Guidelines/best practices for INTR version control? - Studio13

Sorry for the long title and not sure if this needs to be in the Presenter thread or in Engage, but here goes - hope this makes sense 

I've updated to Studio 13 and overall pleased with the product.  Noticing that Presenter apparently embeds the Engage files inside the .ppta file.  This is beneficial from a sharing/review standpoint....send the pptx and ppta file and reviewers can review and even edit the Engage interactions from there...previously you had to also have the .intr file to do much of anything with the interaction.  Problem is, this is not writing back to the original stand-alone .intr file....so the interaction inside the presenter file and the original engage file get out of sync.  I'm concerned that this will create version control issues for us down the road. 

So, finally to the actual question:  Does the Articulate Team or others have any suggestions for best practices on how to handle version control/syncing the original .intr file with what gets embedded in the ppta?   Thanks for your help - love the active community.