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This PR puts, with one exception, every single remaining `by` that lies all by itself on its own line to the previous line, thus matching the current behaviour of `start-port.sh`. The exception is when the `by` begins the second or later argument to a tuple or anonymous constructor; see #3825 (comment). Essentially this is `s/\n *by$/ by/g`, but with manual editing to satisfy the linter's max-100-char-line requirement. The Python style linter is also modified to catch these "isolated `by`s".
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