Sorry I removed my initial post, as I found that it has nothing to do with [space] with further testing.
I am running Jupyter notebook server for Python, on a remote server that I have admin right on Fedora 23.
I am not setting to start my Jupyter notebook server with a user, which prior to that I was playing around starting the server as root.
It was that when the server was run using root, it created some .ipython checkpoint folder as root, which now is preventing me from modifying them.
Manually remove the root-owned .ipython checkpoint folder solved the problem.