What's the best way to structure a Git repo for a new add-on?

Add-on developers,

How do you structure your directories and Git repo when developing an add-on?

I’m attempting my first EE add-on. I’m trying to do it the right way and put it in a Git repository. Most ee_addons in GitHub have a similar structure:

README.txt
extensions/
  ext_project.php
modules/
  project/
    mod.project.php
language/
  english/
    lang.project.php

The obvious solution is to init your git repo in EE’s system directory and only git add your add-on’s files. But, I see a couple problems with this.

1) The README.txt file will live in the system directory of your EE build system. What happens if you’re working on muliple add-ons that each have a README.txt? Do you have separate EE builds for each add on?

2) What if your add-on needs a theme file that lives outside the system directory?

Another option would be to just develop the add on in your EE build system. Then when you’re ready to commit, copy the files over to a separate directory that is only used for committing to git. This feels a little clunky.

I’m sure there is a best practice here, but haven’t seen it documented anywhere.

Appreciate any thoughts!