The manifest target generated by ExtUtils::MakeMaker never removes entries from MANIFEST unless they're matched by anything in MANIFEST.SKIP. That's a feature.
To completely regenerate it from scratch you'll have to delete it first. If you want your manifest target to do something else, you can simply make your Makefile.PL emit a different manifest target, or just define a custom target that does what you mean. -- BOFH excuse #336: the xy axis in the trackball is coordinated with the summer solstice
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