I wonder if it is possible to use nuget to only store references to the required packages in version control (only the package.config and ignore the packages folder).
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I don't know about your first question.
As for having a CI server automatically update the packages, it's doable in theory. You could chain the "List-Package -Installed" and the "Update-Package" commands and have each package updated to the latest version. See the command reference for further details.
Scott Guthrie says this on the topic:
"You can integrate the command-line option with a CI solution and do an update-package command explicitly as part of your build/CI process to pull down updates. Frankly I'm not sure that makes sense for the scenarios we are talking about, though, as typically you want some dev to decide before updating a core runtime dependency to a new version. NuPack's default model would have a developer use NuPack to install a library - and NuPack would automatically check in the package and dependencies to source control. That way another dev (or the CI server) wouldn't need to use NuPack again - they could just sync their source and build. But as I mentioned earlier - if you wanted to explicitly do an update as part of your CI process you could."
Edit:
After your comment I see what you're trying to achieve. I found this long thread in the NuPack discussions list about the issue. A solution will apparently not be part of v1. A custom build task in the CI of your choice and a config in your repo for it is the only solution I see. Please report back with your findings. You got me interested.