Sometimes when contributing to an upstream source, you need to re-base your own repository to be sure there won't be any conflicts. This is just a very quick and dirty way to do it. I will rewrite this post to be more detailed soon.

The following assumes that you have origin set as your source fork, and upstream set to the original source repository.

Typically this is done similar to;

mkdir rustc && cd rustc
git clone git@github.com:luke-nukem/rust.git .
git remote add upstream https://github.com/rust-lang/rust.git

The first thing to do is see what the state of your local repository is with git status

Your branch is up-to-date with 'origin/master'.
Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)

    modified:   _posts/2016-02-27-post.markdown

no changes added to commit (use "git add" and/or "git commit -a")

If you have changes pending, rather than git commiting them, run git stash; this will store your changes on the stack.

Saved working directory and index state WIP on master: 6267421 Initial commit
HEAD is now at 6267421 Initial commit

You can now run git pull --rebase upstream master which will revert you to a clean copy of upstream.

From github.com:Luke-Nukem/Luke-Nukem.github.io
 * branch            master     -> FETCH_HEAD
Current branch master is up to date.

Use git stash list to view the stash stack. Use git stash apply to reapply the most recently stashed work, which you can then commit with git commit. You can also branch a stash with git stash branch testbranch.

Now that you're at a clean state which is equal to upstream minus the changes you committed to your local repo, you can push to your fork origin with;

git push origin master

And now on GitHub, you can make a pull request to the upstream source.