I have resolved the issue by recreating project from CubeMX. There is unkown reason that .cproject file doesn’t have right configuration which was created by CubeMX for systemworkbench. If you go to plugin--> debug in AC6’s location, you can find all scripts related to boards and microcontrollers. When Eclipse could not reach out to this location, then it can not load any of the boards or target MCUs. If configuration is correct then you can select boards and target from build setting. Even though you have selected right target and board in build setting, sometimes, it couldn’t read by RUN or Debug configuration because there is possibility/bug(?) that it doesn’t update details of target and board in .cproject. I am not sure that above information is correct or not.
So, restart everything and recreate the project(you just need to generate code in cubeMX in different location and also state the location of third party library properly) and magic happens. Now, everything is alright.
I am using:
System Workbench for STM32 - C/C++ Embedded Development Tools for MCU
System Workbench for STM32 - C/C++ Debugging Tools for MCU
Eclipse IDE for C/C++ Developers
Version: Neon.3 Release (4.6.3)