Autoupdate: Provide a better information if plugins are under version control or not

Currently we do a simple check if the site is under version control and then disable the autoupdates. If that is the case. This prevents the user from doing autoupdates on plugins even if they are not under version control or any other files for that matter.

We should provide a better way to check if the directory is under version control then core ( or even update core ) and only then not allow the file mods from happening.

This would include checking ignore files for specific directories in the case of git for example.