I have a similar problem where individual projects' POMs inherit from the top-level not from the agregator. To be precise I have a top-level POM and a number of parent POMs (that inherit from the top-level one). These parent POMs correspond to various types of modules, i.e. EAR, WEB, JAR etc. which in turn are inherited by projects' POMs. Parent POMs cannot be merged into the top-level since they operate on different types of projects.
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