Push local to github..missing files

I was following along with the blog tutorial (http://getgrav.org/blog/developing-with-github-part-2) and thought that I got everything done successfully, but now that I've cloned the repo to my server it turns out that index.php and lord knows what else are missing. They weren't even pushed up to the remote and when I make changes (just changed some comments to test), I don't get any indication that I need to commit them. I've checked the .gitignore and it's not there... Anyone have any ideas?

Is it possible to see your Github repo for this? I can perhaps tell what's going on from there.

https://github.com/jacknjeanstudios/myempty.space

I don't see much else missing at an initial glance. I'm not sure why index.php was skipped. Is it still in your local folder? Usually things that are defined in .gitignore are skipped, but index.php is not one of those.

yes. It's still on my local - that site is running fine. Could there be some sort of conflict from the skeleton?

@rhukster apparently there is a .gitignore in the skeleton pkg that has index.php. I had to do git add on the file.

Which skeleton? Blog skeleton doesn't have index.php in .gitignore

https://github.com/getgrav/grav-skeleton-blog-site/blob/develop/.gitignore

Sorry the Sora Article. It turns out that there were some other directories that didn't transfer as well - I just uploaded them.
system/assets vendor/filp/whoops/src/Whoops/Resources/js/zepto.min.js

Now I'm down to a json encode error.