Before today i use Eclipse 3.8 with Sequoyah plugin for Android NDK project.
But today i decide to freshen Eclipse to Juno release with SDK and NDK.
I w
I often solving similar issues that is probably occur when you move or rename the working folder of the project.
.settings
.classpath
.cproject
.project
project.properties
Also this solved issue with Eclipse 4.3 previously ignored build system and user defined compiler flags. Now macros folding dependent on this flags works fine.
If more general: NDK plugin can properly define for you right includes and anything other required to work fine, but you need to clean your project from broken crap, and easiest way to do so is reimport project.