Change git root folder

I have used the Github desktop application to manage my Github repository. I have the following folder structure:

myRepo/
    config/
    mappings/
    src/
    bin/
    eclipse/
    lib/
    README.md
    LICENSE.md

How would I go about making src the main folder of my repository so it will only commit files inside src while retaining the files README.md and LICENSE.md while still having the files inside src inside the src folder, like this:

Thanks in advance.

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