The AndroidManifest.xml file is not pertinent for an NDK build.
You will need to find the appropriate Android.mk file. You may need to add the file name into the LOCAL_SRC_FILES
in that make file, although they may have it set up to compile all the .cpp files in the directory or something more intelligent along those lines. It is, after all, a regular make file.
See here for info on the Android.mk file specifics.
Edit:
I suppose I should add that it would be the LOCAL_SRC_FILES
preceding the relevant include $(BUILD_SHARED_LIBRARY)
for the library you intend to build. Each make file may contain an arbitrary number of targets, although in the simplest case it's usually one make file to build a library.