git - Merge only core functionality of two different branches

So here's the thing:

I have a webapp project I write in Node using Express as a server (in the master branch, and I also have a version of the same app to build a node-webkit desktop app (in the nwjs-sdk branch).

The difference between the two branches are only a handful of files mainly in the root of the directory.

So here's a rough idea of the contents of each branch:

The master branch:

├── package.json
├── node_modules/
├── public
│   ├── css
│   │   ├── cassette.css
│   │   └── style.css
│   ├── data
│   │   └── metadata.json
│   ├── index.html
│   ├── js
│   │   ├── cookie-monster.js
│   │   ├── jquery-3.2.1.min.js
│   │   └── mixtape.js
│   └── tracks
├── README.md
├── readTracks.js
└── server.js

And the nwjs-sdk branch:

├── app
│   ├── css
│   │   ├── cassette.css
│   │   └── style.css
│   ├── data
│   │   ├── metadata.json
│   │   └── tracks.json
│   ├── index.html
│   ├── js
│   │   ├── jquery-3.2.1.min.js
│   │   └── mixtape.js
│   ├── main.js
│   ├── package.json
│   ├── tracks
│   └── uploads
├── package.json
├── readTracks.js
└── writeID3.js

Basically the main diference is that the express server is gone and the public/ dir changes the name to app/

The core functionality of my app is on the public/js/mixtape.js and in index.html (app/js/mixtape.js and app/index.html in the nwjs-sdk branch).

What I want to do is work on the master branch tweaking the core functionality and when everything is ready copy that functionality to the nwjs-sdk branch without breaking the app for node-webkit.

Any ideas on how to use git for this?

via medicengonzo