d3d: Fix silly typo in stencil handling.

Now it works.
Clear alpha only when clearing stencil.

Not sure if this will fix anything.
Warning fixes
Rebase RadarNyan work on Generate version while build on Wiondows
Merge branch 'windows-exe-version' of https://github.com/RadarNyan/ppsspp into verbuild

Conflicts:
	Windows/version.rc