Fix logic error on replying NACK at the end of transfer.
This is also to fix FPGA CI test mbed_hal_fpga_ci_test_shield-i2c/
i2c - test single byte read i2c API.
Better IP initialization sequence:
1. Configure IP pins
2. Select IP clock source and then enable it
3. Reset the IP (SYS_ResetModule)
NOTE1: IP reset takes effect regardless of IP clock. So it doesn't matter if
IP clock enable is before IP reset.
NOTE2: Non-configured pins may disturb IP's state, so IP pinout first and then
IP reset.
NOTE3: IP reset at the end of IP initialization sequence can cover unexpected
situation.