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Although it is recomended that you run each project in its own workspace if there is a need to mix them together you will need to sort through each project and make sure the actions have different definitions that do not overlap.  You will also want to review the web code as well looking for overlaps.
If the two projects do overlap you will need to alter the code in one of the two projects to resolve the conflict. 
For example if both projects have an Action named formHandler.js you will need to change the code paths and project definition. 

So formHandlerAcs.js and formHandlerAnalytics.js or something like that then you will need to merge the app configs and have two different action names in there too.