I had to make some changes to a repo to dockerize it. Initially the submodule pointed at the original repo, so I went back and switched it to a fork and branch, so I could make pull requests as necessary.

Consider putting all your changes in a child theme. Look at my child theme as an example.

add to functions.php in your theme:

https://wordpress.stackexchange.com/questions/120418/completely-disable-categories
http://stackoverflow.com/questions/4249694/how-do-i-remove-a-taxonomy-from-wordpress