I have never used the Android NDK before, I use Eigen for numerical calculations in physics.
Eigen is just a headline, so you can put it wherever you want. You just need to set the path to include in this folder (perhaps in your Android.mk). If you do not need unsupported libraries in Eigen, you only need the "Eigen" folder. The rest is for documentation and tests only. After a brief review of the documentation, I think you can achieve this with
LOCAL_C_INCLUDES := path/to/eigen
inside your Android.mk
A quick and dirty solution is to drop Eigen into the jni folder. But this only works if all sources using Eigen also exist. Thus, you do not need to edit your Android.mk.
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