Use XDocument to do XML operations when generating web.config

parent #778 

@davidfowl , `XmlReader.Create` on CoreCLR always throws exception
```
System.Xml.XmlException: An internal error has occurred.
   at System.Xml.XmlXapResolver.GetEntity(Uri absoluteUri, String role, Type ofObjectToReturn)
   at System.Xml.XmlTextReaderImpl.FinishInitUriString()
   at System.Xml.XmlTextReaderImpl..ctor(String uriStr, XmlReaderSettings settings, XmlParserContext context, XmlResolver uriResolver)
   at System.Xml.XmlReaderSettings.CreateReader(String inputUri, XmlParserContext inputContext)
   at System.Xml.XmlReader.Create(String inputUri, XmlReaderSettings settings, XmlParserContext inputContext)
   at System.Xml.XmlReader.Create(String inputUri)
   at ConsoleApp3.Program.Main(String[] args) in C:\Users\wwa\Documents\Visual Studio Next\Projects\ConsoleApp3\src\ConsoleApp3\Program.cs:line 15
```

So I use
```
XDocument.Parse(File.ReadAllText(webConfigFilePath));
```