Consider an update command

[notmessenger]

This command would be intended to be ran after an upgrade to a new release of this repo. Running it would read in the jsdoc.json file and replace the plugins array and rewrite the file.

The idea being that we won't likely be updating the include and exclude folders very often as well as developers may have customized these entries but plugins will be more universally applied. Prompting the changes would be even better.