Maven shade plugin warning: we have a duplicate - how to fix?

This is my project POM (link to the paste, so you can right click > save as pom.xml)

<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
    <modelVersion>4.0.0</modelVersion>

    <groupId>com.zybnet</groupId>
    <artifactId>excel-reporter</artifactId>
    <version>0.0.1-SNAPSHOT</version>
    <packaging>jar</packaging>

    <name>mvn1</name>
    <url>http://maven.apache.org</url>

    <properties>
        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
    </properties>

    <dependencies>
        <dependency>
            <groupId>junit</groupId>
            <artifactId>junit</artifactId>
            <version>3.8.1</version>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>log4j</groupId>
            <artifactId>log4j</artifactId>
            <version>1.2.17</version>
        </dependency>
        <dependency>
            <groupId>org.apache.poi</groupId>
            <artifactId>poi</artifactId>
            <version>3.8</version>
        </dependency>
        <dependency>
            <groupId>net.sf.jasperreports</groupId>
            <artifactId>jasperreports</artifactId>
            <version>4.6.0</version>
        </dependency>
        <dependency>
            <groupId>org.codehaus.groovy</groupId>
            <artifactId>groovy-all</artifactId>
            <version>2.0.0</version>
        </dependency>
    </dependencies>

    <build>
        <resources>
            <resource>
                <directory>${project.build.sourceDirectory}</directory>
            </resource>
        </resources>
        <plugins>
            <plugin>
                <artifactId>maven-jar-plugin</artifactId>
                <configuration>
                    <finalName>${artifactId}-${version}-tmp</finalName>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-shade-plugin</artifactId>
                <version>1.7.1</version>
                <executions>
                    <execution>
                        <phase>package</phase>
                        <goals>
                            <goal>shade</goal>
                        </goals>
                        <configuration>
                            <filters>
                                <filter>
                                    <artifact>*:*</artifact>
                                    <excludes>
                                        <exclude>META-INF/*.SF</exclude>
                                        <exclude>META-INF/*.DSA</exclude>
                                        <exclude>META-INF/*.RSA</exclude>
                                    </excludes>
                                </filter>
                            </filters>
                            <transformers>
                                <transformer
                                    implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
                                    <mainClass>com.zybnet.Main</mainClass>
                                </transformer>
                            </transformers>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
        </plugins>
    </build>

</project>

I followed the advice of configuring the default jar plugin as advertised in the FAQ, but still when I run mvn package about 20K warnings are issued. Running mvn clean does not help either.

According to this answer, I could manually exclude some dependencies. However, I don't know if it's the right way, and the dependency tree is rather complex so it's difficult to argue where to start.

I know that these issues are not harmful, but I'm used to treat warnings as something that must be fixed. Moreover, I'm a beginner with Maven, so I'd like to understand what's wrong with my understanding, and how to troubleshoot problems.

(Using maven assembly plugin is not an option here)