I've cloned the skwp/dotfiles to use as my own dotfiles. Time to time I have been making commits to my dotfiles for the improvement purposes. Mostly these commits were made to main part of repository.
Now I need to make commit to ~/.zshrc file. This file belongs to prezto repository which is submodule of skwp/dotfiles repository.
The question is how I can make this nested repository as part of my dotfiles? Should I change the remote url to point to my repository? Or is there a way to integrate the prezto to one big repository, and then I can make commits to repository seamlessly no matter which part of repository to push commits to.
You can keep prezto as a submodule, but change its URL to point to a fork of that repo that you own.
Meaning, you need to fork https://github.com/sorin-ionescu/prezto.git, and then change the URL seen in the skwp/dotfiles/.gitmodules file: see "Changing remote repository for a git submodule".
From there, you can make any new commit you want in that submodule, add, commit and push (to your fork), then go back to the main parent repo, add, commit and push (also to your fork).
The other approach, still assuming you have forked the main dotfile repo, would be to un-submodule the prezto submdule: see "un-submodule a git submodule".