Run scan before install or update.

Otherwise it is possible to get into a inconsistent state.
For example if an auto detected dependency is removed.
Closes #381
CmdLine upgrade checks for auto detected mods.
Raise a nice error message instead of a null pointer exception.
Close #605
Fix spurious windows.forms reference.
It was coming from the existence of a GUIMod extension method in a namespace with a using system.windows.forms.
Merge pull request #636 from RichardLake/Issue605

CmdLine: Run scan before install/update, better msg on autoinstalled mods.