Fix very broken clean.bat for msvc install. The way we used subroutines

Fix very broken clean.bat for msvc install. The way we used subroutines
in .bat simply did not work, and it called them in the wrong order,
some several times, and some not at all. So this unrolls all subroutine
calls.

This should fix the issues with clean deleting the wrong files reported
by Dave Page.

While at it, add the "clean dist" option to act like "make distclean",
and no longer remove the flex/bison output files by default. This shuold
fix the problem reported by Pavel Golub in bug #3909.