There seem to be some problems with using the Embedded BSP for the SamD series and the I2C bus. Conflicting declarations for i2c_master_init seems to be just the beginning. No clue where the definition of I2c is anywhere …
Sorry, the BSP structure for SamD devices comes directly from the Atmel’s SDK package and it is indeed one of the least straight-forward ones. We would advise trying to find a sample project from Atmel that matches your hardware the best and then ensuring you reference the equivalent libraries on the VisualGDB side.