Zephyr Workbench, a VSCode extension to manage Zephyr on STM32.
It enables users to easily create, develop, and debug Zephyr applications.
Main features:
Install host dependencies.
Import toolchain and SDK.
Create, configure, build and manage apps.
Debug STM32.
You can directly download it from the VSCode marketplace
For more details, visit the Zephyr Workbench
The problem you describe are related to CubeMX, up to version 4.13; you should upgrade to 4.14, then regenerate your project in a new directory: the result should be a lot cleaner
Please keep us informed in case of further problems,