I have created two versions of the same app (paid and free) without problems. Instead of duplicating the assets folder, I used the "Linked source" functionality of Eclipse to reference the other project's assets folder (the physical assets folder is inside the paid version, the free version links to it). This has worked quite nicely.
Now I've encountered a specific problem though:
I have more content (more music) in the paid version that is unused in the free version. I tried filtering them in the free version using resource filters on the linked folders. In the package explorer that displays fine - I thought that would be enough to make it work.
However, when I inspected the resulting APKs, I noticed that the free version APK is about the same size. Opening them revealed that the free version - despite resource filtering - included all the content of the paid version. It seemed to completely ignore the filtering.
I wonder if there is any way to do this, or even a more elegant solution to the whole problem?
I am using libGDX by the way, so the structure is generally that I have a general common project that gets included by the two Android versions and Desktop version.