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Site running as Azure Web App throws exception on startup

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We're developing a new Commerce solution and we have test/prod environments running as web apps in Azure with automated deployment. 

I configured the solution for Azure using this documentation, and initially it worked fine - but when I made a new deploy to test today, we got this exception on startup:

[NullReferenceException: Object reference not set to an instance of an object.]
   EPiServer.Web.Hosting.VirtualPathRegistrationHandler.CreateVirtualPathProviderInstance(ProviderSettings providerSettings) +59
   EPiServer.Web.Hosting.VirtualPathRegistrationHandler.RegisterVirtualPathProvidersFromSettings(ProviderSettingsCollection settings) +172
   EPiServer.Web.Hosting.VirtualPathRegistrationHandler.RegisterVirtualPathProviders(InitializationEngine context, ProviderSettingsCollection settings) +40
   EPiServer.Framework.Initialization.Internal.VirtualPathProviderInitialization.RegisterVirtualPathProviders(InitializationEngine context) +179
   EPiServer.Framework.Initialization.Internal.ModuleNode.Execute(Action a, String key) +54
   EPiServer.Framework.Initialization.Internal.ModuleNode.Initialize(InitializationEngine context) +122
   EPiServer.Framework.Initialization.InitializationEngine.InitializeModules() +247
[InitializationException: Initialize action failed for Initialize on class EPiServer.Framework.Initialization.Internal.VirtualPathProviderInitialization, EPiServer.Framework.AspNet, Version=11.3.2.0, Culture=neutral, PublicKeyToken=8fe83dea738b45b7]
   EPiServer.Framework.Initialization.InitializationEngine.InitializeModules() +774
   EPiServer.Framework.Initialization.InitializationEngine.ExecuteTransition(Boolean continueTransitions) +198
   EPiServer.Framework.Initialization.InitializationModule.EngineExecute(HostType hostType, Action`1 engineAction) +876
   EPiServer.Framework.Initialization.InitializationModule.FrameworkInitialization(HostType hostType) +225
   EPiServer.Global..ctor() +103
   ASP.global_asax..ctor() +42

It's been about a month since last time I deployed to this environment, and the codebase has changed a lot (and we've also installed new versions of EPiServer Nuget packages), so it's hard to say what change has caused this (if any). It works fine locally. 

Would very much appreciate it if anyone could give us a nudge in the right direction here.

Versions are: EPiServer.CMS v.11.3.2, EPiServer Commerce v.11.6.1


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