Hi,
The –set-section-alignment argument is used by MSBuild projects to align the embedded bootloader to the specified boundary. You can find the implementation details in the <VisualGDB directory>\MSBuild\Targets\binary.targets file.
If you are using an older toolchain that doesn’t support it, you can either try patching binary.targets to remove the -set-section-alignment part, or simply copy arm-none-eabi-objcopy.exe from a newer toolchain. Objcopy is only used for translating between various file formats (ELF/HEX/binary) and won’t affect the output of the compiler.