github changes not staged for commit

Have you tried

git add .

This recurses into sub-directories, whereas I don't think * does.

See here

in my case, I needed a

 git add files
 git commit -am 'what I changed'
 git push

the 'a' on the commit was needed.

Is week1 a submodule?

Note the relevant part from the output of the git status command:

(commit or discard the untracked or modified content in submodules)

Try cd week1 and issuing another git status to see what changes you have made to the week1 submodule.

See http://git-scm.com/book/en/Git-Tools-Submodules for more information about how submodules work in Git.

WARNING! THIS WILL DELETE THE ENTIRE GIT HISTORY FOR YOUR SUBMODULE. ONLY DO THIS IF YOU CREATED THE SUBMODULE BY ACCIDENT. CERTAINLY NOT WHAT YOU WANT TO DO IN MOST CASES.

I think you have to go inside week1 folder and delete the .git folder:

sudo rm -Rf .git

then go back to top level folder and do:

git add .

then do a commit and push the code.