I guess we still need Choose Nodes, but need to merge all the packages...

I wonder why it installed the references at all. Usually it should not add the reference if it already finds one which doesn't have a Paket flag.

(this would also lead to a workaround)

I've also already noticed this behavior, but since it leads to no problems during the build and the result assemblies also have no problems at runtime and it's only weird display in the Solution Explorer, I haven't reported this one ;)

Currently a Choose node is generated per package and contains all assemblies, contained in the package as well as framework ones. Only the references already present without Paket flag will be removed from the list of references to include.

To deduplicate the nodes, we would need to collect framework references together with the conditions when each of it should be inserted and provide separate Choose nodes for them.
When removing packages, we would need to consider which of those references should also be removed, as not referenced anymore by any of the remaining packages.

I have the same behavior. If you add to an empty F# project nuget packages - FSharp.Data and WindowsAzure.Storage you will see System.Xml.Linq twice under References node in the Solution Explorer:

Although I have 3 System.Xml entries and 2 System.Xml.Linq entries in our solution it doesn't affect the build process.

Paket version 3.11.2.0

packet.lock:

  remote: https://www.nuget.org/api/v2
    FSharp.Core (4.0.0.1)
    FSharp.Data (2.3.2)
      Zlib.Portable (>= 1.11) - framework: portable-net45 sl5 win8, portable-net45 win8, portable-net45 win8 wp8 wpa81
    Microsoft.Azure.KeyVault.Core (1.0) - framework: >= net40, wpv8.0
    Microsoft.Data.Edm (5.7) - framework: >= net40, winv4.5, wpv8.0, wpav8.1
    Microsoft.Data.OData (5.7) - framework: >= net40, winv4.5, wpv8.0, wpav8.1
      Microsoft.Data.Edm (5.7)
      System.Spatial (5.7)
    Microsoft.Data.Services.Client (5.7) - framework: >= net40
      Microsoft.Data.OData (5.7)
    Newtonsoft.Json (9.0.1) - framework: >= net40, winv4.5, wpv8.0, wpav8.1
    System.Spatial (5.7) - framework: >= net40, winv4.5, wpv8.0, wpav8.1
    WindowsAzure.Storage (7.1.2)
      Microsoft.Azure.KeyVault.Core (>= 1.0) - framework: >= net40, wpv8.0
      Microsoft.Data.OData (>= 5.6.4) - framework: >= net40, winv4.5, wpv8.0, wpav8.1
      Microsoft.Data.Services.Client (>= 5.6.4) - framework: >= net40
      Newtonsoft.Json (>= 6.0.8) - framework: >= net40, winv4.5, wpv8.0, wpav8.1
    Zlib.Portable (1.11) - framework: portable-net45 sl5 win8, portable-net45 win8, portable-net45 win8 wp8 wpa81```

can you please zip that sample project and attach it here? thanks

Yes, it is in attachment.

ConsoleApplication1.zip

Ok one System.Xml.Linq.dll is coming from FSharp.Data and one from Microsoft.WindowsAzure.Storage

we could somehow store if we already emitted the reference for a given framework and only reference it once. So it would be ommited for Microsoft.WindowsAzure.Storage.

Is it worth it?

I believe this goes into the category of "should fix". It's (I believe) mostly harmless but it's something that can confuse users and is not expected.

so what do we do? removing the second reference?

Reordering choose nodes by grouping by target framework (see @mexx 's comment) is not what I want to do before we know how nuget is doing this in vNext.