The file components/libraries/timer/app_timer_freertos.c does not have the function app_timer_cnt_get() defined. Compiling libraries that require it (like external/lwip/src/port/nrf_platform_port.c) fails when using FreeRTOS.
Two simple source code problems discovered from the new SDK when enabling commissioning and compiling with -DCOMMISSIONING_ENABLED
There seems to be a ending parenthesis missing from ble_ncfgs.c line 503:
UNUSED_RETURN_VALUE(sd_ble_gap_phy_update(p_ble_evt->evt.gap_evt.conn_handle, &phys);
The file ipv6_medium_ble.c needed an additional header to compile (external Makefile project, gcc)
#include "app_error.h"
With these changes I was able to proceed.
Pertti