AOSP build system handles the shared libraries differently from Eclipse-ADT.
You will need to extract that .so from your apk and create an Android.mk to it.
To extract the .so, just unzip the apk and get it from libs
folder.
Here is an example for the Android.mk to libfoo.so shared library:
LOCAL_PATH:= $(call my-dir)
# prebuilt shared library
include $(CLEAR_VARS)
LOCAL_MODULE := libfoo
LOCAL_SRC_FILES := libfoo.so
LOCAL_MODULE_SUFFIX := .so
LOCAL_MODULE_CLASS := SHARED_LIBRARIES
LOCAL_MODULE_PATH := $(TARGET_OUT)/lib
LOCAL_MODULE_TAGS := optional
include $(BUILD_PREBUILT)