Where to put Elastic Beanstalk config commands that are only run once on spin-up?

Commands can be run conditionally using the test: modifier. You specify a test to be done. If the test returns 0, the command is run, otherwise it is not.

If the last command in your config file touches a file, and the commands above that you only want to run once check for the existence of that file, then those commands will only run the first time.

commands:
  01-do-always:
    command: run_my_script
  02-do-on-boot:
    command: script_to_run_once
    test: test ! -f .semaphore
  99-signal-startup-complete:
    command: touch .semaphore

On Windows it would be something like this

commands:
  01-do-always:
    command: run_my_script
  02-do-on-boot:
    command: script_to_run_once
    test: if exists c:\\path\\to\\semaphore.txt (exit 0) else (exit 1)
  99-signal-startup-complete:
    command: date > c:\\path\\to\\semaphore.txt