Setting up virtual directory throws

[jaykay-design]

Using version 0.9.4
I have set up virtual directories manually like this:
/.well-known => site\wwwroot.well-known (Directory)
/.well-known/acme-challenge => site\letsencrypt.well-known\acme-challenge (Directory)

When using the UI with option "Update Application Settings and Virtual Application (if needed)" i get this exception.

Microsoft.Azure.Management.WebSites.Models.DefaultErrorResponseException: Operation returned an invalid status code 'BadRequest' at Microsoft.Azure.Management.WebSites.WebAppsOperations.d__46.MoveNext() --- End of stack trace from previous location where exception was thrown --- at System.Runtime.CompilerServices.TaskAwaiter.ThrowForNonSuccess(Task task) at System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(Task task) at Microsoft.Azure.Management.WebSites.WebAppsOperationsExtensions.d__83.MoveNext() --- End of stack trace from previous location where exception was thrown --- at System.Runtime.CompilerServices.TaskAwaiter.ThrowForNonSuccess(Task task) at System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(Task task) at Microsoft.Azure.Management.WebSites.WebAppsOperationsExtensions.UpdateConfiguration(IWebAppsOperations operations, String resourceGroupName, String name, SiteConfigResource siteConfig) at LetsEncrypt.Azure.Core.Services.PathProvider.d__4.MoveNext() in D:\a\1\s\LetsEncrypt.SiteExtension.Core\Services\PathProvider.cs:line 0 --- End of stack trace from previous location where exception was thrown --- at System.Runtime.CompilerServices.TaskAwaiter.ThrowForNonSuccess(Task task) at System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(Task task) at LetsEncrypt.Azure.Core.Services.PathProvider.d__3.MoveNext() in D:\a\1\s\LetsEncrypt.SiteExtension.Core\Services\PathProvider.cs:line 43 --- End of stack trace from previous location where exception was thrown --- at System.Runtime.CompilerServices.TaskAwaiter.ThrowForNonSuccess(Task task) at System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(Task task) at LetsEncrypt.Azure.Core.Services.PathProvider.d__6.MoveNext() in D:\a\1\s\LetsEncrypt.SiteExtension.Core\Services\PathProvider.cs:line 92 --- End of stack trace from previous location where exception was thrown --- at System.Runtime.CompilerServices.TaskAwaiter.ThrowForNonSuccess(Task task) at System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(Task task) at System.Runtime.CompilerServices.TaskAwaiter.ValidateEnd(Task task) at LetsEncrypt.SiteExtension.Controllers.HomeController.d__1.MoveNext() in D:\a\1\s\LetsEncrypt-SiteExtension\Controllers\HomeController.cs:line 80

Without using that option and going ahead the page gets stuck on "/letsencrypt/Home/PleaseWait".
I then click on " Nothing happens? click here" and proceed but finally get this exception:

[DefaultErrorResponseException: Operation returned an invalid status code 'BadRequest']
Microsoft.Azure.Management.WebSites.d__46.MoveNext() +3003
System.Runtime.CompilerServices.TaskAwaiter.ThrowForNonSuccess(Task task) +99
System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(Task task) +58
Microsoft.Azure.Management.WebSites.d__83.MoveNext() +260
System.Runtime.CompilerServices.TaskAwaiter.ThrowForNonSuccess(Task task) +99
System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(Task task) +58
Microsoft.Azure.Management.WebSites.WebAppsOperationsExtensions.UpdateConfiguration(IWebAppsOperations operations, String resourceGroupName, String name, SiteConfigResource siteConfig) +52
LetsEncrypt.Azure.Core.Services.d__4.MoveNext() in D:\a\1\s\LetsEncrypt.SiteExtension.Core\Services\PathProvider.cs:0
System.Runtime.CompilerServices.TaskAwaiter.ThrowForNonSuccess(Task task) +99
System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(Task task) +58
LetsEncrypt.Azure.Core.Services.d__3.MoveNext() in D:\a\1\s\LetsEncrypt.SiteExtension.Core\Services\PathProvider.cs:43
System.Runtime.CompilerServices.TaskAwaiter.ThrowForNonSuccess(Task task) +99
System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(Task task) +58
LetsEncrypt.Azure.Core.Services.d__6.MoveNext() in D:\a\1\s\LetsEncrypt.SiteExtension.Core\Services\PathProvider.cs:92
System.Runtime.CompilerServices.TaskAwaiter.ThrowForNonSuccess(Task task) +99
System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(Task task) +58
LetsEncrypt.Azure.Core.Services.d__5.MoveNext() in D:\a\1\s\LetsEncrypt.SiteExtension.Core\Services\KuduFileSystemAuthorizationChallengeProvider.cs:37
System.Runtime.CompilerServices.TaskAwaiter.ThrowForNonSuccess(Task task) +99
System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(Task task) +58
LetsEncrypt.Azure.Core.Services.d__5.MoveNext() in D:\a\1\s\LetsEncrypt.SiteExtension.Core\Services\BaseHttpAuthorizationChallengeProvider.cs:55
System.Runtime.CompilerServices.TaskAwaiter.ThrowForNonSuccess(Task task) +99
System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(Task task) +58
LetsEncrypt.Azure.Core.Services.d__5.MoveNext() in D:\a\1\s\LetsEncrypt.SiteExtension.Core\Services\AcmeService.cs:44
System.Runtime.CompilerServices.TaskAwaiter.ThrowForNonSuccess(Task task) +99
System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(Task task) +58
LetsEncrypt.Azure.Core.d__16.MoveNext() in D:\a\1\s\LetsEncrypt.SiteExtension.Core\CertificateManager.cs:231
System.Runtime.CompilerServices.TaskAwaiter.ThrowForNonSuccess(Task task) +99
System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(Task task) +58
LetsEncrypt.Azure.Core.d__17.MoveNext() in D:\a\1\s\LetsEncrypt.SiteExtension.Core\CertificateManager.cs:244
System.Runtime.CompilerServices.TaskAwaiter.ThrowForNonSuccess(Task task) +99
System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(Task task) +58
LetsEncrypt.SiteExtension.Controllers.d__7.MoveNext() in D:\a\1\s\LetsEncrypt-SiteExtension\Controllers\HomeController.cs:238
System.Runtime.CompilerServices.TaskAwaiter.ThrowForNonSuccess(Task task) +99
System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(Task task) +58
System.Web.Mvc.Async.TaskAsyncActionDescriptor.EndExecute(IAsyncResult asyncResult) +97
System.Web.Mvc.Async.<>c__DisplayClass8_0.b__1(IAsyncResult asyncResult) +17
System.Web.Mvc.Async.WrappedAsyncResult1.CallEndDelegate(IAsyncResult asyncResult) +10 System.Web.Mvc.Async.WrappedAsyncResultBase1.End() +49
System.Web.Mvc.Async.AsyncControllerActionInvoker.EndInvokeActionMethod(IAsyncResult asyncResult) +49
System.Web.Mvc.Async.<>c__DisplayClass11_0.b__0() +58
System.Web.Mvc.Async.<>c__DisplayClass11_2.b__2() +228
System.Web.Mvc.Async.<>c__DisplayClass7_0.b__1(IAsyncResult asyncResult) +10
System.Web.Mvc.Async.WrappedAsyncResult1.CallEndDelegate(IAsyncResult asyncResult) +10 System.Web.Mvc.Async.WrappedAsyncResultBase1.End() +49
System.Web.Mvc.Async.AsyncControllerActionInvoker.EndInvokeActionMethodWithFilters(IAsyncResult asyncResult) +49
System.Web.Mvc.Async.<>c__DisplayClass3_6.b__4() +35
System.Web.Mvc.Async.<>c__DisplayClass3_1.b__1(IAsyncResult asyncResult) +100
System.Web.Mvc.Async.WrappedAsyncResult1.CallEndDelegate(IAsyncResult asyncResult) +10 System.Web.Mvc.Async.WrappedAsyncResultBase1.End() +49
System.Web.Mvc.Async.AsyncControllerActionInvoker.EndInvokeAction(IAsyncResult asyncResult) +44
System.Web.Mvc.<>c.b__152_1(IAsyncResult asyncResult, ExecuteCoreState innerState) +11
System.Web.Mvc.Async.WrappedAsyncVoid1.CallEndDelegate(IAsyncResult asyncResult) +29 System.Web.Mvc.Async.WrappedAsyncResultBase1.End() +49
System.Web.Mvc.Controller.EndExecuteCore(IAsyncResult asyncResult) +64
System.Web.Mvc.<>c.b__151_2(IAsyncResult asyncResult, Controller controller) +13
System.Web.Mvc.Async.WrappedAsyncVoid1.CallEndDelegate(IAsyncResult asyncResult) +22 System.Web.Mvc.Async.WrappedAsyncResultBase1.End() +49
System.Web.Mvc.Controller.EndExecute(IAsyncResult asyncResult) +45
System.Web.Mvc.Controller.System.Web.Mvc.Async.IAsyncController.EndExecute(IAsyncResult asyncResult) +10
System.Web.Mvc.<>c.b__20_1(IAsyncResult asyncResult, ProcessRequestState innerState) +28
System.Web.Mvc.Async.WrappedAsyncVoid1.CallEndDelegate(IAsyncResult asyncResult) +29 System.Web.Mvc.Async.WrappedAsyncResultBase1.End() +49
System.Web.Mvc.MvcHandler.EndProcessRequest(IAsyncResult asyncResult) +45
System.Web.Mvc.MvcHandler.System.Web.IHttpAsyncHandler.EndProcessRequest(IAsyncResult result) +9
System.Web.CallHandlerExecutionStep.System.Web.HttpApplication.IExecutionStep.Execute() +577
System.Web.HttpApplication.ExecuteStepImpl(IExecutionStep step) +132
System.Web.HttpApplication.ExecuteStep(IExecutionStep step, Boolean& completedSynchronously) +163

[jaykay-design]

Ok, so according to the source code a virtual application has to be set up for the challenge directory, but, If I do that then it seems as some setup from the root's application is inherits which is not available in this child application.
I tested accessing the challenge file manually when it is all set up using a virtual directory instead and that seems to work.