I am new to GitHub and finding it incredibly hard to learn.  I am following the instructions here to create new repositories from an existing directory containing the project and typing git init ... etc.  
However I created a repository in the wrong place and then deleted it by going into Settings at github.com.  Then, when I tried to re-push the files  the way I wanted it, one of the subfolders is now black (the one I had just deleted the repository for) and now not clickable - i.e. does not appear to be there.  See statistics_project1 in screenshot below.
It's very hard to troubleshoot a problem like this. There is no error message or explanatory text when you hover over the black sub-folder.
This post seems similar but I don't know. The solution looks complicated. Cannot remove submodule from Git repo
Could someone please tell me what a black 'unclickable' folder means in a github repository?
 
     
     
    