This won't work. "make bootstrap" must be preceeded by "configure",
and if configure.bat does not have the right line ends, then that will
fail.
This situation worries me less: if configure.bat fails to run, the
user will know something is wrong with the batch file. It's the
mysterious error message produced by Make that prompted my suggestion.
I've seen 2 Emacs maintainers trip on this just this last month.
But if you have a better idea, I'm open to suggestions.
(Btw, my testing indicates that cmd.exe from Windows 2K and XP
succeeds running a batch file even if its lines end in the Unix-style
single LF, and also if there's more than one CR character before the
newline.)