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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.
XOgastan is an API that allow to write programs that takes in input the file containing the ast generated by gcc and to analyze them. Using it you can collect informations about the generic C program represented by the AST (Tree) dumped by gcc.