I must not understand. You say you are running the v1.0.1 blink sketch, then you say everything failed. How did you upload the blink sketch?
How are you running the new download? I navigate to that directory with Nautilus and run that shell script. It should have the IDE version and any modification in the title of the IDE window.
I created a link of that shell script (right mouse click using Nautilus), and moved the link to my desktop. That eliminates all that stuff in between.