Click New button to make new builder, and choose program.
Type the name of builder(for example, Native Builder), and enter the path of bash.exe of cygwin under Location. Set path of bin folder of Cygwin as Working Directory. Put in the following command in the Arguments box.
--login -c "cd /cygdrive/c/Users/user/development/adt-bundle-windows-x86_64/android-ndk-r8e && ./ndk-build -C /cygdrive/c/Users/user/workspace2/HelloNDK"
"/cygdrive/c/Users/user/development/adt-bundle-windows-x86_64/android-ndk-r8e" is my path of android ndk. You should change it to your path. Be aware that cygwin use different path writing against dos's. "/cygdrive/c/Users/user/workspace2/HelloNDK" is my path to android ndk project. You should change it to your path also.
Now move to Refresh tab. Check Refresh resources upon completion. Click Specific resources and then click Specify resources button. check libs folder of android ndk project.
Move to Build Options tab. Choose Allocate console, During auto builds. If you don't want to see ndk log, click Launch in background. Check specify working set of relevant resources. Click Specify resources button and select jni folder and all the files in it.
Click ok, and you will see new builder. Now ndk will be built automatically when you clean or build the ndk project(libs and obj folder will be created). Very nice!!