maven package后的war包里出现jar包冲突问题，而打包前可在eclipse正常运行， 也无jar包冲突

Question

打包前并无jar包冲突问题，项目里的Maven Dependencies也无重复jar，项目也可正常在eclipse中的server（非eclipse自带）里跑起来。但打包后手动部署在tomcat里会有jar包冲突导致的问题，删重复的jar后（主要指hibernate-entitymanager的jar）正常跑起来，但想知道为啥有这种问题，求教。

另一个项目里，一样的pom.xml文件，maven package打包，并无上面的情况。但我这个项目maven clean 又打包了很多次，还是出现jar重复的情况。

pom.xml主要配置：

<dependencies>
        <dependency>
            <groupId>commons-codec</groupId>
            <artifactId>commons-codec</artifactId>
            <version>1.9</version>
        </dependency>

        <dependency>
            <groupId>org.apache.commons</groupId>
            <artifactId>commons-lang3</artifactId>
            <version>3.4</version>
        </dependency>

        <dependency>
            <groupId>redis.clients</groupId>
            <artifactId>jedis</artifactId>
            <version>2.6.2</version>
        </dependency>

        <dependency>
            <groupId>junit</groupId>
            <artifactId>junit</artifactId>
            <version>4.12</version>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>org.springframework</groupId>
            <artifactId>spring-test</artifactId>
            <version>4.1.7.RELEASE</version>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>net.sf.json-lib</groupId>
            <artifactId>json-lib</artifactId>
            <classifier>jdk15</classifier>
            <version>2.4</version>
        </dependency>
        <!-- Spring Framework -->
        <dependency>
            <groupId>org.springframework</groupId>
            <artifactId>spring-context</artifactId>
            <version>4.1.7.RELEASE</version>
        </dependency>
        <dependency>
            <groupId>org.springframework</groupId>
            <artifactId>spring-context-support</artifactId>
            <version>4.1.7.RELEASE</version>
        </dependency>
        <dependency>
            <groupId>org.springframework</groupId>
            <artifactId>spring-web</artifactId>
            <version>4.1.7.RELEASE</version>
        </dependency>
        <dependency>
            <groupId>org.springframework</groupId>
            <artifactId>spring-beans</artifactId>
            <version>4.1.7.RELEASE</version>
        </dependency>
        <dependency>
            <groupId>org.springframework</groupId>
            <artifactId>spring-webmvc</artifactId>
            <version>4.1.7.RELEASE</version>
        </dependency>
        <dependency>
            <groupId>org.springframework</groupId>
            <artifactId>spring-tx</artifactId>
            <version>4.1.7.RELEASE</version>
        </dependency>
        <dependency>
            <groupId>org.springframework</groupId>
            <artifactId>spring-aspects</artifactId>
            <version>4.1.7.RELEASE</version>
        </dependency>
        <dependency>
            <groupId>org.springframework.data</groupId>
            <artifactId>spring-data-jpa</artifactId>
            <version>1.8.2.RELEASE</version>
        </dependency>
        <dependency>
            <groupId>org.springframework.hateoas</groupId>
            <artifactId>spring-hateoas</artifactId>
            <version>0.17.0.RELEASE</version>
        </dependency>
        <dependency>
            <groupId>org.hibernate</groupId>
            <artifactId>hibernate-entitymanager</artifactId>
            <version>4.2.5.Final</version>
        </dependency>
        <dependency>
            <groupId>org.hibernate</groupId>
            <artifactId>hibernate-ehcache</artifactId>
            <version>4.2.5.Final</version>
        </dependency>
        <dependency>
            <groupId>mysql</groupId>
            <artifactId>mysql-connector-java</artifactId>
            <version>5.1.18</version>
        </dependency>
        <dependency>
            <groupId>log4j</groupId>
            <artifactId>log4j</artifactId>
            <version>1.2.17</version>
        </dependency>
        <dependency>
            <groupId>com.fasterxml.jackson.core</groupId>
            <artifactId>jackson-core</artifactId>
            <version>2.6.0</version>
        </dependency>
        <dependency>
            <groupId>com.fasterxml.jackson.core</groupId>
            <artifactId>jackson-databind</artifactId>
            <version>2.6.0</version>
        </dependency>
        <dependency>
            <groupId>com.fasterxml.jackson.core</groupId>
            <artifactId>jackson-annotations</artifactId>
            <version>2.6.0</version>
        </dependency>
        <dependency>
            <groupId>commons-fileupload</groupId>
            <artifactId>commons-fileupload</artifactId>
            <version>1.3.1</version>
        </dependency>
        <dependency>
            <groupId>commons-dbcp</groupId>
            <artifactId>commons-dbcp</artifactId>
            <version>1.4</version>
        </dependency>
        <dependency>
            <groupId>javax.servlet</groupId>
            <artifactId>servlet-api</artifactId>
            <version>2.5</version>
            <scope>provided</scope>
        </dependency>
        <dependency>
            <groupId>jstl</groupId>
            <artifactId>jstl</artifactId>
            <version>1.2</version>
        </dependency>
        <dependency>
            <groupId>javax.servlet.jsp.jstl</groupId>
            <artifactId>jstl-api</artifactId>
            <version>1.2</version>
            <exclusions>
                <exclusion>
                    <artifactId>jsp-api</artifactId>
                    <groupId>javax.servlet.jsp</groupId>
                </exclusion>
                <exclusion>
                    <artifactId>servlet-api</artifactId>
                    <groupId>javax.servlet</groupId>
                </exclusion>
            </exclusions>
        </dependency>
        <dependency>
            <groupId>org.slf4j</groupId>
            <artifactId>slf4j-log4j12</artifactId>
            <version>1.7.12</version>
        </dependency>
        <dependency>
            <groupId>org.apache.ant</groupId>
            <artifactId>ant</artifactId>
            <version>1.9.4</version>
        </dependency>
        <dependency>
            <groupId>joda-time</groupId>
            <artifactId>joda-time</artifactId>
            <version>2.8.2</version>
        </dependency>
        <!-- MarkdownJ -->
        <dependency>
            <groupId>org.markdownj</groupId>
            <artifactId>markdownj</artifactId>
            <version>0.3.0-1.0.2b4</version>
        </dependency>
        <dependency>
            <groupId>org.apache.httpcomponents</groupId>
            <artifactId>httpclient</artifactId>
            <version>4.5</version>
        </dependency>
        <dependency>
            <groupId>org.eclipse.jgit</groupId>
            <artifactId>org.eclipse.jgit</artifactId>
            <version>4.0.1.201506240215-r</version>
        </dependency>
        <dependency>
            <groupId>commons-io</groupId>
            <artifactId>commons-io</artifactId>
            <version>2.4</version>
        </dependency>
        <dependency>
            <groupId>com.rabbitmq</groupId>
            <artifactId>amqp-client</artifactId>
            <version>3.5.4</version>
        </dependency>


        <dependency>
            <groupId>org.zywx.appdo.facade</groupId>
            <artifactId>appdo-facade-user</artifactId>
            <version>4.0-SNAPSHOT</version>
            <exclusions>
                <exclusion>
                    <groupId>org.hibernate.javax.persistence</groupId>
                    <artifactId>hibernate-jpa-2.0-api</artifactId>
                </exclusion>
            </exclusions>
        </dependency>

        <dependency>
            <groupId>org.zywx.appdo.facade</groupId>
            <artifactId>appdo-facade-mam</artifactId>
            <version>4.0-SNAPSHOT</version>
            <exclusions>
                <exclusion>
                    <groupId>org.hibernate.javax.persistence</groupId>
                    <artifactId>hibernate-jpa-2.0-api</artifactId>
                </exclusion>
            </exclusions>
        </dependency>

        <dependency>
            <groupId>org.zywx.appdo.facade</groupId>
            <artifactId>appdo-facade-omm</artifactId>
            <version>4.0-SNAPSHOT</version>
            <exclusions>
                <exclusion>
                    <groupId>org.hibernate.javax.persistence</groupId>
                    <artifactId>hibernate-jpa-2.0-api</artifactId>
                </exclusion>
            </exclusions>
        </dependency>

        <dependency>
            <groupId>com.101tec</groupId>
            <artifactId>zkclient</artifactId>
            <version>0.4</version>
            <exclusions>
                <exclusion>
                    <groupId>org.apache.zookeeper</groupId>
                    <artifactId>zookeeper</artifactId>
                </exclusion>
            </exclusions>
        </dependency>

        <dependency>
            <groupId>jaxen</groupId>
            <artifactId>jaxen</artifactId>
            <version>1.1.6</version>
        </dependency>



        <dependency>
            <groupId>org.springframework.data</groupId>
            <artifactId>spring-data-redis</artifactId>
            <version>1.4.1.RELEASE</version>
        </dependency>
        <!-- ehcache 相关依赖 -->
        <dependency>
            <groupId>net.sf.ehcache</groupId>
            <artifactId>ehcache</artifactId>
            <version>2.8.1</version>
        </dependency>

        <!-- 二维码 -->
        <!-- https://mvnrepository.com/artifact/com.google.zxing/core -->
        <dependency>
            <groupId>com.google.zxing</groupId>
            <artifactId>core</artifactId>
            <version>3.3.0</version>
        </dependency>
        <dependency>
            <groupId>org.jodd</groupId>
            <artifactId>jodd</artifactId>
            <version>3.3.8</version>
        </dependency>
    </dependencies>
    <build>
        <finalName>Pkgs</finalName>
        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-compiler-plugin</artifactId>
                <version>3.3</version>
                <configuration>
                    <source>1.7</source>
                    <target>1.7</target>
                    <encoding>UTF-8</encoding>
                </configuration>
            </plugin>
        </plugins>
    </build>

就是不懂为啥会打包会重复jar呢，小白求教。