ok I got that to work now and can display un-calibrated plot graph.
when compiling compass_tutorial03.c after modifying calibration data I get error
pi@INS-RPi2-01 ~/BerryIMU/compass_tutorial03_calibration $ gcc -o compass_tutorial03 compass_tutorial03.c
/tmp/ccwU8pZV.o: In function `main':
compass_tutorial03.c:(.text+0x354): undefined reference to `atan2'
collect2: ld returned 1 exit status
You were right though, it was just file name and paths incorrect.