If you teach according to the official guide, the file tsconfig.json in section "compilerOptions" add "outDir": "dist",
To Transpolar folded .js files in the dist folder and not mixed with .ts
And in the settings SystemJS (systemjs.config.js) specify that folder (8-9 stitching about):
var map = {
'app': 'dist', // initially there is a folder app
Transfer to Cordoba index file, configure SystemJS, dist, styles, and library files. Themselves already :)