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Eclipse Maven Build Is not Including Dependencies on Generated Jar File

I'm not a very experienced Java user in terms of compilation with maven, eclipse, etc...
I'm trying to build a small proyect with some maven dependencies, and my idea is to include all the dependencies in the ganarated Jar.
This is the content of 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/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>amgrd</groupId>
<artifactId>testFlink</artifactId>
<packaging>jar</packaging>
<version>0.0.1-SNAPSHOT</version>
<name>testFlink</name>
<description>testFlink</description>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<flink.version>0.10.0</flink.version>
<jdk.version>1.8</jdk.version>
</properties>
<dependencies>
<dependency>
<groupId>org.apache.flink</groupId>
<artifactId>flink-java</artifactId>
<version>${flink.version}</version>
</dependency>
<dependency>
<groupId>org.apache.flink</groupId>
<artifactId>flink-streaming-java</artifactId>
<version>${flink.version}</version>
</dependency>
<dependency>
<groupId>org.apache.flink</groupId>
<artifactId>flink-clients</artifactId>
<version>${flink.version}</version>
</dependency>
<dependency>
<groupId>org.apache.flink</groupId>
<artifactId>flink-connector-kafka_2.11</artifactId>
<version>0.10.0</version>
</dependency>
</dependencies>
<build>
<sourceDirectory>${project.basedir}/src/main/java</sourceDirectory>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<archive>
<manifestEntries>
<Main-Class>StreamingWordCount</Main-Class>
</manifestEntries>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<configuration>
<source>${jdk.version}</source>
<target>${jdk.version}</target>
</configuration>
</plugin>
</plugins>
</build>
</project>
I splitted it on three parts to remark the piece of XML that should be configuring the project to include the jars in the generated file.
Then I show the context menu of the project and click on Run as... -> Maven --> And I type the target "package".
The generated jar does not contain dependencies, only pom.xml, manifest and my source code classes.
Thank you in advance

There should be two jars in your target directory after you build. One that only contains your classes, and one with all the classes. The latter has the suffix jar-with-dependencies.jar.

How can I execute a simple jar?

I'm trying to make a simple batch file with maven commands to execute the installation and execute the jar main class.
But the compile JAR does not have the dependencies and I get error
Exception in thread "main" java.lang.NoClassDefFoundError:
akka/actor/ActorSystem
This is my simple script
call mvn clean dependency:copy-dependencies
call mvn package
call cd target
call java -jar distributed-1.0.0.jar
pause
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>distributed</groupId>
<artifactId>distributed</artifactId>
<version>1.0.0</version>
<dependencies>
<!-- https://mvnrepository.com/artifact/org.scala-lang/scala-library -->
<dependency>
<groupId>org.scala-lang</groupId>
<artifactId>scala-library</artifactId>
<version>2.11.0</version>
</dependency>
<!-- https://mvnrepository.com/artifact/com.typesafe.akka/akka-actor -->
<dependency>
<groupId>com.typesafe.akka</groupId>
<artifactId>akka-actor_2.11</artifactId>
<version>2.5.16</version>
</dependency>
</dependencies>
<build>
<sourceDirectory>src</sourceDirectory>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<configuration>
<outputDirectory>src/main/java/resources/lib
</outputDirectory>
</configuration>
</plugin>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.5.1</version>
<configuration>
<source/>
<target/>
</configuration>
</plugin>
<plugin>
<!-- Build an executable JAR -->
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>3.1.0</version>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<classpathPrefix>lib/</classpathPrefix>
<mainClass>com.ipca.distributed.Implementations</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
</plugins>
</build>
</project>
What do I need here??

I think the easiest solution to create a runnable jar is to use Maven Assembly Plugin, or Maven Shade Plugin, or One Jar Plugin or even Spring Boot Plugin ( it's not weird if it works ). You can find some more details on how to use each one here.
These plugins are doing exactly you are trying to do with the 2 combined plugins that you have ( maven-dependency-plugin and maven-jar-plugin ).

Execution of Scala and Maven project

I have created a simple maven project of Scala in eclipse's scala ide using below details -
Artifact Id - scala-archetype-simple
Group Id - net.alchim31.maven
After created the project I have modified the pom.xml file.
<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>scalapoc</artifactId>
<version>0.0.1</version>
<name>${project.artifactId}</name>
<description>Test scala app</description>
<properties>
<maven.compiler.source>1.6</maven.compiler.source>
<maven.compiler.target>1.6</maven.compiler.target>
<encoding>UTF-8</encoding>
<scala.version>2.11.5</scala.version>
<scala.compat.version>2.11</scala.compat.version>
</properties>
<dependencies>
<dependency>
<groupId>org.scala-lang</groupId>
<artifactId>scala-library</artifactId>
<version>${scala.version}</version>
</dependency>
<!-- Test -->
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.11</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.specs2</groupId>
<artifactId>specs2-core_${scala.compat.version}</artifactId>
<version>2.4.16</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.specs2</groupId>
<artifactId>specs2-junit_${scala.compat.version}</artifactId>
<version>2.4.16</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.scalatest</groupId>
<artifactId>scalatest_${scala.compat.version}</artifactId>
<version>2.2.4</version>
<scope>test</scope>
</dependency>
</dependencies>
<build>
<sourceDirectory>src/main/scala</sourceDirectory>
<testSourceDirectory>src/test/scala</testSourceDirectory>
<plugins>
<plugin>
<!-- see http://davidb.github.com/scala-maven-plugin -->
<groupId>net.alchim31.maven</groupId>
<artifactId>scala-maven-plugin</artifactId>
<version>3.2.0</version>
<executions>
<execution>
<goals>
<goal>compile</goal>
<goal>testCompile</goal>
</goals>
<configuration>
<args>
<!-- <arg>-make:transitive</arg> -->
<arg>-dependencyfile</arg>
<arg>${project.build.directory}/.scala_dependencies</arg>
</args>
<archive>
<manifest>
<mainClass>App.scala</mainClass>
</manifest>
</archive>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.18.1</version>
<configuration>
<useFile>false</useFile>
<disableXmlReport>true</disableXmlReport>
<!-- If you have classpath issue like NoDefClassError,... -->
<!-- useManifestOnlyJar>false</useManifestOnlyJar -->
<includes>
<include>**/*Test.*</include>
<include>**/*Suite.*</include>
</includes>
</configuration>
</plugin>
</plugins>
</build>
</project>
I have also added manifest entry inside plugin tag.
<archive>
<manifest>
<mainClass>App.scala</mainClass>
</manifest>
</archive>
I have only one App.scala file and one test file available in project. Build was successful. But when trying to execute the jar using java -jar <jar_name> getting below error -
no main manifest attribute, in scalapoc-0.0.1.jar
When trying to execute the command java -cp scalapoc-0.0.1.jar com.test.scalapoc.App.scala getting below error -
Error: Could not find or load main class com.test.scalapoc.App.scala
Please suggest what to be needed to execute the jar.

try
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<configuration>
<archive>
<manifest>
<mainClass>com.test.scalapoc.App</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
.scala is for source only, source is not executable
archive tag is part of the configuration of a plugin
see https://maven.apache.org/shared/maven-archiver/examples/classpath.html#Make
UPDATE 2018-06-05:
To create a standalone jar (without need to defined a classpath with scala-library and other dependencies on command line), you should create a jar that included other classes/jar.
see:
Apache Maven Shade Plugin – Executable JAR and the rest of the doc of the plugin for tuning & configuration
or the old one-jar tool Deliver Your Java Application in One-JAR™ !

ClassNotFound Maven War

I'm building a multi-module Maven web app project, but I'm having trouble deploying the WAR on my Tomcat server.
My project structure is
MyApp
MyAppSchemas
MyAppUtils
MyAppWs
Here's the problem. When I try to deploy my generated war on my local Tomcat server, I get the following error:
Apr 19, 2017 1:42:43 PM org.apache.catalina.core.StandardContext filterStart
SEVERE: Exception starting filter ApiOriginFilter
java.lang.ClassNotFoundException: io.swagger.api.ApiOriginFilter
APIOriginFilter is a class generated in the MyAppSchemas module. I've included the MyAppSchemas jar as a dependency in the MyAppWs pom:
<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>
<parent>
<groupId>io.swagger</groupId>
<artifactId>MyApp</artifactId>
<version>1.0</version>
</parent>
<artifactId>MyAppWs</artifactId>
<name>MyAppWs</name>
<packaging>war</packaging>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>2.3</version>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<classpathPrefix>APP-INF/lib</classpathPrefix>
</manifest>
</archive>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>2.0.2</version>
<configuration>
<source>1.6</source>
<target>1.6</target>
</configuration>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>io.swagger</groupId>
<artifactId>MyAppSchemas</artifactId>
<version>1.0</version>
</dependency>
<dependency>
<groupId>io.swagger</groupId>
<artifactId>MyAppUtils</artifactId>
<version>1.0</version>
</dependency>
</dependencies>
</project>
Bottom line: how do I include other submodules on my war runtime classpath?

This can be achieved by adding your classes to an external jar and marking it as a dependency.
Add the dependency via a System scope
<dependency>
..
<scope>system<scope>
<systemPath>your jar path</systemPath>
</dependency>
Then define using the plugin as below
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<includes>
<include>directory path/*.jar</include>
</includes>
</configuration>
</plugin>
</plugins>
</build>

maven ear with war overlay

i have following war project:
<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>
...
<properties>
<failOnMissingWebXml>false</failOnMissingWebXml>
</properties>
<dependencies>
...
<dependency>
<groupId>com.sixgroup.rdx.common</groupId>
<artifactId>rdx-common-web</artifactId>
<type>war</type>
</dependency>
<dependency>
<groupId>com.sixgroup.rdx.common</groupId>
<artifactId>rdx-common-web</artifactId>
<version>${rdx-common.version}</version>
<type>jar</type>
<classifier>classes</classifier>
</dependency>
...
</dependencies>
<build>
<plugins>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<!-- <version>3.3</version> -->
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>2.1.1</version>
<configuration>
<overlays>
<overlay>
<groupId>com.sixgroup.rdx.common</groupId>
<artifactId>rdx-common-web</artifactId>
<exludes>
<exclude>WEB-INF/lib/*.jar</exclude>
<exclude>WEB-INF/classes/**/*.class</exclude>
</exludes>
</overlay>
</overlays>
</configuration>
</plugin>
<plugin>
<groupId>pl.project13.maven</groupId>
<artifactId>git-commit-id-plugin</artifactId>
</plugin>
</plugins>
</build>
</project>
this generates a beautiful war with the common-web .xhtml Files in the root dir and the classes of the common-web as jar in the web-inf/lib folder.
But now when i build the ear, the overlay of this war is ignored, so the excludes don't work and because of this i get an error when deploying (A component named 'FooBar' is already defined in this module)
This is the webModule in my ear-pom:
<webModule>
<groupId>${project.groupId}</groupId>
<artifactId>rdp-pricedata-web</artifactId>
<bundleFileName>rdp-pricedata-web.war</bundleFileName>
<unpack>true</unpack>
</webModule>
is there a way to force the ear to accept the overlay in the war?