Update to work with IPython comm infrastructure (https://github.com/ipython/ipython/pull/4195)
Fix shell reply message handling, and kill an unnecessary reply message.
Comment out old files code

This code is in here because SageCell version 1 let a user upload files to act upon.  When we rewrote the cell server, we decided uploading files was a hardly-used feature, so we put it on the back burner and never got around to implementing it.  It is potentially useful, though, and this code works around some browser problems, so I'm leaving the code in, but commented out.
mention in readme that you need to apply IPython PR 4195 now.