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Cloud Computing infrastructures and Grid Computing platforms are representatives of a new breed of systems that leverage the modularity paradigm to assemble large-scale dynamic applications from modules contributed by different, possibly untrustworthy providers. Increased susceptibility to faults, diminished accountability, and complex system configuration are major challenges when assembling and operating such systems. In this paper, we describe how to solve these problems by retrofitting module management systems with the ability to deploy modules to execution environments with adjustable degree of isolation. We give a formal definition of the underlying hierarchical Module Isolation Problem and devise an online algorithm to solve it in an incremental fashion. We discuss how to apply our approach to a state-of-the-art module management system and demonstrate its effectiveness by an experimental evaluation.