I found the TypeScript Build tab in the properties of a typescript project. And on that tab was an interesting feature called: 'Combine JavaScript output into file: '. This seems to work like intended but it seems to mess up intellisense for some reason.
When the option to combine the js output files is on, intellisense stops working (ctrl+space doesn't do anything). But syntax highlighting, building, and refactoring still works. It does this until the option is turned off and VS has restarted.
I installed the Visual Studio 2013 Update 2 CTP 2 and removed the original typescript plugin (because it's included in the update?). Web Essentials is enabled, it doesn't crash any more with the new update, and disabling it doesn't fix the intellisense.
What is going on? How do I get this to work?