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Rebase your fork's master repo to match upstream's
(master) $ git rebase upstream/master
Branch it before you work
Create new local repo to work on issue or feature
(master) $ git checkout -b branch_name
Make all your changes in the local branch_name branch and commit with a nice, short subject and a detailed message
(branch_name) $ git add <all modified or new files>
(branch_name) $ git commit
Adding feature so and so to module blah.
Here I will add more information about what the entire commit is about.
Ready to push your changes for a PR?
(branch_name) $ git push origin branch_name
Now use Github's web UI to create your PR.
Updating a Pull Request?
Need to make more changes either because you received feedback for your PR or because you're not done yet?
(branch_name) $ git add <all modified or new files>
(branch_name) $ git ci --amend
* By using --amend you get to keep all your changes as one single commit, which is much cleaner imho :)
What if Github website says that your PR cannot be merged?
First, let's rebase your master to reflect upstream's master