typescript automatically creating js files after running npm start

The issue is most likely with your tsconfig.json - this is the file (usually located in your project root, alongside package.json) that contains the configuration for your TypeScript build. By default, it just compiles the files in place, leading to the situation you're describing where your source folder fills up with compiled Javascript files. The options you'll need to add will depend on what you want the end result to be:

If you want all the resulting files to be concatenated into a single output file:

{
    "compilerOptions": {
        "outFile": "./dist/app.js"
    }
}

If you want all the resulting files to be output into a separate folder (but still as individual files):

{
    "compilerOptions": {
        "outDir": "./dist"
    }
}

Of course, if there's already a tsconfig.json there, you'll want to add these options, rather than replacing the entire thing.

There are a massive amount of options available for configuring the TypeScript build process - if you want to tweak it some more, you can find info on the wiki, or if you need some more examples, let me know and I'll edit them into the answer.

In fact, when running the "npm run start" command, both TypeScript compiler and lite-server are started. If you only want to run the HTTP server, you could run the following command:

$ npm run lite

This way TypeScript files won't be compiled again at startup and you will use the previously compiled JS files to execute your Angular2 application.