Duplicated source code can harm maintainability of software systems. Duplo is a tool to find duplicated code blocks in large C, C++, Java, C# and VB.Net systems.
Nmdepend is a lightweight 'link-time' dependency analyzer for C++. It uses object files and libraries instead of source-code as input. It can help to manage 'cross-directory' dependencies. Dependencies can be visualized in combination with Graphviz.