How to wire Angular2 + Webpack + Node + Express?

First of all, I have it wired and working, but I am somewhat discontent with the result and have a feeling it can be improved.

(The current result can be found here - https://github.com/MarkKharitonov/Angular2WebpackNodeExpress/tree/v0.0.1.)

The directory structure is:

C:.
│   .gitignore
│   package.json
│   tsconfig.json
│   tslint.json
│   typings.json
│   webpack.config.js
│
├───dist
│   └───server
│           api.js
│           api.js.map
│           main.js
│           main.js.map
│
└───src
    ├───client
    │       app.component.ts
    │       index.html
    │       main.ts
    │       polyfills.ts
    │       tsconfig.json
    │       vendor.ts
    │
    └───server
            api.ts
            main.ts
            tsconfig.json

Right now the dist folder has only the server side files compiled from ./src/server. They are placed there by the IntelliJ IDEA, because ./src/server/tsconfig.json requests compilation on save.

The client side bundling occurs in memory courtesy of webpack-dev-server. The ./src/client/tsconfig.json does not request compilation on save.

The things I dislike about my current setup are described here - https://github.com/MarkKharitonov/Angular2WebpackNodeExpress/tree/v0.0.1#problems, namely:

1. webpack is going to take care of any plain .js files under ./src/client - they would be bundled and placed under ./dist/client automatically. But what about plain .js files under ./src/server ? Do I need a task runner for that (gulp, grunt, whatever ...) or is there a solution within webpack?
2. I have three tsconfig.json files - ./src/client/tsconfig.json, ./src/server/tsconfig.json and ./tsconfig.json. The three files share most of the options, but not all. Right now I copy them in each of the three files - not very good.
3. In addition, because the typings folder is at the root I have to start all the top level TypeScript files (.\src\client\main.ts, .\src\client\polyfills.ts, .\src\client\vendor.ts and .\src\server\main.ts) with /// <reference path="../../typings/index.d.ts" />.

Hence the questions:

1. Can webpack also handle the server side files, but differently from the client side ones? I.e. transpile - yes, copy to dist - yes, bundle - no? Please, bear in mind I am using webpack-dev-server.
2. Is it possible to inherit tsconfig.json configuration so that I could avoid duplicating many options across the three files I have?
3. Is it possible to avoid the inclusion of /// <reference path="../../typings/index.d.ts" /> in the top level TypeScript files when the file layout is similar to mine ?

I know these are three questions instead of one, but I feel they are all closely related and the answer to one could also be the answer to another.