I have following structure

└───src
    ├───external
    │   └───lib
    └───App
        ├───Class

src/external/lib/ contains 2 files, lib.js and lib.d.ts.
In src/App/Class/Class.ts I am importing ../../external/lib/lib and it works fine, but generates following structure:

└───dist
    └───App
        ├───Class

With JS files in dist/App/Class. My config is:

{
  "compilerOptions": {
    "module": "commonjs",
    "sourceMap": false,
    "target": "ES5",
    "noImplicitAny": true,
    "outDir": "./dist",
    "rootDir": "./src"
  },
  "files": [
    "src/main.ts"
  ]
}

So I thought what rootDir property should solve this problem and transfer entire structure to dist folder. Am I doing something wrong?