Issue with remote GitHub repository

Question

Now, here is the format of the folder on my Linux machine:

/phd_simulations
    /ns-3
    /pybindgen
    /scenario

So ns-3, pybindgen, and scenario are all directories themselves...

Is this the correct workflow for git? There is no Linux desktop client (yet), so bear with me:

git init
git add .
git commit -m "First commit"
git remote add origin https://github.com/username/some-proj-name.git

git push

Right?

When I view the repository on GitHub.com, it only seems to be adding the folders themselves, NOT the contents.

I haven't used Git extensively yet (still learning), and I know I've done this successfully in the past, so I don't know what the deal is now.

Answer 1

It would add the folder only when those folders, locally on your computer, have a .git in them.
That would make them nested git repo, in which case, you should them as gray folder on GitHub.
See "Why github display gray folder to when I create a new repository?"

If you want just their files, remove (or move) the .git out of the way, and re-init your repo (add, commit, push --force).
Make sure you don't need the history of those nested repo first.