I was really missing the Auto-Reset Feature for the Arduino-BT, therefore I did it myself. It can be added to existing V06 boards but it would be nice to have it in future versions of the Arduino-BT.
It can be easily done by setting the iWRAP parameters to configure a WT-11 GPIO pin as DTR (e.g. PIO7) and connecting it to the ATmega reset pin using a little curcuit. The curcuit is needed because the WT-11 DTR signal is not inverted (this could be configured) and because the WT-11 uses 3,3V logic.
You will also need a slightly adapted version of avrdude which clears the DTR signal when closing the connection, otherwise the reset will only work once. An experimental patch can be found here: https://savannah.nongnu.org/patch/?6866
The auto-reset should be configurable via a jumper to disable it because for normal operation you don't want that the ATmega resets every time you open a bluetooth connection.
This is the iWRAP command for PIO7:
SET CONTROL MSC DCE 00 80 00 00 00 00
The curcuit and its connections has to look like this:
Part list: R1 100 kOhm R2 100 Ohm C1 22 nF D1 1N4148 Q1 BC547C
Similar types of D1 and Q1 will also work.