document that logs go to stderr and why kubectl exec runs are missing from kubectl logs

[realyota]

Adds a ## Logging section to the README:

• log messages go to stderr, stdout only carries the command output (since Logs of CLI commands should go to stderr? #969), so saving the log to a file needs 2>&1
• docker logs / kubectl logs only show the container's main process, so commands started with docker exec / kubectl exec don't appear there; running them through the API puts their logs into the container log

The section sits before ## Common CLI Usage, so generate_manual.sh doesn't overwrite it.