The way I’d go about this is build your standalone application but build into it a bullet proof API that will allow others and yourself leverage the power of your application.
Whichever way you look at it there will be a fair amount of coding to be done each time you visit a different CMS as they all have different ways of dealing with things. If your app has good API controls others could then make their own modules for other CMS’s that you never knew existed, thus not limiting you to the likes of WordPress and Joomla.
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