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The point to use the plugin is that you will use the capabilities of the mobile SDK lifecycle tracking with all of the mobile metrics that come along like launch, crash, install ....

If you use default javascript implementation you won't have these metrics which won't make sense to not have them if you are tracking an app. Make sure you use the SDKs provided by Adobe.

IOS doc

Android doc

I played with it in the past and wrote a tutorial: PhoneGap android app and Adobe Mobile Services · alcazes/Adobe-Analytics-from-A-To-Z Wiki · GitHub

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