Switched to "Atmel Studio", actually I didn't know that Atmel Studio can be combined with the Arduino World. Loading an .ino File, Studio creates the required environment and the library structure automatically.
Instead of progamming the CPU via USB I use JTAG and the Atmel Dragon as Interface. Works pretty well except some low frequented crashes by Atmel Studio.
In Atmel Studio compiler warnings cannot be detected, so everything seems to be allright and you can implement your application using instanced objects from library.