Sorry, System Workbench for STM32 is not open-source.
The setting menu is crashing because no compiler prefix option is found.
Are you sure your generated project is using the “fr.ac6.managedbuild.toolchain.gnu.cross.exe.debug” or “fr.ac6.managedbuild.toolchain.gnu.cross.exe.release” toolchain. The compiler prefix is usually set to its default value “arm-none-eabi-” automatically.
It might be quicker to compare your .cproject to the one from a new project created from the IDE to identify the mismatches.