How to store firmware configuration or image in source-control?
For libraries only add comment next to #include with version number and author's name if the library is in Library Manager or the download location if it is not in Manager. 

Example:

#include &lt;MemoryFree.h&gt; // https://github.com/mpflaga/Arduino-MemoryFree
#include &lt;Ethernet.h&gt; // Ethernet 2.00


Put NINA firmware version in some comment at the top of the main sketch file. The firmware is part of the Arduino boards package so no need to store it in your repo. If you modified the firmware, publish source code in your fork of the official repository and there you can then release the binary too.

Put public certificate keys and similar files in sketch folder in subfolder called extras or data.

And write a README file for your repository.