The current docblock for `WP_Upgrader::run` indicates the default value for the `clear_working` key of the `$options` argument is `false`. However, in the code directly below, the default is shown to be `true. This change updates the docblock to correct the default.
This commit also reorders the `$defaults` to match the order they appear in the docblock.
Props paulkevan.
Fixes#55450.
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