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The Metatag module needs to be able to automatically import settings from Nodewords during its hook_install() implementation to make the upgrade process seamless. If possible this should be included with v1.0.
Once we have reached a 1.0 release, one of the immediate tasks to be done is to work on a migration script from Nodewords for D6 to Metatags. We'll likely have to try and support both 6.x-1.x and 6.x-2.x branches. Leaving as postponed for now as this is *not* a stable release blocker.