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I've often wondered the same. You basically end up having to have all three in your init.el file, since there doesn't appear to be a good rhyme or reason are to which packages are contained in which repositories.

As I've said elsewhere, we will sort this out in the end. Right now MELPA tends to be the latest and greatest and marmalade is more stable (read 'less exciting') releases. It would be good to have this recognized per-package though so hopefully we will merge the strategies of both repositories into a single repository that can do any one of those things for any package configuration.

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