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.