You have a number of problems to solve:
- How to regroup the source and header files ideally
- How to automate the code modifications to carry this out
In both cases, you need a robust C++ parser with full name resolution to determine the dependencies accurately.
Then you need machinery that can reliably modify the C++ source code.
Our DMS Software Reengineering Toolkit with its C++ Front End could be used for this. DMS has been used for large-scale C++ code restructuring; see http://www.semdesigns.com/Company/Publications/ and track down the first paper "Case Study: Re-engineering C++ Component Models Via Automatic Program Transformation". (There's an older version of this paper you can download from there, but the published one is better). AFAIK, DMS is the only tool to have ever been applied to transforming C++ on large scale.
This SO discussion on reorganizing code addresses the problem of grouping directly.
