When upgrading projects with nuget packages from Vx20XX to VS2015, you might have a problem with nuget packages. 
Example of error message:
This project references NuGet package(s) that are missing on this computer. Enable NuGet Package Restore to download them. 
Update 2016-02-06: I had a link to the information but it does not work anymore. I suspect that a recent path has solved the problem ???
I fixed my problem writing a little program that do MSBuild-Integrated package restore vs. Automatic Package Restore
You can download executable of the tool here.
Please let me know the result :-) !

Code as reference:
<Window x:Class="FixNuGetProblemsInVs2015.MainWindow"
        xmlns="http://schemas.microsoft.com/winfx/2006/xaml/presentation"
        xmlns:x="http://schemas.microsoft.com/winfx/2006/xaml"
        xmlns:d="http://schemas.microsoft.com/expression/blend/2008"
        xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006"
        xmlns:local="clr-namespace:FixNuGetProblemsInVs2015"
        mc:Ignorable="d"
        Title="Fix NuGet Packages problems in Visual Studio 2015 (By Eric Ouellet)" Height="350" Width="525">
    <Grid>
        <Grid.RowDefinitions>
            <RowDefinition Height="Auto"></RowDefinition>
            <RowDefinition Height="Auto"></RowDefinition>
            <RowDefinition Height="*"></RowDefinition>
            <RowDefinition Height="Auto"></RowDefinition>
        </Grid.RowDefinitions>
        <Grid.ColumnDefinitions>
            <ColumnDefinition Width="Auto"></ColumnDefinition>
            <ColumnDefinition Width="10"></ColumnDefinition>
            <ColumnDefinition></ColumnDefinition>
        </Grid.ColumnDefinitions>
        <TextBlock Grid.Row="0" Grid.Column="0">Root directory of projects</TextBlock>
        <Grid Grid.Row="0" Grid.Column="2">
            <Grid.ColumnDefinitions>
                <ColumnDefinition></ColumnDefinition>
                <ColumnDefinition Width="Auto"></ColumnDefinition>
            </Grid.ColumnDefinitions>
            <TextBox Grid.Column="0" Name="DirProjects"></TextBox>
            <Button Grid.Column="1" VerticalAlignment="Bottom" Name="BrowseDirProjects" Click="BrowseDirProjectsOnClick">Browse...</Button>
        </Grid>
        <!--<TextBlock Grid.Row="1" Grid.Column="0">Directory of NuGet Packages</TextBlock>
        <Grid Grid.Row="1" Grid.Column="2">
            <Grid.ColumnDefinitions>
                <ColumnDefinition></ColumnDefinition>
                <ColumnDefinition Width="Auto"></ColumnDefinition>
            </Grid.ColumnDefinitions>
            <TextBox Grid.Column="0" Name="DirPackages"></TextBox>
            <Button Grid.Column="1"  Name="BrowseDirPackages" Click="BrowseDirPackagesOnClick">Browse...</Button>
        </Grid>-->
        <TextBox Grid.Row="2" Grid.Column="0" Grid.ColumnSpan="3" Name="TxtLog" IsReadOnly="True"></TextBox>
        <Button Grid.Row="3" Grid.Column="0" Click="ButtonRevertOnClick">Revert back</Button>
        <Button Grid.Row="3" Grid.Column="2" Click="ButtonFixOnClick">Fix</Button>
    </Grid>
</Window>
using System;
using System.Collections.Generic;
using System.ComponentModel;
using System.Diagnostics;
using System.IO;
using System.Linq;
using System.Text;
using System.Threading.Tasks;
using System.Windows;
using System.Windows.Controls;
using System.Windows.Data;
using System.Windows.Documents;
using System.Windows.Forms;
using System.Windows.Input;
using System.Windows.Media;
using System.Windows.Media.Imaging;
using System.Windows.Navigation;
using System.Windows.Shapes;
using System.Xml;
using System.Xml.Linq;
using Application = System.Windows.Application;
using MessageBox = System.Windows.MessageBox;
/// <summary>
/// Applying recommanded modifications in section : "MSBuild-Integrated package restore vs. Automatic Package Restore"
/// of : http://docs.nuget.org/Consume/Package-Restore/Migrating-to-Automatic-Package-Restore
/// </summary>
namespace FixNuGetProblemsInVs2015
{
    /// <summary>
    /// Interaction logic for MainWindow.xaml
    /// </summary>
    public partial class MainWindow : Window
    {
        public MainWindow()
        {
            InitializeComponent();
            DirProjects.Text = @"c:\prj";
            // DirPackages.Text = @"C:\PRJ\NuGetPackages";
        }
        private void BrowseDirProjectsOnClick(object sender, RoutedEventArgs e)
        {
            FolderBrowserDialog dlg = new FolderBrowserDialog();
            dlg.SelectedPath = DirProjects.Text;
            if (dlg.ShowDialog() == System.Windows.Forms.DialogResult.OK)
            {
                DirProjects.Text = dlg.SelectedPath;
            }
        }
        //private void BrowseDirPackagesOnClick(object sender, RoutedEventArgs e)
        //{
        //  FolderBrowserDialog dlg = new FolderBrowserDialog();
        //  dlg.SelectedPath = DirPackages.Text;
        //  if (dlg.ShowDialog() == System.Windows.Forms.DialogResult.OK)
        //  {
        //      DirPackages.Text = dlg.SelectedPath;
        //  }
        //}
        // private string _dirPackages;
        private void ButtonFixOnClick(object sender, RoutedEventArgs e)
        {
            DoJob(false);
        }
        private void ButtonRevertOnClick(object sender, RoutedEventArgs e)
        {
            DoJob(true);
        }
        private void DoJob(bool revert = false)
        {
            TxtLog.Text = "";
            string dirProjects = DirProjects.Text;
            // _dirPackages = DirPackages.Text;
            if (!Directory.Exists(dirProjects))
            {
                MessageBox.Show("Projects directory does not exists: " + dirProjects);
                return;
            }
            //if (!Directory.Exists(_dirPackages))
            //{
            //  MessageBox.Show("Packages directory does not exists: " + _dirPackages);
            //  return;
            //}
            RecurseFolder(dirProjects, revert);
        }
        private void RecurseFolder(string dirProjects, bool revert = false)
        {
            if (revert)
            {
                Revert(dirProjects);
            }
            else
            {
                FixFolder(dirProjects);
            }
            foreach (string subfolder in Directory.EnumerateDirectories(dirProjects))
            {
                RecurseFolder(subfolder, revert);
            }
        }
        private const string BackupSuffix = ".fix_nuget_backup";
        private void Revert(string dirProject)
        {
            foreach (string filename in Directory.EnumerateFiles(dirProject))
            {
                if (filename.ToLower().EndsWith(BackupSuffix))
                {
                    string original = filename.Substring(0, filename.Length - BackupSuffix.Length);
                    if (File.Exists(original))
                    {
                        File.Delete(original);                                          
                    }
                    File.Move(filename, original);
                    Log("File reverted: " + filename + " ==> " + original);
                }
            }
        }
        private void FixFolder(string dirProject)
        {
            BackupFile(System.IO.Path.Combine(dirProject, "nuget.targets"));
            BackupFile(System.IO.Path.Combine(dirProject, "nuget.exe"));
            foreach (string filename in Directory.EnumerateFiles(dirProject))
            {
                if (filename.ToLower().EndsWith(".csproj"))
                {
                    FromProjectFileRemoveNugetTargets(filename);
                }
            }
        }
        private void BackupFile(string path)
        {
            if (File.Exists(path))
            {
                string backup = path + BackupSuffix;
                if (!File.Exists(backup))
                {
                    File.Move(path, backup);
                    Log("File backup: " + backup);
                }
                else
                {
                    Log("Project has already a backup: " + backup);
                }
            }
        }
        private void FromProjectFileRemoveNugetTargets(string prjFilename)
        {
            XDocument xml = XDocument.Load(prjFilename);
            List<XElement> elementsToRemove = new List<XElement>();
            foreach (XElement element in xml.Descendants())
            {
                if (element.Name.LocalName == "Import")
                {
                    var att = element.Attribute("Project");
                    if (att != null)
                    {
                        if (att.Value.Contains("NuGet.targets"))
                        {
                            elementsToRemove.Add(element);
                        }
                    }
                }
                if (element.Name.LocalName == "Target")
                {
                    var att = element.Attribute("Name");
                    if (att != null && att.Value == "EnsureNuGetPackageBuildImports")
                    {
                        elementsToRemove.Add(element);
                    }
                }
            }
            if (elementsToRemove.Count > 0)
            {
                elementsToRemove.ForEach(element => element.Remove());
                BackupFile(prjFilename);
                xml.Save(prjFilename);
                Log("Project updated: " + prjFilename);
            }
        }
        private void Log(string msg)
        {
            TxtLog.Text += msg + "\r\n";
        }
    }
}