Not sure what vcs is. You provide a link?
a version control system. like git.
As long as you aren’t version controlling al themes/plugins.
What I would do for the themes/plugins on version control, use the individual options and disable plugin and automatic updates for those.
Right now I have everything ina git repo witht he exception of my .htaccess, wp-config, uploads, and cache directory.
So yes I do have themes and plugins in my git repo.
Basically I am fine with with everything getting updated when it comes to security/minor releases. When I have time I go though and update everything locally and push to production. But production always needs to stay secure.
Right now it doesn’t looks like the plugin will update anything including yesterdays minor update because I have it in git. Is this by design and can i change this behavior?
Not at this point, I’m afraid.
I personally avoid version-controlling anything besides individual plugins/themes specifically because of this issue and the many moving parts.
Not sure there is a solution from our end.