Don't try this at home! NuGet will hurt your brain.

nasty.fs

let RemoveFilesFromProj packageInstallPath (package : IPackage) (project : IProjectSystem) (localRepo : IPackageRepository) =
    let packagesConfig = "packages.config"
    let otherPackages =
        (XDocument.Parse <| project.OpenFile(packagesConfig).ReadToEnd())
            .Descendants(XName.Get "package")
        |> Seq.filter (fun p -> p.Attribute(XName.Get "id").Value <> package.Id)
        |> Seq.map (fun p -> localRepo.FindPackage(p.Attribute(XName.Get "id").Value, new SemanticVersion(p.Attribute(XName.Get "version").Value), true, true))
    let inUseByOtherPackages =
        otherPackages
        |> Seq.map (fun p -> getFiles project p)
        |> Seq.reduce
            (fun acc next -> 
                let a, f, c, b = acc
                let a', f', c', b' = next
                (Seq.append a a', Seq.append f f', Seq.append c c', Seq.append b b'))
        |> fun (a, f, c, b) ->
                Seq.distinctBy (fun (assembly : IPackageAssemblyReference) -> assembly.Name) a,
                Seq.distinctBy (fun (frameworkRef : FrameworkAssemblyReference) -> frameworkRef.AssemblyName) f,
                c
                |> Seq.filter (fun (contentFile : IPackageFile) ->
                    not <| fileTransformers.ContainsKey(Path.GetExtension contentFile.EffectivePath))
                |> Seq.distinctBy (fun contentFile -> contentFile.EffectivePath, contentFile.TargetFramework.Version),
                Seq.distinctBy (fun (buildFile : IPackageFile) -> buildFile.EffectivePath, buildFile.TargetFramework.Version) b
    let assemblyReferencesToDelete, frameworkReferencesToDelete, contentFilesToDelete, buildFilesToDelete =
        let a, f, c, b = getFiles project package
        let a', f', c', b' = inUseByOtherPackages
        Seq.filter (fun (assembly : IPackageAssemblyReference) -> Seq.exists (fun (assembly' : IPackageAssemblyReference) -> assembly.Name = assembly'.Name) a' |> not) a,
        Seq.filter (fun (assembly : FrameworkAssemblyReference) -> Seq.exists (fun (assembly' : FrameworkAssemblyReference) -> assembly.AssemblyName = assembly'.AssemblyName) f' |> not) f,
        Seq.filter (
            fun (contentFile : IPackageFile) -> 
                Seq.exists (
                    fun (contentFile' : IPackageFile) -> 
                        (contentFile.EffectivePath, contentFile.TargetFramework.Version) = (contentFile'.EffectivePath, contentFile'.TargetFramework.Version)) c' |> not) c,
        Seq.filter (
            fun (buildFile : IPackageFile) -> 
                Seq.exists (
                    fun (buildFile' : IPackageFile) -> 
                        (buildFile.EffectivePath, buildFile.TargetFramework.Version) = (buildFile'.EffectivePath, buildFile'.TargetFramework.Version)) b' |> not) b
    project.DeleteFiles(contentFilesToDelete, otherPackages, fileTransformers)
    assemblyReferencesToDelete |> Seq.iter (fun a -> project.RemoveReference(a.Name))
    buildFilesToDelete
    |> Seq.map (fun bf -> Path.Combine(packageInstallPath, bf.Path))
    |> Seq.iter (fun fullPath -> project.RemoveImport(fullPath))