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In order to make significant progress in solving challenging problems in Computational Science & Engineering (CS&E), we need to integrate a large amount of software written by different groups of experts. Modern Lean/Agile methodologies would seem to provide a good foundation for research-driven development of complex CS&E software. Here, we describe issues related to the integration of CS&E software and propose different integration processes tailored to the special challenges in CS&E. We also describe practical experience with some of these tailored integration strategies related to Trilinos and some of its important application customers at Sandia National Labs.