System Workbench for STM32

Good idea adding it to external tools.

This batch file might help:

@echo off

set flasherdir=your path to the flasher

set binfile=%~dpn1.bin
set binname=%~n1.bin

cd %flasherdir%

if exist %binfile% (
echo Starting to flash %binname%
ac6_stm32flash.exe -erasesector -loader algo\stm32f4xx.bin
ac6_stm32flash.exe -prog -loader .\algo\stm32f4xx.bin -binary %binfile%
echo Resetting board
ac6_stm32reset.exe
) else (
echo Cannot find bin file: %binname%
)

exit

Save the script to, say, "flash.bat", and put its full path+name in the "Location:" field of the ext.tool run configuration.
Use whatever you prefer as working directory.
For the "Arguments:" field, click "Variables..." button, and choose "selected_resource_loc".

To use it to flash a .bin you just need to click on any .elf or .bin file in the project explorer to select it and then run the tool by clicking the External tools button.
The batch script tries to change the extension to .bin; if the file is found, it first partly erase the flash, then flash the binary and finally resets the board.

It works for me, but YMMV.
If your target board catches fire, your cat is teleported to Mars or you start speaking ancient tongues, I take no responsibility!