Our project layout (for historical reasons) is such that our Application.mk and Android.mk files live in the same directory as AndroidManifest.xml, rather than in a jni subdirectory.

This works fine for ndk-build, by executing it as
ndk-build NDK_APPLICATION_MK=Application.mk

With the old (shell-based) ndk-gdb, it was also possible to support this, if somewhat hackishly, by executing it as
GNUMAKE="make NDK_APPLICATION_MK=Application.mk" ndk-gdb

However, there does not appear to be any way at all to get this to work with the new Python-based ndk-gdb. The script's invocation of make does not seem to have any way for the user to inject additional command-line arguments.