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.
Timers don't stop when you are paused on breakpoint unless you specifically ask the DBG component to freeze them. Search for "freeze register" in the DBG section of your reference manual for more information.