I really like the TypeScript support and the integration with Test Explorer. The Run All in the Test Explorer is picking up the generated *.js files. I'd like to have it ignore them and only run the *.ts files. Web Essentials is installed and creating the .js and .min.js files when I save. As a work-a-round I've configured it not to generate those files for now.
Comments: Did you try setting the testing mode in the options menu to only include .ts files? 
Comments: Did you try setting the testing mode in the options menu to only include .ts files? 