It seems that, for the second screenshot, you do not create an Ac6 System Workbench project, but a standard Eclipse project, perhaps a Makefile CDT project, where you set up the compiler manually in the Makefile and debug configuration.
Please follow the tutorial on Getting started with System Workbench for STM32 to create your first project, it will be simpler.
Regarding the project definition files, their names are “.project” and “.cproject”, meaning they are hidden files on Linux. To see them you should either use the “-a” option of “ls” on the command line or parameterize the file explorer to show hidden files. In the project explorer view of System Workbench for STM32, open the “View Menu”, select “Customize view” and deselect “.* resources”.