I recently converted a large project to build with Maven. The project contained both C++ and Java code, and produced a web application, a standalone server application, plus a number of small command line tools. The project used a large number of open-source Java libraries, and Maven tamed these easily. The native C++ library proved harder, and this is the approach I took.
The code snippets below are part of a complete example that builds a tiny Java/C++ application under Linux. This should port easily to other Unix-like platforms, and may provide some help to performing the same task under Windows. The example is available in tar.gz and zip formats.