EF.cs

//Some change may be needed here, depending on your version
public static XNamespace edmx = "http://schemas.microsoft.com/ado/2009/11/edmx";
public static XNamespace xmlnsssdl = "http://schemas.microsoft.com/ado/2009/11/edm/ssdl";
public static XNamespace xmlnsedm = "http://schemas.microsoft.com/ado/2009/11/edm";
public static XNamespace xmlnscs = "http://schemas.microsoft.com/ado/2009/11/mapping/cs";
		
void Main()
{
  string rootDir = @"C:\Users\Admin\Documents\visual studio 2013\Projects\ConsoleApplication2\ConsoleApplication2";
  string BackupDestination = @"C:\Users\Admin\Documents\visual studio 2013\Projects\ConsoleApplication2\ConsoleApplication2\Backup";
  string resultFilePath = rootDir + @"\ReportServer.edmx";
  
  string[] files = new string[]
  {
	  rootDir + @"\SimpleAccount.edmx",
  };
	
	Backup(rootDir, BackupDestination);
	MergeEDMX(files, resultFilePath);
	ReplacePrefixes(resultFilePath);
	ReorderNavigationProperties(resultFilePath);
}

private static void MergeEDMX(string[] files, string ResultFile)
{
	Console.WriteLine ("Merging EDMX");

	foreach (string file in files)
	{
		XDocument doc = XDocument.Load(file);
		XDocument docresult = XDocument.Load(ResultFile);
		
		//SSDL
		Console.WriteLine ("Merging SSDL");
		
		MergeNodes(docresult.Root.Descendants(xmlnsssdl + "EntityContainer").First(),
			doc.Root.Descendants(xmlnsssdl + "EntityContainer").Elements(),
			docresult.Root.Descendants(xmlnsssdl + "EntityContainer").Elements(),
			(x,y) => x.Attribute("Name").Value == y.Attribute("Name").Value);
			
		MergeNodes(docresult.Root.Descendants(xmlnsssdl + "Schema").First(),
			doc.Root.Descendants(xmlnsssdl + "Schema").Elements().Where(x=> x.Name != xmlnsssdl + "EntityContainer"),
			docresult.Root.Descendants(xmlnsssdl + "Schema").Elements().Where(x=> x.Name != xmlnsssdl + "EntityContainer"),
			(x,y) => x.Attribute("Name").Value == y.Attribute("Name").Value);
		
		Console.WriteLine ("Done SSDL");
		//CSDL
		Console.WriteLine ("Merging CSDL");
		
		MergeNodes(docresult.Root.Descendants(xmlnsedm + "EntityContainer").First(),
			doc.Root.Descendants(xmlnsedm + "EntityContainer").Elements(),
			docresult.Root.Descendants(xmlnsedm + "EntityContainer").Elements(),
			(x,y) => x.Attribute("Name").Value == y.Attribute("Name").Value);
		
		//Import NavigationProperties. First we go to already existant entities (OldEntities) to read existing NavProp
		//Then we import those Elements to the new entity (NewEntity) in the loop
		
		var OldEntities = docresult.Root.Descendants(xmlnsedm + "EntityType");
		var NewEntities = doc.Root.Descendants(xmlnsedm + "EntityType");
		
		foreach (var NewEntity in NewEntities)
		{
			var OldEntity = OldEntities.FirstOrDefault(x=> x.Attribute("Name").Value == NewEntity.Attribute("Name").Value);
			
			if (OldEntity == null)
				continue;
							
			NewEntity.Add(OldEntity
							.Elements(xmlnsedm + "NavigationProperty")
							.Where(x=> x.Attribute("Relationship").Value.Contains(".LNK_")));
		}
			
		NewEntities = NewEntities.Union(doc.Root.Descendants(xmlnsedm + "Schema").Elements().Where(x=> x.Name != xmlnsedm + "EntityContainer"));
		//
		
		//Merge the itens inside the Schema (except EntityContainer)
		MergeNodes(docresult.Root.Descendants(xmlnsedm + "Schema").First(),
			NewEntities.ToList(),
			docresult.Root.Descendants(xmlnsedm + "Schema").Elements().Where(x=> x.Name != xmlnsedm + "EntityContainer"),
			(x,y) => x.Attribute("Name").Value == y.Attribute("Name").Value);
		
		Console.WriteLine ("Done CSDL");
		//C-S
		
		Console.WriteLine ("Merging C-S");
		
		//Merge the itens inside EntityContainer in the C-S layer
		MergeNodes(docresult.Root.Descendants(xmlnscs + "EntityContainerMapping").First(),	
			doc.Root.Descendants(xmlnscs + "EntitySetMapping"),
			docresult.Root.Descendants(xmlnscs + "EntitySetMapping"),
			(x,y) => x.Attribute("Name").Value == y.Attribute("Name").Value);
		
		//Merge the functions (requires different attribute comparing) 
		MergeNodes(docresult.Root.Descendants(xmlnscs + "EntityContainerMapping").First(),
			doc.Root.Descendants(xmlnscs + "FunctionImportMapping"),
			docresult.Root.Descendants(xmlnscs + "FunctionImportMapping"),
			(x,y) => x.Attribute("FunctionImportName").Value == y.Attribute("FunctionImportName").Value);
			
		Console.WriteLine ("Done C-S");
		
		docresult.Save(ResultFile);
	}
	 
	Console.WriteLine("Done Merging");
}

//Deletes old nodes that exist in a ParentTarget and in the NewChilds when the comparer returns true 
private static void MergeNodes(XElement ParentTarget, IEnumerable<XElement> NewChilds, IEnumerable<XElement> OldChilds, Func<XElement, XElement, bool> ChildComparer)
{
	(from OldFunc in OldChilds
	 from NewFunc in NewChilds
	where ChildComparer(OldFunc, NewFunc)
	select OldFunc).Remove();
	
	//Add new functions
	ParentTarget.Add(NewChilds);
}

//Reorders the navigation properties of an EDMX 
private void ReorderNavigationProperties(string EDMXFilePath)
{
	Console.WriteLine ("Reordering navigation properties");

	XDocument doc = XDocument.Load(EDMXFilePath);
	
	foreach (var Entity in doc.Root.Descendants(edmx + "Runtime")
									.Descendants(edmx + "ConceptualModels")
									.Descendants(xmlnsedm + "Schema")
									.Descendants(xmlnsedm + "EntityType"))
	{
		Entity.ReplaceNodes(
			Entity.Descendants()
			.Where (x => x.Parent == Entity)	//Descendentes directos
			.OrderBy (x => x.Name == xmlnsedm + "NavigationProperty" ? x.Attribute("Name").Value : "a" ));
	}
	
	doc.Save(EDMXFilePath);
	
	Console.WriteLine("Done");
}

//Replace the  prefixes of the other models. 
private void ReplacePrefixes(string FilePath)
{
	Console.WriteLine ("Replacing database prefixes");
	
	string CorrectPrefix = "Model";
	var text = File.ReadAllText(FilePath);
	
	text = text.Replace("SimpleAccountModel", CorrectPrefix);
	
	File.WriteAllText(FilePath, text);
	
	Console.WriteLine ("Done");
}


public void Backup(string source, string destination)
{
	string DoBackups;
	Console.WriteLine ("Do backups first? y/n");
	
	do
	{
		DoBackups = Console.ReadLine();
	} while (DoBackups != "y" && DoBackups != "n");

	if (DoBackups == "y")
	{
		Console.WriteLine ("Performing backups");
		
		DoBackup(source, destination);
		
		Console.WriteLine ("Done");
	}
	else
		Console.WriteLine ("Ignoring backups...");
}

//Backs up all .edmx and .Designer.cs in the Source directory.
public void DoBackup(string Source, string Destination)
{
	DirectoryInfo srcDir = new DirectoryInfo(Source);
	DirectoryInfo dstDir = new DirectoryInfo(Destination);
	
	var files = from file in srcDir.GetFiles()
				where file.Extension == ".edmx"
					|| file.Name.Contains(".Designer.cs")
				select file;
	
	foreach (FileInfo FileName in files)
	{
		if (!dstDir.Exists)
			dstDir.Create();
			
		System.IO.File.Copy(FileName.FullName, dstDir.FullName + "\\" + FileName.Name, true);
	}
}