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You can copy stuff from \Windows to \Program Files\whatever as part of your Rom Kitcen OEM package (there are plenty of examples of this out there), but you'll end up with 2 copies in the final rom. Funky, but works. Only issue there is total rom space used, if its a massive app.
You may be able to tweak your registry entries instead, so any registry references to \Program Files\Foo\bar.exe point to \Windows\bar.exe instead - that's worth a shot to try first.
Subfolders in your OEM package would be ignored, as far as I can tell.
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