How to make a new branch for PR?
Go to your rAthena fork on your github account, https://github.com/<yourusername>/rathena
Make sure, you're in "master" branch first, so it will makes new branch based on "master"
Make new branch by click that "branch" and just type branch name that you want. Example "idea" (thank anubisK that inspired a cool name for sample branch)
Branch created.
Pull your local first, you will get this notif about latest pull contains new branch.
Now, make new branch on your local, make sure the active branch is "master".
Add new branch with same name "idea".
New branch created. Now set the tracked branch.
Well, now u're in "idea" branch, you can edit something. I tried to edit README.txt and README.md. Save your changes.
Commit & Push it, make sure your changes in "idea" branch not in master branch.
Give a little log messages.
Now, go to Github again, look at your new branch commits. Mine, https://github.com/cydh/rathena/commits/idea. OK nothing to here, I just want to show you the changes.
Now, browse source on idea branch. Like mine, https://github.com/cydh/rathena/tree/idea
You can click "compare" or "compare & pull request", or by enter this URL https://github.com/cydh/rathena/commits/idea
After done you comparing, hit that "Create pull request"!
Give a little notice maybe? "Create pull request!"
OK, your new Pull Request is ready, you can wait until it merged or rejected.
Once it merged or rejected, you can delete the "idea" branch, it won't bothers your "master" branch fork.
Then, for sync your master branch, just do like on my other guide how to update forked repo.
You should do those steps before making new PR, because this won't mess your forked repo & the master branch's commits. Just try asked someone who already mess their fork, he/she have to reset their fork (delete current fork and refork) to make their "master" branch clear.