Development tools for Zephyr on STM32Workbench for Zephyr: VS Code extension to set up, build, flash and debug Zephyr applications on STM32.Devicetree manager: browse, edit and visualize Zephyr devicetree, STM32CubeMX-like for Zephyr.
Under Debug Configurations, the debugger tab, there is a Configuration script section, with a button for Automated Generation or User Defined. If you set it to "User Defined", then your changes won't get overridden.