unlink './Makefile';
rename './Makefile', './Makefile.old'
system('nmake clean') if $^0 =~ m/Win32/;
before the call to ExtUtils::MakeMaker to get rid of the old Makefile (which I think is the issue).
Alternatively you can simply EDIT the Makefile after it is created to delete the section that is causing you issues. After the call to MakeMaker add some perl to make any edits you need to keep omake happy.
You can add any amount of cleanup, prompting, etc, etc code to Makefile.PL. For example it is not uncommon to automatically pick a C/C++ compiler based on platform (see Inline::CPP distro Makefile.PL) or hunt down libraries (and prompt if not found) etc, etc.
|