Today I updated my Windows 10 PC to Threshold 2. The update went fine apart from Visual Studio refusing to run any of my Universal Windows 10 projects (including new ones).<
I managed to fix the problem by checking the box "Compile with .NET Native tool chain" under project's "Properties --> Build" -tab.
similarly in official troubleshooting page this Native and cleanup tips are mentioned
Turns out that my Visual Studio projects must be on my C:/ drive and not a storage drive. All fixed.
Since correct answer does not work for me, I found another bad solution: change your package name for debugging purposes.
Important: you should stop debugging via stop button, not via App`s close button.