The threat or concern that a proliferation of diverging variants of the Android platform will result in the inability of some devices to properly run apps written with the Android SDK. With a large number of custom versions of the Android platform emerging, the concern is that interoperability will be weakened as a result of the potential for applications built specifically for one variant or device not being able to work with others.
Google has created an Android compatibility program to help quell fears of Android fragmentation and has also deemed the idea of Android fragmentation a "bogeyman" in a recent blog, but concerns about device-specific apps leading to interoperability issues persist nonetheless.
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