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Feel free to recommend a better title or changes to my explanation below!
I am using Windows Azure Websites (for the first time) and have connected it to a solution in Visual Studio Online (also my first time). I was also able to connect to Visual Studio Online, create a project, throw up a master page and web form connected to a master page and my Azure website updated itself. Great!
My Issue
If I add another project to the solution it seems that this new project overwrites the files in the first one. I can't figure out how to set this up so:
Project 1 -> deploy to wwwroot (happens by default great!)
Project 2 -> deploy to wwwroot/sub/directory/ (doesn't seem to work)
Could somebody explain how to configure project 2 so that when the solution auto deploys to an Azure Website that it goes to a specific location?
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Create or open an Azure cloud service project in Visual Studio. In Solution Explorer, right-click the project, and, from the context menu, select Convert > Convert to Azure Cloud Service Project. In Solution Explorer, right-click the newly created Azure project, and, from the context menu, select Publish.
Scroll all the way to the bottom then add a new application where ever you want like Project2 below. 
Basically the 'Project2' part is the URL after the root '/' and the 'site\wwwroot\Project2' is where the actual folder should live under the site root
Download the publishing profile and import it in Visual Studio, then add the application name after your site name like below. Also remember to update the destination URL as well
hope that helps
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