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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.

Eclipse, JavaFX: Code runs in IDE, but not in runnable jar

I'm currently trying to port my project to javafx11. For testing, I'm trying to create a runnable jar file with the hello-world-example from the tutorial page. I included the vm-modules, to prevent the error
Error: JavaFX runtime components are missing, and are required to run this application.
In eclipse, everything works fine, but when I export the project as a runnable jar file, the error returns when I try to run the jar.
When I export the jar-file, I choose the same run configuration as the app and I chose to extract required libraries into generated jar.
EDIT: As it was recommended, I'm currently trying to create a runnable jar with maven. The bhild succeds, but I can't execute it.
The pom.xml looks like this
<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>Mpp_App</groupId>
<artifactId>Mpp_App</artifactId>
<version>0.0.1-SNAPSHOT</version>
<packaging>jar</packaging>
<name>Dacemo</name>
<build>
<sourceDirectory>src</sourceDirectory>
<resources>
<resource>
<directory>src</directory>
<excludes>
<exclude>**/*.java</exclude>
</excludes>
</resource>
</resources>
<plugins>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.0</version>
<configuration>
<release>11</release>
</configuration>
</plugin>
<plugin>
<groupId>org.openjfx</groupId>
<artifactId>javafx-maven-plugin</artifactId>
<version>0.0.2</version>
<configuration>
<mainClass>Start</mainClass>
</configuration>
</plugin>
<plugin>
<!-- Build an executable JAR -->
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.4</version>
<configuration>
<archive>
<manifest>
<mainClass>Start</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>com.jfoenix</groupId>
<artifactId>jfoenix</artifactId>
<version>9.0.8</version>
</dependency>
<!-- https://mvnrepository.com/artifact/com.itextpdf/itextpdf -->
<dependency>
<groupId>com.itextpdf</groupId>
<artifactId>itextpdf</artifactId>
<version>5.5.13</version>
</dependency>
<!-- https://mvnrepository.com/artifact/com.googlecode.json-simple/json-simple -->
<dependency>
<groupId>com.googlecode.json-simple</groupId>
<artifactId>json-simple</artifactId>
<version>1.1.1</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.apache.pdfbox/pdfbox -->
<dependency>
<groupId>org.apache.pdfbox</groupId>
<artifactId>pdfbox</artifactId>
<version>2.0.15</version>
</dependency>
</dependencies>
</project>
On trying to execute it, I get the error
Could not find or laod main class Start
Caused by: java.lang.NoClassDefFoundError: javafx/application/Application
Is the Start.java defined wrongly? In the eclipse project structure, the Start.java lies in the default package.

NoClassDefFoundError: Maven intermodule dependency

I have my Storm application (maven) project structured as follow:
parent-project/
├── pom.xml
├── storm-application/
└── pom.xml
├── utils/
└── pom.xml
I structured my pom.xml files as follow:
parent-project:pom.xml
<modelVersion>4.0.0</modelVersion>
<groupId>my.project</groupId>
<artifactId>parent-project</artifactId>
<packaging>pom</packaging>
<version>1.0-SNAPSHOT</version>
<modules>
<module>utils</module>
<module>storm-application</module>
</modules>
<build>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
</plugins>
</pluginManagement>
</build>
storm-application:pom.xml
<parent>
<groupId>my.project</groupId>
<artifactId>parent-project</artifactId>
<version>1.0-SNAPSHOT</version>
</parent>
<groupId>my.project.parent-project</groupId>
<artifactId>storm-application</artifactId>
<packaging>jar</packaging>
<dependencies>
<dependency>
<groupId>my.project.parent-project</groupId>
<artifactId>utils</artifactId>
<version>1.0-SNAPSHOT</version>
</dependency>
<dependency> ...storm dependency... </dependency>
</dependencies>
<build>
<sourceDirectory>src/main/java</sourceDirectory>
<testSourceDirectory>src/test/java</testSourceDirectory>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>3.1.1</version>
<configuration>
<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>
</build>
utils:pom.xml
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>my.project</groupId>
<artifactId>parent-project</artifactId>
<version>1.0-SNAPSHOT</version>
</parent>
<groupId>my.project.parent-project</groupId>
<artifactId>utils</artifactId>
<packaging>jar</packaging>
<dependencies>
... some project related dependencies ...
</dependencies>
<build>
<sourceDirectory>src/main/java</sourceDirectory>
<testSourceDirectory>src/test/java</testSourceDirectory>
</build>
My objective would be to include the sibling module utilsin storm-application.
I need to include the module utils directly in the jar package of the storm-applicationmodule.
In fact, if I run the main function directly from IntelliJ it works, because it recognize the project structure, but if I try to deploy the application with Storm I get this error:
Exception in thread "main" java.lang.NoClassDefFoundError: my/project/parent-project/utils/MyClass
at my.project.parent-project.storm-application.MainClass.main(MainClass.java:116)
Caused by: java.lang.ClassNotFoundException: my.project.parent-project.utils.MyClass
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:338)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
... 1 more
I even tried to use the maven-assembly-plugin to include all the dependency in the package but I still get the same error.
Update
So what I was missing was that the assembly creates a second jar on the form name-version-jar-with-dependencies.
Plus, the storm dependency should be of <scope>provided</scope> otherwise it complains.
Still, I'm wondering if there would be an easier way to achieve this inter-module dependency.

I found a cleaner way to do so. Instead of using the assembly plugin, I use the shade plugin, so that the fat jar keeps the standard name.
Finally, this is the storm-application/pom.xml that, for me, works:
<parent>
<groupId>my.project</groupId>
<artifactId>parent-project</artifactId>
<version>1.0-SNAPSHOT</version>
</parent>
<groupId>my.project.parent-project</groupId>
<artifactId>storm-application</artifactId>
<packaging>jar</packaging>
<dependencies>
<dependency>
<groupId>my.project.parent-project</groupId>
<artifactId>utils</artifactId>
<version>1.0-SNAPSHOT</version>
</dependency>
<dependency> ...storm dependency... </dependency>
</dependencies>
<build>
<sourceDirectory>src/main/java</sourceDirectory>
<testSourceDirectory>src/test/java</testSourceDirectory>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>3.2.1</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>

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>

Not generating OSGI-INF folder

I am new to OSGI.I have been having trouble to get OSGI-INF folder in generated jar file.
I need to have folder structure like as below
META-INF
OSGI-INF
Com.mine.cq
I am using Eclipse and m2e plugin. When I run my project I am getting BUILD SUCCESS. And I am getting the below folder structure in that generated jar file.
META-INF
Com.mine.cq
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/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>com.mine.cq</groupId>
<artifactId>mineCore</artifactId>
<version>0.0.1-SNAPSHOT</version>
<packaging>jar</packaging>
<name>mineCore</name>
<url>http://maven.apache.org</url>
<properties>
<file.encoding>utf-8</file.encoding>
</properties>
<build>
<defaultGoal>install</defaultGoal>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-enforcer-plugin</artifactId>
<version>1.0-alpha-3</version>
<executions>
<execution>
<id>enforce-java</id>
<goals>
<goal>enforce</goal>
</goals>
<configuration>
<rules>
<requireMavenVersion>
<message>Project must be built with Maven 2.0.7 or higher</message>
<version>2.0.7</version>
</requireMavenVersion>
<requireJavaVersion>
<message>Project must be compiled with Java 5 or higher</message>
<version>1.5.0</version>
</requireJavaVersion>
</rules>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.felix</groupId>
<artifactId>maven-bundle-plugin</artifactId>
<version>1.4.3</version>
<extensions>true</extensions>
<configuration>
<instructions>
<Export-Package>
com.mine.cq.mineCore.*
</Export-Package>
<Import-Package>
*;resolution:=optional,
javax.servlet;version=2.4,
javax.servlet.http;version=2.4
</Import-Package>
<Embed-Dependency>
</Embed-Dependency>
<Embed-Transitive>true</Embed-Transitive>
<Include-Resource>{maven-resources}</Include-Resource>
<Sling-Bundle-Resources>/var/classes</Sling-Bundle-Resources>
</instructions>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-scm-plugin</artifactId>
<version>1.0</version>
<configuration>
<goals>install</goals>
</configuration>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>3.8.1</version>
<scope>test</scope>
</dependency>
</dependencies>
</project>
Why OSGI-INF folder is not in the .jar file? I need to set some information in OSGO-INF folder since I have to register my component as a OSGI service.
Please guide me to get it done.

Although being pretty late, I'll post my 2 cents about this issue for future reference.
As already pointed out, you can have the "packaging" of the bundle set to "jar" if you follow the instructions given in Maven bundle plugin documentation.
There is just a little gotcha: with that configuration, you need to explicitly add <exportScr>true</exportScr> inside the plugin configuration in order to properly create the SCR xml file (also remember to adjust manifest location, since in the documentation that piece is absent!).
You can see an example here (that's totally different from yours, but I assume you can easily reduce it on your code, if you're still interested):
<?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.massimobono.karaf.examples</groupId>
<artifactId>user-example</artifactId>
<version>0.0.1-SNAPSHOT</version>
<packaging>jar</packaging>
<build>
<plugins>
<plugin>
<!-- Here you specifiy that you want to use the manifest file generated by maven bundle plugin -->
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>3.0.2</version>
<configuration>
<archive>
<manifestFile>${project.build.outputDirectory}/META-INF/MANIFEST.MF</manifestFile>
</archive>
</configuration>
</plugin>
<!-- Here you generate the whole MANIFEST by using maven-bundle-plugin -->
<plugin>
<groupId>org.apache.felix</groupId>
<artifactId>maven-bundle-plugin</artifactId>
<version>3.2.0</version>
<extensions>true</extensions> <!-- make sure this is present -->
<executions>
<execution>
<id>bundle-manifest</id>
<phase>process-classes</phase>
<goals>
<goal>manifest</goal>
</goals>
</execution>
</executions>
<configuration>
<manifestLocation>${project.build.outputDirectory}/META-INF/</manifestLocation> <!-- make sure this is present! in the example of maven bundle plugin documentation, this piece is NOT present -->
<exportScr>true</exportScr> <!-- be sure to add this line as well -->
<supportedProjectTypes>
<supportedProjectType>jar</supportedProjectType>
<supportedProjectType>bundle</supportedProjectType>
<supportedProjectType>war</supportedProjectType>
</supportedProjectTypes>
<instructions>
<Bundle-SymbolicName>${project.groupId}.${project.artifactId}</Bundle-SymbolicName>
<_dsannotations>*</_dsannotations>
</instructions>
</configuration>
</plugin>
</plugins>
</build>
<properties>
<maven.compiler.source>1.8</maven.compiler.source>
<maven.compiler.target>1.8</maven.compiler.target>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
<dependencies>
<dependency>
<groupId>org.osgi</groupId>
<artifactId>org.osgi.core</artifactId>
<version>6.0.0</version>
<scope>provided</scope>
</dependency>
<!-- https://mvnrepository.com/artifact/org.osgi/org.osgi.service.component.annotations -->
<dependency>
<groupId>org.osgi</groupId>
<artifactId>org.osgi.service.component.annotations</artifactId>
<version>1.3.0</version>
</dependency>
</dependencies>
</project>

Your pom.xml needs to have a packaging type of "bundle" rather than "jar". If you want the packaging type to be "jar", use this:
http://felix.apache.org/site/apache-felix-maven-bundle-plugin-bnd.html#ApacheFelixMavenBundlePlugin%28BND%29-AddingOSGimetadatatoexistingprojectswithoutchangingthepackagingtype
EDIT: Oh! That's only problem one. The other problem is that I don't think you can generate
OSGI-INF with the maven-bundle-plugin. You need to create the OSGI-INF folder yourself within src/main/resources or use a plugin that generates OSGI-INF.
The maven-scr-plugin can generate OSGI-INF, but it's only useful if you are using SCR. Maven SCR Plugin - Not generating OSGI-INF folder