Directory Reorg, LED libraries, gpio_init at startup

This PR has a mishmash of things we did over the past week. The most significant is probably a directory reorganization, to clean things up and prepare obelisk-ob1 to be the home for more advanced firmware development.

After the reorg we built some easy LED libraries, 'led_control.h', and then made two binaries for scripts to leverage. The binaries are 'led_alternate' and 'led_flash_green', and they are each used by the upgrade script.

Then I added a tool to run gpio_init at startup, so that tools like the upgrade script don't need to worry about initializing the gpios before setting the led patterns.

Finally I updated the upgradeOB1.sh script to set the LEDs.

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As I don't have test hardware with me, none of these changes have been tested.