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Maven assembly jar execution Could not find or load main class Caused by: java.lang.ClassNotFoundException

I have been trying, for several days now, to create an executable jar file for my muli-module maven project, sadly I have had no luck on doing it.
I know that there are a lot of similar questions already, but, even by following the answers, i cannot manage to run the jar I make.
I am using the maven-assembly plugin, so that my jar contains all the required dependencies, here is the 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 https://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<artifactId>tam-authentication</artifactId>
<name>tam-authentication</name>
<description>authentication tam project</description>
<parent>
<groupId>com.netcomgroup.eu</groupId>
<artifactId>TAM</artifactId>
<version>0.0.1-SNAPSHOT</version>
</parent>
<properties>
<java.version>11</java.version>
</properties>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
</plugin>
</plugins>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<archive>
<manifest>
<mainClass>"fully qualified class name"</mainClass>
</manifest>
</archive>
</configuration>
<executions>
<execution>
<id>make-assembly</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</pluginManagement>
</build>
<dependencies>
...
dependencies from other modules
...
</dependencies>
</project>
futhermore i have another probably related problem regarding jar creation with a common library included:
using Eclipse as IDE, whenever I run as > maven install on the multimodule project, I often get jars failing over correct imports, that I need to delete and import again to complete the java building process correctly. Sometimes i simply must run maven install several times in a row to make the jar building process succeed.
I don't know if the second problem is related but i guess there is some mistake I cannot see in the multi module project jar building.

First of all, as per your pom.xml you did not provide the fully qualified Main class name in your dependency. Second if you provided the Main class name, then after "mvn clean install", it would create 2 jars - one with artifact name and one with "jar-with-dependencies" and you have to user "jar-with-dependencies".
Also i don't think you need to use pluginManagement tag as an extra step. I have just modified a bit your pom below, please try this and check.
<?xml version="1.0" encoding="UTF-8"?>
4.0.0
<artifactId>tam-authentication</artifactId>
<name>tam-authentication</name>
<description>authentication tam project</description>
<parent>
<groupId>com.netcomgroup.eu</groupId>
<artifactId>TAM</artifactId>
<version>0.0.1-SNAPSHOT</version>
</parent>
<properties>
<java.version>11</java.version>
</properties>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<mainClass>{Your fully qualified Main class eg - abc.cde.Main}</mainClass>
</manifest>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
</plugin>
</plugins>
</build>
<dependencies>
...
dependencies from other modules
...
</dependencies>

Maven custom directory structure - no sources to compile despite specifying sourceDirectory

I am using a custom directory structure and have specified the directory in sourcedirectory tag. But still I get the message No sources to compile. Although the build is successful.
My directory structure:
So instead of src/main/java, I am using java. (And I have a reason to do that, so right now it's not possible to switch to src/main/java)
Here's my pom.xml:
<artifactId>application</artifactId>
<name>application</name>
<packaging>jar</packaging>
<properties>
<maven.compiler.source>1.8</maven.compiler.source>
<maven.compiler.target>1.8</maven.compiler.target>
<maven.test.skip>true</maven.test.skip>
</properties>
<build>
<sourceDirectory>java</sourceDirectory>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.7.0</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
<excludes>
<exclude>**/old/**/*.java</exclude>
</excludes>
<includes>
<include>java/com/**/*.java</include>
</includes>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<configuration>
<source>1.8</source>
<target>1.8</target>
<excludes>
<exclude>**/old/**/*.java</exclude>
</excludes>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<classpathPrefix>lib/</classpathPrefix>
<mainClass>com.start.Start</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
</plugins>
</build>
When I run command mvn clean package, I get following output:
The source is not compiled and resultant jar is empty. All the sources I have referred for using custom directory structure with maven say that using sourceDirectory should solve the problem. But in my case it doesn't solve
EDIT
I am using custom directory structure as using standar directory structure did not work for me. Hers' my question related to that:
Getting error in linking a source folder in eclipse maven
EDIT2:
I am linking source in java directory. That is, on the file system, application->java does not exist, but in eclipse through link source option, I have added the Java source folder from a different directory. Therefore it appears in eclipse. Also I have run maven commands with mvn command line as well as through eclipse.

If I understand your issue correctly, You have an application folder and the actual source (java) folder is from somewhere else in the file system.
And you linked the external folder as java source through eclipse for compilation.
By linking in Eclipse, maven will not automatically know where the source files are. Maven follows standard directory structure for looking up java and test files.
You can use this Build Helper plugin to customize the way maven looks up sources.
An example talked here

This is your problem: <include>java/com/**/*.java</include>
You should not include the sourcedirectory, just the paths relative to it.

Follow these steps of this working example and compare it step by step with your project to figure out what's wrong:
create a folder.
create inside the folder a pom.xml with the following content:
<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.yourdomain.yourproject</groupId>
<artifactId>yourapp</artifactId>
<version>1.0-SNAPSHOT</version>
<packaging>jar</packaging>
<name>yourapp</name>
<url>http://maven.apache.org</url>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<maven.javadoc.skip>true</maven.javadoc.skip>
</properties>
<dependencies>
</dependencies>
<build>
<plugins>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>2.9</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.5</version>
</plugin>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<archive>
<manifest>
<mainClass>com.yourdomain.yourproject.content.Main</mainClass>
</manifest>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<appendAssemblyId>false</appendAssemblyId>
</configuration>
<executions>
<execution>
<id>make-assembly</id> <!-- this is used for inheritance merges -->
<phase>package</phase> <!-- bind to the packaging phase -->
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-release-plugin</artifactId>
<version>2.5.1</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-deploy-plugin</artifactId>
<version>2.8.2</version>
<dependencies>
<dependency>
<groupId>org.jvnet.wagon-svn</groupId>
<artifactId>wagon-svn</artifactId>
<version>1.12</version>
</dependency>
</dependencies>
</plugin>
</plugins>
</build>
</project>
create this folder structure inside your root folder:
src/main/java/com/yourdomain/yourproject/content/
create a Main.java in content folder with the following content:
package com.yourdomain.yourproject.content;
public class Main
{
public static void main(String[] args)
{
System.out.println("HELLO");
}
}
go back to your root folder and execute mvn clean install
a target folder will be created with the jar in there.
you can execute it with java -jar target/yourapp-1.0-SNAPSHOT.jar

When running Java jar file my dependency classes aren't found

I currently have a maven project with 1 dependency. When I build it using mvn package and run it I get a ClassNotFoundException for the classes in my dependency. When I export it as a normal jar in Intellij I still get the same error. I have tried just about everything including setting -cp in the command line. Note that the main class is being found, just not the classes in my dep
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>me.jaredstef</groupId>
<artifactId>hawkeyecountdownbot</artifactId>
<version>1.0</version>
<packaging>jar</packaging>
<name>hawkeyecountdownbot</name>
<url>http://maven.apache.org</url>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
<dependencies>
<dependency>
<groupId>org.twitter4j</groupId>
<artifactId>twitter4j-core</artifactId>
<version>[4.0,)</version>
<scope>compile</scope>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.4</version>
<configuration>
<archive>
<manifest>
<mainClass>me.jaredstef.hawkeyecountdownbot.HawkHeart</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.2</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
</plugins>
</build>
</project>
EDIT:
Stacktrace:
Exception in thread "main" java.lang.NoClassDefFoundError: twitter4j/TwitterException
at java.lang.Class.getDeclaredMethods0(Native Method)
at java.lang.Class.privateGetDeclaredMethods(Class.java:2701)
at java.lang.Class.privateGetMethodRecursive(Class.java:3048)
at java.lang.Class.getMethod0(Class.java:3018)
at java.lang.Class.getMethod(Class.java:1784)
at sun.launcher.LauncherHelper.validateMainClass(LauncherHelper.java:544)
at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:526)
Caused by: java.lang.ClassNotFoundException: twitter4j.TwitterException
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
... 7 more

It looks like it's failing to find a dependent class (twitter4j.TwitterException) which is used in a method signature of a class you are using from your own code.
How do you get this compiled without error?
If that works though it may be an issue of incompatible versions of the twitter4j library to be present: one at compile time (with the TwitterException) and a different one at runtime (without the TwitterException).
This may be caused by your allowing to use "4.0 or higher" in the dependency. It may help to define an exact version there to track this down.

When you run a JAR file with the -jar switch, class path defined on the command line (or in environment variables) is ignored.
You will have to add a Class-Path manifest attribute that includes the location of your dependencies.
Maven-Jar-Plugin (or more exactly, the Maven Archiver configuration) supports this by using the addClasspath and classpathPrefix options. Note that you still have to ensure that the dependency libs end up in that directory (e. g. by using maven-assembly-plugin or by manually copying the dependencies there). Or build a fat jar with maven-assembly-plugin that includes all dependencies.

I will suggest you to do following:
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>2.2-beta-4</version>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<archive>
<manifest>
<mainClass>Main_Class</mainClass>
</manifest>
</archive>
</configuration>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
<finalName>Final_Jar_Name</finalName>

Eclipse / Maven: "Could not find the main class" Errors While Building Executable JAR

Updated: "Could not find the main class" turned out to be a red herring: In the line immediately before public static void main(String[] args) my class attempts to load a resource bundle from a file that was not included in the JAR. Failure to load this resource produced reporting that lead me in the wrong direction:
Caused by: java.util.MissingResourceException: Can't find bundle for base name propFile, locale en_US
at java.util.ResourceBundle.throwMissingResourceException(ResourceBundle.java:1427)
at java.util.ResourceBundle.getBundleImpl(ResourceBundle.java:1250)
at java.util.ResourceBundle.getBundle(ResourceBundle.java:705)
at com.foo.bar.MyApp(MyApp.java:103)
Could not find the main class: com.foo.bar.MyApp. Program will exit.
I'm developing on Win 7 64-bit with Eclipse Juno and JDK 1.6_45, both 32-bit. I'm generating an executable JAR with a mvn clean install invocation.
When I attempt to launch the app I've received "Could not find the main class" or "Failed to load Main-Class manifest attribute"
Similar ground has been covered here and here. I've read through these answers and the basic maven examples, but I'm still failing to end up
with an executable JAR.
I've attempted to execute the app with both java -jar MyApp-jar-with-dependencies and java -cp MyApp-jar-with-dependencies com.foo.bar.MyApp invocations
I find it particularly confusing that the MANIFEST.MF (contined within META-INF within the JAR) specifically lists my target main class, and the MyApp.class file is present in the directory tree at the correct location (com\foo\bar\MyApp.class).
I have refactored my package name and class name a few times over the course of development. Might this action have caused some referencing/classpath hiccup? Where else could the main class lookup failing?
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>
<parent>
[...]
</parent>
<groupId>com.foo.bar</groupId>
<artifactId>MyApp</artifactId>
<packaging>jar</packaging>
<version>2.0.0.0-SNAPSHOT</version>
<name>MY APP</name>
<url>http://maven.apache.org</url>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<issues-product>APP</issues-product>
<issues-component>MY_APP</issues-component>
</properties>
<dependencies>
[...]
</dependencies>
<build>
<finalName>${project.artifactId}</finalName>
<plugins>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>2.3.2</version>
<configuration>
<source>1.6</source>
<target>1.6</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-checkstyle-plugin</artifactId>
<version>${maven.checkstyle.version}</version>
<configuration>
[...]
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-pmd-plugin</artifactId>
<version>${maven.pmd.version}</version>
<configuration>
[...]
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>${maven.javadoc.version}</version>
</plugin>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<version>2.2.2</version>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<mainClass>com.foo.bar.MyApp</mainClass>
</manifest>
</archive>
</configuration>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
<pluginManagement>
[...]
</pluginManagement>
</build>
<reporting>
[...]
</reporting>
<scm>
[...]
</scm>
</project>
My MANIFEST.MF within the the output JAR:
Manifest-Version: 1.0
Archiver-Version: Plexus Archiver
Created-By: Apache Maven
Built-By: myname
Build-Jdk: 1.6.0_45
Main-Class: com.foo.bar.MyApp

I'm not sure why yours isn't working, here is a cut-n-paste from my working maven project. You should only have to replace com.pictureu.mains.MainGui with your main class to test
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<archive>
<manifest>
<mainClass>com.pictureu.mains.MainGui</mainClass>
</manifest>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
</plugin>

Playn mvn clean install error "NoClassDefFoundError: playn/core/game

so for a long time now i have been searching the web constantly looking at other peoples problems and fixes hoping they will be reverent to my issue, but i cant seem to find anyone with the same issue involving playn.
i can run "mvn test" the the cmd and mu little project runs perfectly, however when i come to finally exporting the project using "mvn clean install" and attemt to run the myApp-core-1.0-SNAPSHOT.jar i get an Exception:
Exception in thread "main" java.NoClassDefFoundError: playn/core/game
im just wondering if anone has come across this problem in the past and can point me in the right direction to overcoming it, since this app is my A-level coursework and is due to be handed in soon i am very worried i may not reach the deadline for handing in dates, i really hope this doesnt happen D:
this is my myApp-core 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/maven-
v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>com.ALevelWork</groupId>
<artifactId>zombiepanic</artifactId>
<version>1.0-SNAPSHOT</version>
</parent>
<artifactId>zombiepanic-core</artifactId>
<packaging>jar</packaging>
<name>ZombiePanic Core</name>
<dependencies>
<dependency>
<groupId>com.googlecode.playn</groupId>
<artifactId>playn-jbox2d</artifactId>
<version>${playn.version}</version>
</dependency>
<dependency>
<groupId>com.googlecode.playn</groupId>
<artifactId>playn-core</artifactId>
<version>${playn.version}</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<!-- Build an executable JAR -->
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<classpathPrefix>lib/</classpathPrefix>
<mainClass> ZombiePanic.core.ZombiePanic</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
</plugin>
</plugins>
<resources>
<!-- include the source files in our main jar for use by GWT -->
<resource>
<directory>${project.build.sourceDirectory}</directory>
</resource>
<!-- and continue to include our standard resources -->
<resource>
<directory>${basedir}/src/main/resources</directory>
</resource>
</resources>
</build>
</project>
Thanks in advance,
Jacob

i have fixed this problem by following this tutorial (http://jameswilliams.be/blog/entry/255), i was not linking the zombiepanic-core to the java backend (zombiepanic-java) to do this you need to firstly add this plug-in into the java backend pom.xml:
<plugin>
<groupId>org.sonatype.plugins</groupId>
<artifactId>jarjar-maven-plugin</artifactId>
<version>1.5</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>jarjar</goal>
</goals>
<configuration>
<rules />
</configuration>
</execution>
</executions>
once you have done this, link it to the core class (zombiepanic-core) by adding this also into the java backend pom.xml:
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<configuration>
<archive>
<manifest>
<mainClass>com.YourPackage.java.JarJarDemoJava</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
remember to link the main class to your java backend version, for example ZombiePanicJava instead of the core version which is just ZombiePanic.