I have seen this anti pattern in some diffrent code bases both Java and dotNet.

When selecting build artifact always go “all in”. If maven is the tool the it is maven poms that shall be under version control. The IDE resources like eclipse .project and .classpath is and shall be treated as generated resources. By that I mean not under version control!

In the eclipse case use the maven plugin eclipse:eclipse or even better use the IDE plugin m2Eclipse.