Why to reinvent wheel..?
You could use existing systems, like Debian package-system (deb), RPM-system like Fedora Core/RedHat, or Gentoo's Emerge.
All working, proven technologies.
Would you like to have a go at porting one of them to Windows, then?
Also, what about a GUI?
I would very much like to see an RPM or DEB based Cygwin, but I've never had a suitably large chunk of free time to devote to such an undertaking. I recently tried to get rpm-4.4.1 working on Cygwin, but although it compiled, it segfaulted immediately on startup. Of course, really we would need a native Windows port, which would be even harder.
Max.
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