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I have an ASP.NET Web API project created on Windows using Visual Studio. How can I set this up for use with DNX/DNVM (on a Mac)?

Switching to Git solved the source control compatibility with TFS. But I wasn't able to find references to getting a project working across both these development environments.

I'm assuming as a first step the project will have to be migrated to ASP.NET 5/vNext but wondering other problems lurk around the corner with different project members using different environments.

I get an error when I run - git:(master):dnx . kestrel

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As you mentioned yes you will have to migrate any namespace changes. I have a project that is developed across both. Also changing csproj files to xproj. Support is coming for some kind of interop between the different project types but its not here yet.

For build, publish, deploy from git without relying on VS publish capabilities or MSBuild you can follow my blog post here.
Basically you use DNU to publish and then kudu to deploy.