Choose 'Android Native' as the configuration type.Here's how to debug native code in Android Studio: Update June 2016: In Android Studio 2.1 the default run configuration supports native debugging so there should be no need to do the below unless you're using an older version. It wasn't the case at the time of the initial question - thanks for all the downvotes since then :) please look at donturner's answer below. Update: the debugging support is out now.
However it should be out soon - they recently mentioned mid-June as a target. The SDK tools team said that the NDK support wasn't part of the first previews of Android Studio 1.3. Actually, the advertised NDK support isn't available yet, even if you download the ndk-bundle and update Android Studio to the latest version in the canary channel (1.3-preview3 as of now).
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