[VersionControl] Check repository state before certain operations.

[mkrueger]

During rebase the version control seemed to do something with the repository that caused an invalid state. It may be the add/remove file handling in version control file system extension to cause that.

This patch prevents the extension to handle add/remove events during a git operation..

Fixes VSTS #900751

[Therzok]

The build failed

[sevoku]

@mkrueger ping wrt build