Using PersistenceJS, there is a persistence.reset API that will clear the database. PersistenceJS website
For development / testing, you can browse the content and delete webSQL, IndexedDB, cookies, etc., looking for your domain name at this URL in Chrome:
chrome:
There you can delete all storage for the domain or only certain local storage objects. Yes, the URL only means cookies, but the interface at this URL includes all types of offline storage.
It would be great if the Chrome Developer Tools interface had the ability to right-click and delete the storage object on the Resources tab along with content validation. But for now, all I know is the settings / cookies URL.
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