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Failed to package a jar with dependencies with mvn

I am using mvn to build a simple Java code, I expect mvn could package a signle jar including all dependencies.
When I ran command "mvn clean package", it always generate a jar "myapp-1.0-SNAPSHOT.jar", it doesn't contain any dependenies.
However, when I ran command "mvn clean compile assembly:single", it can generate expected jar, jar name becomes "myapp-1.0-SNAPSHOT-jar-with-dependencies.jar", it contains all dependecies.
I am confused why the command "mvn clean package" doesn't work? what's wrong in my pom.xml or what's missing in pom.xml? Could anybody give some helps?
The following is my pom file.
<?xml version="1.0" encoding="UTF-8"?>
<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.barry.app</groupId>
<artifactId>myapp</artifactId>
<version>1.0-SNAPSHOT</version>
<packaging>jar</packaging>
<name>myapp</name>
<!-- FIXME change it to the project's website -->
<url>http://www.example.com</url>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<maven.compiler.source>1.7</maven.compiler.source>
<maven.compiler.target>1.7</maven.compiler.target>
</properties>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.11</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.apache.kafka</groupId>
<artifactId>kafka-clients</artifactId>
<version>3.1.0</version>
</dependency>
</dependencies>
<build>
<pluginManagement><!-- lock down plugins versions to avoid using Maven defaults (may be moved to parent pom) -->
<plugins>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<archive>
<manifest>
<mainClass>com.barry.app.App</mainClass>
</manifest>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
<executions>
<execution>
<id>make-assembly</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</pluginManagement>
</build>
</project>

Dependency 'javax:javaee-api:6.0' not found

I'm a computer science student and I'm currently making my first steps in using JEE. To retry an example of my study material, I tried to build a web-application using IntelliJ Community. As there is no offical possibility to do so with the community version, I tried to use maven following this tutorial: https://www.shortn0tes.com/2017/01/tutorial-intellij-idea-community.html
Now I get an error about the dependency injection of javax in the pom.xml:
Dependency 'javax:javaee-api:6.0' not found
Is there anything that I need to add/configure in my IntelliJ IDE? I know that the tutorial is maybe not super modern anymore, but I'd just like to follow the example of my university material.
Thank you very much!
Here my pom.xml:
<?xml version="1.0" encoding="UTF-8"?>
<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>org.example</groupId>
<artifactId>test</artifactId>
<version>1.0-SNAPSHOT</version>
<packaging>war</packaging>
<name>test Maven Webapp</name>
<!-- FIXME change it to the project's website -->
<url>http://www.example.com</url>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<maven.compiler.source>1.7</maven.compiler.source>
<maven.compiler.target>1.7</maven.compiler.target>
</properties>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.11</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>javax</groupId>
<artifactId>javaee-api</artifactId>
<version>6.0</version>
<scope>provided</scope>
</dependency>
</dependencies>
<build>
<finalName>test</finalName>
<pluginManagement><!-- lock down plugins versions to avoid using Maven defaults (may be moved to parent pom) -->
<plugins>
<plugin>
<groupId>org.apache.tomcat.maven</groupId>
<artifactId>tomcat7-maven-plugin</artifactId>
<version>2.2</version>
<configuration>
<port>8888</port>
<path>/</path>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<plugin>
<artifactId>maven-clean-plugin</artifactId>
<version>3.1.0</version>
</plugin>
<!-- see http://maven.apache.org/ref/current/maven-core/default-bindings.html#Plugin_bindings_for_war_packaging -->
<plugin>
<artifactId>maven-resources-plugin</artifactId>
<version>3.0.2</version>
</plugin>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.0</version>
</plugin>
<plugin>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.22.1</version>
</plugin>
<plugin>
<artifactId>maven-war-plugin</artifactId>
<version>3.2.2</version>
</plugin>
<plugin>
<artifactId>maven-install-plugin</artifactId>
<version>2.5.2</version>
</plugin>
<plugin>
<artifactId>maven-deploy-plugin</artifactId>
<version>2.8.2</version>
</plugin>
</plugins>
</pluginManagement>
</build>
</project>

Eclipse Maven Java import not resolved

I am having a problem with Eclipse Luna-1 resolving dependencies using the M2 Maven extension to Eclipse. See screen shot below, I appear to have a build path that has in it the correct .jar files, and these file are present in the .m2 repository. All shown in the screenshot. The build does not appear to be looking in the repository JAR files to satisfy the imports.
Screen shot of eclipse problem
pom.xml
<?xml version="1.0" encoding="UTF-8"?>
<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>org.ladbury</groupId>
<artifactId>NavigationDisplay</artifactId>
<version>0.0.1-SNAPSHOT</version>
<name>Navigation Display</name>
<description>receives navigation data via UDF and displays the results</description>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<maven.compiler.source>1.8</maven.compiler.source>
<maven.compiler.target>1.8</maven.compiler.target>
<client.directory>C:\Users\GJWood\navigate</client.directory>
<client.main.class>main.NavClient</client.main.class>
</properties>
<dependencies>
<dependency>
<groupId>org.jfree</groupId>
<artifactId>jcommon</artifactId>
<version>1.0.23</version>
</dependency>
<dependency>
<groupId>org.jfree</groupId>
<artifactId>jfreechart</artifactId>
<version>1.0.19</version>
</dependency>
</dependencies>
<build>
<directory>target</directory>
<outputDirectory>target/classes</outputDirectory>
<finalName>${project.artifactId}-${project.version}</finalName>
<testOutputDirectory>target/test-classes</testOutputDirectory>
<sourceDirectory>src/main/java</sourceDirectory>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.5.1</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>3.0.2</version>
<configuration>
<archive>
<manifest>
<mainClass>${client.main.class}</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
</plugins>
</build>
</project>

Maven clean and package doesn't generate surefire reports

I have a multi-module maven project where module A/B/C depends on module D.
Plugin maven-surefire-plugin is used for test phrase.
However,
mvn clean package
doesn't generate surefire-reports under **/target/
And
mvn clean; mvn package
could generate surefire-reports as expected.
This confused me a lot. Although the workaround for me is simply splitting to two mvn commands but I would like to know why?
Versions:
maven 3.3.3
jdk 1.7.0
maven-surefire-plugin 2.14
Root Pom:
<?xml version="1.0" encoding="UTF-8"?>
<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/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>org.jzako.test</groupId>
<artifactId>FeedbackSystem</artifactId>
<packaging>pom</packaging>
<version>1.0-SNAPSHOT</version>
<name>FeedbackSystem</name>
<url>http://maven.apache.org</url>
<dependencies>
<dependency>
<groupId>org.testng</groupId>
<artifactId>testng</artifactId>
<version>6.8.21</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-all</artifactId>
<version>1.10.19</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.powermock</groupId>
<artifactId>powermock-api-mockito</artifactId>
<version>1.6.2</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.powermock</groupId>
<artifactId>powermock-module-testng</artifactId>
<version>1.6.2</version>
<scope>test</scope>
</dependency>
</dependencies>
<modules>
<module>ModuleA</module>
<module>ModuleB</module>
<module>ModuleC</module>
<module>Utility</module>
</modules>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<configuration>
<source>1.7</source>
<target>1.7</target>
<encoding>UTF-8</encoding>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.14</version>
<configuration>
<forkMode>never</forkMode>
</configuration>
</plugin>
</plugins>
</build>
</project>
Module A Pom:
<?xml version="1.0"?>
<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"
xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>org.jzako.test</groupId>
<artifactId>FeedbackSystem</artifactId>
<version>1.0-SNAPSHOT</version>
</parent>
<groupId>org.jzako.test</groupId>
<artifactId>ModuleA</artifactId>
<version>1.0-SNAPSHOT</version>
<name>ModuleA</name>
<build>
<plugins>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<archive>
<manifest>
<mainClass>org.jzako.test.main.LightweightFeedbackStatisticsMain</mainClass>
</manifest>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
<executions>
<execution>
<id>make-assembly</id>
<phase>package</phase>
<goals>
<goal>assembly</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
<resources>
<resource>
<directory>${basedir}/../conf/dev</directory>
</resource>
</resources>
<testResources>
<testResource>
<directory>${basedir}/../conf/dev</directory>
</testResource>
</testResources>
</build>
<dependencies>
<dependency>
<groupId>org.jzako.test</groupId>
<artifactId>Utility</artifactId>
<version>1.0-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
</dependencies>
</project>
Multi-module Relationship
Module A/B/C depends on Utility Module and no dependencies among Module A/B/C.
Update:
It seems everything's fine for a single maven module projects. Something related to the multi-modules?

How to exclude folder with files from war maven assembly

I wanna exclude folder marked with red line. How can I do it?
Here is my 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/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>com.test</groupId>
<artifactId>Test</artifactId>
<packaging>war</packaging>
<version>1.0</version>
<url>http://maven.apache.org</url>
<properties>
<spring-version>4.1.0.RELEASE</spring-version>
<spring-security-version>3.2.3.RELEASE</spring-security-version>
<hibernate-version>4.3.4.Final</hibernate-version>
</properties>
<dependencies>
<!-- a lot of dependencies -->
</dependencies>
<build>
<finalName>Test</finalName>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>2.3.2</version>
<configuration>
<source>1.5</source>
<target>1.5</target>
</configuration>
</plugin>
</plugins>
</build>
</project>
Should I do anything with maven-compiler-plugin configuration?

This should give you the answer you need: http://maven.apache.org/plugins/maven-war-plugin/examples/including-excluding-files-from-war.html
Here is an example where we exclude all JAR files from WEB-INF/lib:
<project>
...
<build>
<plugins>
<plugin>
<artifactId>maven-war-plugin</artifactId>
<version>2.6</version>
<configuration>
<packagingExcludes>WEB-INF/lib/*.jar</packagingExcludes>
</configuration>
</plugin>
</plugins>
</build>
...
</project>
This doesn't have anything to do with the maven compiler plugin, but the maven war plugin.