Tim,
i got so frustrated with my inability to get CB working with Arduino , that i pretty much gave up in June. I went with Atom + PlatformIO. (Latter is real good btw). But Atom is just not cutting for me.
I just ran the latest CB (svn 10912) with oBFusCATed's wizard and "Blink" example worked -wizard worked great, file structures, build just fine. In my iternal wizdom i didn't select "upload to board once compiled" flag. So now i'm trying to figure out how to do just that.