doc: clarify how to trigger automatic stage0 updates

This PR clarifies that to trigger the automatic stage0 update mechanism,
you should modify `stage0/src/stdlib_flags.h` (not `src/stdlib_flags.h`).
The update-stage0 process will then overwrite it with the contents of
`src/stdlib_flags.h`, bringing them back in sync.

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Co-Authored-By: Claude <noreply@anthropic.com>