Paul is correct. As explained in our release notes, Icenium now handles integrated plugins in a new way. When you enable them, they are no longer listed in the Plugins folder. Moreover, for Apache Cordova 3.0.0 projects and later, you do not need to add <script> includes in your index.html for the integrated plugins.
You can read more about working with core, custom, and integrated plugins in our documentation. As for dropping SQLite support in the simulator - in reality, Icenium has never supported the integrated plugins in the simulator. As stated here, in the device simulator, Icenium switches to WebSQL. However, the team is working on improving plugin support in the simulator and now the device simulator supports the Telerik EQATEC Analytics plugin.
You've missed the Icenium Visual Studio Integration keynote? It has been recorded and posted here.
Looking for tips & tricks directly from the Icenium team? Check out our blog!
Share feedback and vote for features on our Feedback Portal.