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Maven's pom.xml is independent of the IDE. M2e should not require that its information should be stored in the pom. Perhaps in a file called m2e.xml, .m2e, or similar, or in one of the eclipse-specific files like .project.
m2e does not require m2e-specific configuration in pom.xml, but provides an option to include such configuration if the user chooses to do so. See also bug 350414, which discusses related enhancement request.
Moved to https://github.com/eclipse-m2e/m2e-core/issues/