Display warning message on the Updates screen when a VCS is in use

[johnbillion]

When a version control system is in use, an appropriate warning message should be shown on the Updates screen, recommending that updates be performed via their VCS instead. The update action shouldn't be blocked, though.

Similarly, for every plugin and theme that has an update available, WordPress should check whether the individual plugin or theme's directory is under version control and present a similar warning because updating a plugin or theme will completely wipe out its directory, therefore allowing version history to be lost.

The WP_Upgrader::is_vcs_checkout( ... ) method can be used to detect VCS usage.