diag: Update Diag over STM to support new command protocol

Diag over STM command protocol currently supported is version 1
protocol. The protocol has been changed and labeled as version
2. Make modifications to support version 2 Diag over STM command
protocol.

Change-Id: I6853d8d2a6ed35166a9be28a464aa7c0dfe844b0
Signed-off-by: Dixon Peterson <dixonp@codeaurora.org>