I've compiled an Arduino program via a Makefile and have the resulting hex file.
From the Mac command line, how do I upload this hex file to my STM32 Cortex M3 board? For an ATMEL processor I would use avrdude.
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There are several different tools for uploading binaries to a Cortex M3. Depending on the board (not chip) configuration, they include (ht: Majenko):
Many Arduino flavors use a board with some kind of USB or FT232 adapter. In this case:
The dfu-util project supports a Mac version of dfu-util, their command line DFU tool.
Note that this answer is identical for any binaries which run on the processor, be they Arduino sketches or programs developed with other frameworks.