Hi, Bongmaster: Your problem is interesting. Could you please restart the Arduino software and see if you still get that arduino-0011 message? Alternatively, you could tweak the code at line 43-ish to switch to Arduino 0011 mode. Let me know how it works out for you.
And hello, Justin: Thanks for your kind words. I saw your release with interest. I believe that bitlash may represent a somewhat "thicker client" approach 
Regarding framing and flow control: nothing special. The protocol is line-oriented and straightforward to automate, especially since you can set the prompt to something distinctive if '>' won't work for your application.
Happy to answer follow-ups.
Cheers,
-br