Solves the problem with typescript->javascript compilation and module path aliases (compilerOptions.paths).

CustomModuleLoader.ts

import customModuleLoader = require('module');

export class CustomModuleLoader {
  public cOptions: any = require('../tsconfig.json').compilerOptions;

  public replacePaths: any = {};

  constructor() {
    Object.keys(this.cOptions.paths).forEach(alias => {
      this.replacePaths[alias.replace(/\*.?/, '(.*)')] = this.cOptions.paths[alias][0].replace(/\*.?/, '$1');
    });
  
    (<any>customModuleLoader)._originalResolveFilename = (<any>customModuleLoader)._resolveFilename;
  
    (<any>customModuleLoader)._resolveFilename = (request: string, parent: customModuleLoader, isMain: boolean) => {
      Object.keys(this.replacePaths).forEach(matchString => {
        let regex = new RegExp(matchString);
        if (request.match(regex)) {
          request = [process.cwd(), this.cOptions.outDir, request.replace(regex, this.replacePaths[matchString])].join('/');
        }
      })
      return (<any>customModuleLoader)._originalResolveFilename(request, parent, isMain);
    }
  }
};