Hi - I also had problems compiling the new RFBee Arduino 1.0 files on Linux. To resolve this, I opened all the files in a good text editor (Sublime Text editor) and saved all the files with Unix line endings. Then, I changed line 26 of RFBeeCore.h from this:
#include “RFBEEGlobals.h”
to:
#include “RFBeeGlobals.h”
Then on my Linux system the example sketch compiled happily 
Regarding the use of AT commands, it seems in the new Arduino firmware for Arduino 1.0, the approach is to set the various configuration parameters and modes directly in the code. As a developer I think I like this approach, although there is no documentation other than the example sketch to get you going. Anyway, looking at the code in RFBeeConfig.cpp allowed me to change a couple of simple things - for example I wanted to set the destination and source address of my RFBees so I did that by hacking RFBeeConfig.cpp (lines 37 and 38) like this:
EEPROM.write(CONFIG_DEST_ADDR,2);
EEPROM.write(CONFIG_MY_ADDR,1);
Maybe there is a better way, and I’m sure the library will improve over time. Thanks to the author for their fantastic work by the way…