TypeScript: Unexpected reserved word

I have a project in WebStorm IDE & Node.js. I created a file named "mongo-manager.ts" which I used in the routes\index.js file. It worked seamlessly.

Then I did 2 things:

1. WebStorm had always asked me whether or not to compile TypeScript to JavaScript and I had always ignored it, but then once I clicked on "yes" and since then after solving some errors it's compiling now ts files successfully to js.
2. I converted index.js into index.ts and now I still have index.js which is an output of the compilation.

Ever since then, when I try to run my app (using the triangular green button in WebStorm which in turn uses the command line: "C:\Program Files (x86)\JetBrains\WebStorm 11.0.1\bin\runnerw.exe" "C:\Program Files\nodejs\node.exe" bin\www), I get this error:

import mongodb = require('mongodb');

^^^^^^

SyntaxError: Unexpected reserved word

Now, there's no specific problem with the "import" statement because if I omit it, the next non JavaScript statement throws the same exception. It just tries to treat TypeScript like it was JavaScript.

I've found these questions: Typescript: unexpected reserved word in PHPStorm, Unable to import in typescript file in nodejs

They suggest either to use "tsc" rather than node.exe, or to make sure that I run with node.exe the js file rather than the ts file.

Now the thing is that the file that node.exe runs directly is "www" which is a JavaScript file and in turn calls app.js which is still JavaScript, but later the files index.ts and mongo-manager.ts are called, so I have a hybrid of both js and ts.

And another and most important thing is that my code has already worked seamlessly even though it's hybrid and without taking any of the suggestions in these questions, until I answered WebStorm "yes" to the question whether to compile TypeScript to JavaScript, which had always appeared.

Anyway, I only want my app working again, no matter how.

Any help will be profoundly appreciated!