you may recreate your own eclipse project (using cross cgc or ac6 toolchain ) based on the cubemx ac6 project and files.
create your project aside cubnemx folder and then link all file and folder as it is done on ac6 or atollic project.
i’ve done that even before ac6 was supported by CubeMX using the attolic generated codes.
it maye look painfull first time but as all project have same stucture it easy to re-use copy paste and addapt the base project.
I’m confident that is working under linux (i have doen it for several project with a different eclispe arm plugin and same project build on win7/linux plaftrom)