package.rpc: don't override package-user-dir

Put what we used to override package-user-dir with as the first element
of package-directory-list instead; that way, if a user has packages
installed there, package.el can still find them.

fixes #799

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I'm fairly sure this works, but as this change is a bit delicate, it would be good to have some more "real world" testing before merging it.