[Solved]-Disable javascript facet in a m2e project-eclipse

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>