The problem is that at the present time, when you create the package, you specify in the .nuspec file the path to which the file will end up. So right now, everything is pretty hardcoded to go to / Content.
We discussed the possibility of adding virtual folders or placeholders to your .nuspec file. The end user can then define the mapping to say that all $ scripts files go to / public / js, etc.
You can see the discussion here http://nuget.codeplex.com/discussions/256542
We can create a problem for this and make people vote for it.
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