cli.md: add --plugin-dir and minor edits

Изменения

Address changes from picodata!928 (merged)

Версия: Picodata 24.3.0-59-g26b11774

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• Changes should be cherry-picked to 24.2: no
• Staging: https://docs.binary.picodata.io/picodata/asabirov_add_plugin_dir_option/reference/cli/#run