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.
Same here, with Workbench Eclipse plugin on Debian Linux, with STM32F7 Discovery board.
Acutally it doesn't seem to be a problem of USB 2 or 3: I had to switch between two USB 2 ports, one is working, the other gives a timeout error. Don't know why.