Hybrid App with Ionic - Newbie questions

Hi all

I’m developing my first hybrid application with Ionic/Cordova. I did the initial project setup with this generator: https://github.com/diegonetto/generator-ionic

I also read a lot about the project structure. As far as I understood it, the plugins and platforms directory shouldn’t be in version control. They are generated during the build process.

Now my question, where should I put the native android code? There is a class generated named CordovaApp in platforms/android//CordovaApp.java
Is this the source folder ?

Then I have some trouble with remote debugging. The application on my tablet isn’t able to make a connection to my server. this only works if a chrome browser is running on the tablet, which already made a connection. Otherwise if I close the browser, the application can’t establish the connection.
I also read that the debuggable=true flag must be set in the file androidManifest.xml. This file is generated through the build process. Is there also a possibility to define it in config.xml?