I do something very similar - although my naming is slightly different, for me it would be moodle-plugins28/theme/essential and moodl-plugins27/theme/essential for example, so I have a separate folder for the plugins based on moodle version, which does involve some duplication when a plugin is appropriate for several versions but the folders, as Michael mentioned, follow the structure of the moodle folders, so I can just copy it across into a new moodle code folder and its all done.
General developer forum
How are you deploying moodle?
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