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The resource folder is not supposed to be used for application data like databases. Furthermore resource_filename does not work for Zip file which means that you can fall back to root_folder in all situations anyways except for those where resource_filename of pkg_resources is doing scary things anyways.
I just thought about this to be used for development, not in production. But the zip concern is a valid one (and as there is configuration support now that it's easy to specify a dev db.
There is open_resource, but sometimes one does not need an open file but the filename.
I've thought of something like this: http://paste.pocoo.org/show/217837/
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