first of all, clean the configuration with mvn eclipse:clean, it will remove all configuration from the .project file.
then make a new one with mvn eclipse:eclipse, just with the configuration and dependencies on your pom.xml.
edit: and configure the project natures that you need:
<plugin> <groupid>org.apache.maven.plugins</groupid> <artifactid>maven-eclipse-plugin</artifactid> <configuration> <projectnatures> <projectnature>org.eclipse.jdt.core.javanature</projectnature> <projectnature>org.eclipse.wst.common.modulecore.modulecorenature</projectnature> </projectnatures> <additionalprojectnatures> [... the ones you need or empty...] <projectnature>org.springframework.ide.eclipse.core.springnature</projectnature> </additionalprojectnatures> </configuration> </plugin>
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