Your on the right track. You want them in MSI form actually as that's actually whats stored in the DB and contains the version information of the config. Later you can just import it right back from the MSI if needed using "add package".
Awwww - I was so close! I saw Add Package but never bothered to see what files it filtered - and it clearly that MSI is one of them! So close :-)
Thanks for the fast response - I can get cracking with my clean up now.