command. This too for CodeSniffer which is in comparison with locally installed PHPCS negligibly slower without the hassle of version conflicts per project etc Currently we run Grunt, NPM, PHPCS, Bower, PHP, PHPUnit all from docker 
)
But back on topic: why not add those to a global gitignore in the VM then? I’d rather see you illustrate the best way and explain why then to go against such a commonly accepted method ( https://github.com/github/gitignore / http://augustl.com/blog/2009/global_gitignores/ )