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Getting "java.lang.NoClassDefFoundError: org/apache/kafka/clients/consumer/KafkaConsumer" when I try to run the Java -jar command after maven build [duplicate]

Is there a way to force maven(2.0.9) to include all the dependencies in a single jar file?
I have a project the builds into a single jar file. I want the classes from dependencies to be copied into the jar as well.
Update: I know that I cant just include a jar file in a jar file. I'm searching for a way to unpack the jars that are specified as dependencies, and package the class files into my jar.

You can do this using the maven-assembly plugin with the "jar-with-dependencies" descriptor. Here's the relevant chunk from one of our pom.xml's that does this:
<build>
<plugins>
<!-- any other plugins -->
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
</plugin>
</plugins>
</build>

With Maven 2, the right way to do this is to use the Maven2 Assembly Plugin which has a pre-defined descriptor file for this purpose and that you could just use on the command line:
mvn assembly:assembly -DdescriptorId=jar-with-dependencies
If you want to make this jar executable, just add the main class to be run to the plugin configuration:
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<archive>
<manifest>
<mainClass>my.package.to.my.MainClass</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
If you want to create that assembly as part of the normal build process, you should bind the single or directory-single goal (the assembly goal should ONLY be run from the command line) to a lifecycle phase (package makes sense), something like this:
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<executions>
<execution>
<id>create-my-bundle</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
...
</configuration>
</execution>
</executions>
</plugin>
Adapt the configuration element to suit your needs (for example with the manifest stuff as spoken).

If you want to do an executable jar file, them need set the main class too. So the full configuration should be.
<plugins>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
<configuration>
<!-- ... -->
<archive>
<manifest>
<mainClass>fully.qualified.MainClass</mainClass>
</manifest>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
</plugin>
</plugins>

Method 1: Copy the dependencies' JAR files into target/lib and then add them to the JAR's classpath in MANIFEST:
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<configuration>
<outputDirectory>${project.build.directory}/lib</outputDirectory>
<excludeTransitive>false</excludeTransitive>
<stripVersion>false</stripVersion>
</configuration>
<executions>
<execution>
<id>copy-dependencies</id>
<phase>package</phase>
<goals>
<goal>copy-dependencies</goal>
</goals>
</execution>
</executions>
</plugin>
<!-- Add LIB folder to classPath -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.4</version>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<classpathPrefix>lib/</classpathPrefix>
</manifest>
</archive>
</configuration>
</plugin>
Method 2: Unpack all dependencies and repack their classes and resources into one flat JAR. Note: The overlapping resources will be randomly lost!
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<executions>
<execution>
<phase>package</phase>
<goals><goal>single</goal></goals>
</execution>
</executions>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
</plugin>

There's the shade maven plugin. It can be used to package and rename dependencies (to omit dependency problems on the classpath).

You can use the newly created jar using a <classifier> tag.
<dependencies>
<dependency>
<groupId>your.group.id</groupId>
<artifactId>your.artifact.id</artifactId>
<version>1.0</version>
<type>jar</type>
<classifier>jar-with-dependencies</classifier>
</dependency>
</dependencies>

If you (like me) dont particularly like the jar-with-dependencies approach described above,
the maven-solution I prefer is to simply build a WAR-project,
even if it is only a stand-alone java application you are building:
Make a normal maven jar-project, that will build your jar-file (without the dependencies).
Also, setup a maven war-project (with only an empty src/main/webapp/WEB-INF/web.xml file, which will avoid a warning/error in the maven-build), that only has your jar-project as a dependency, and make your jar-project a <module> under your war-project. (This war-project is only a simple trick to wrap all your jar-file dependencies into a zip-file.)
Build the war-project to produce the war-file.
In the deployment-step, simply rename your .war-file to *.zip and unzip it.
You should now have a lib-directory (which you can move where you want it) with your jar and all the dependencies you need to run your application:
java -cp 'path/lib/*' MainClass
(The wildcard in classpath works in Java-6 or higher)
I think this is both simpler to setup in maven (no need to mess around with the assembly plugin) and also gives you a clearer view of the application-structure (you will see the version-numbers of all dependent jars in plain view, and avoid clogging everything into a single jar-file).

http://fiji.sc/Uber-JAR provides an excellent explanation of the alternatives:
There are three common methods for constructing an uber-JAR:
Unshaded. Unpack all JAR files, then repack them into a single JAR.
Pro: Works with Java's default class loader.
Con: Files present in multiple JAR files with the same path (e.g.,
META-INF/services/javax.script.ScriptEngineFactory) will overwrite one
another, resulting in faulty behavior.
Tools: Maven Assembly
Plugin, Classworlds Uberjar
Shaded. Same as unshaded, but rename (i.e., "shade") all packages of all dependencies.
Pro: Works with Java's default class loader.
Avoids some (not all) dependency version clashes.
Con: Files
present in multiple JAR files with the same path (e.g.,
META-INF/services/javax.script.ScriptEngineFactory) will overwrite one
another, resulting in faulty behavior.
Tools: Maven Shade Plugin
JAR of JARs. The final JAR file contains the other JAR files embedded within.
Pro: Avoids dependency version clashes. All
resource files are preserved.
Con: Needs to bundle a special
"bootstrap" classloader to enable Java to load classes from the
wrapped JAR files. Debugging class loader issues becomes more complex.
Tools: Eclipse JAR File Exporter, One-JAR.

My definitive solution on Eclipse Luna and m2eclipse:
Custom Classloader (download and add to your project, 5 classes only)
:http://git.eclipse.org/c/jdt/eclipse.jdt.ui.git/plain/org.eclipse.jdt.ui/jar%20in%20jar%20loader/org/eclipse/jdt/internal/jarinjarloader/;
this classloader is very best of one-jar classloader and very fast;
<project.mainClass>org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader</project.mainClass>
<project.realMainClass>my.Class</project.realMainClass>
Edit in JIJConstants "Rsrc-Class-Path" to "Class-Path"
mvn clean dependency:copy-dependencies package
is created a jar with dependencies in lib folder with a thin classloader
<build>
<resources>
<resource>
<directory>src/main/java</directory>
<includes>
<include>**/*.java</include>
<include>**/*.properties</include>
</includes>
</resource>
<resource>
<directory>src/main/resources</directory>
<filtering>true</filtering>
<includes>
<include>**/*</include>
</includes>
<targetPath>META-INF/</targetPath>
</resource>
<resource>
<directory>${project.build.directory}/dependency/</directory>
<includes>
<include>*.jar</include>
</includes>
<targetPath>lib/</targetPath>
</resource>
</resources>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<mainClass>${project.mainClass}</mainClass>
<classpathPrefix>lib/</classpathPrefix>
</manifest>
<manifestEntries>
<Rsrc-Main-Class>${project.realMainClass} </Rsrc-Main-Class>
<Class-Path>./</Class-Path>
</manifestEntries>
</archive>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<executions>
<execution>
<id>copy-dependencies</id>
<phase>package</phase>
<goals>
<goal>copy-dependencies</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</pluginManagement>
</build>

Putting Maven aside, you can put JAR libraries inside the Main Jar but you will need to use your own classloader.
Check this project: One-JAR link text

I was trying to do sth similar, but I didn't want all jars to be included. I wanted to include some specific directories from the given dependency. In addition classifier tag was already occupied, so I couldn't do:
<dependencies>
<dependency>
<groupId>your.group.id</groupId>
<artifactId>your.artifact.id</artifactId>
<version>1.0</version>
<type>jar</type>
<classifier>jar-with-dependencies</classifier>
</dependency>
</dependencies>
I used maven-dependency-plugin and unpack goal
And unpacked what I wanted to the ${project.build.directory}/classes, otherwise it will be omitted
Because it was in the classes directory, maven finally placed it in the jar
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<executions>
<execution>
<id>unpack</id>
<phase>prepare-package</phase>
<goals>
<goal>unpack</goal>
</goals>
<configuration>
<artifactItems>
<artifactItem>
<groupId>my.group</groupId>
<artifactId>my.artifact</artifactId>
<classifier>occupied</classifier>
<version>1.0</version>
<type>jar</type>
</artifactItem>
</artifactItems>
<outputDirectory>${project.build.directory}/classes</outputDirectory>
<includes>aaa/**, bbb/**, ccc/**</includes>
</configuration>
</execution>
</executions>
</plugin>

This post may be a bit old, but I also had the same problem recently. The first solution proposed by John Stauffer is a good one, but I had some problems as I am working this spring. The spring's dependency-jars I use have some property files and xml-schemas declaration which share the same paths and names. Although these jars come from the same versions, the jar-with-dependencies maven-goal was overwriting theses file with the last file found.
In the end, the application was not able to start as the spring jars could not find the correct properties files. In this case the solution propose by Rop have solved my problem.
Also since then, the spring-boot project now exist. It has a very cool way to manage this problem by providing a maven goal which overload the package goal and provide its own class loader. See spring-boots Reference Guide

Have a look at this answer:
I am creating an installer that runs as a Java JAR file and it needs to unpack WAR and JAR files into appropriate places in the installation directory. The dependency plugin can be used in the package phase with the copy goal and it will download any file in the Maven repository (including WAR files) and write them where ever you need them. I changed the output directory to ${project.build.directory}/classes and then end result is that the normal JAR task includes my files just fine. I can then extract them and write them into the installation directory.
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<executions>
<execution>
<id>getWar</id>
<phase>package</phase>
<goals>
<goal>copy</goal>
</goals>
<configuration>
<artifactItems>
<artifactItem>
<groupId>the.group.I.use</groupId>
<artifactId>MyServerServer</artifactId>
<version>${env.JAVA_SERVER_REL_VER}</version>
<type>war</type>
<destFileName>myWar.war</destFileName>
</artifactItem>
</artifactItems>
<outputDirectory>${project.build.directory}/classes</outputDirectory>
</configuration>
</execution>
</executions>

Thanks
I have added below snippet in POM.xml file and Mp problem resolved and
create fat jar file that include all dependent jars.
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
<configuration>
<descriptorRefs>
<descriptorRef>dependencies</descriptorRef>
</descriptorRefs>
</configuration>
</plugin>
</plugins>

I found this to be the clearest answer; other answers here were missing things that weren't obvious to me such as mvn clean package command for example, and adding the plugin separately as a dependancy also. All of which are probably obvious to more habitual maven users.
https://howtodoinjava.com/maven/executable-jar-with-dependencies/

To make it more simple, You can use the below plugin.
<plugin>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
<executions>
<execution>
<goals>
<goal>repackage</goal>
</goals>
<configuration>
<classifier>spring-boot</classifier>
<mainClass>
com.nirav.certificate.CertificateUtility
</mainClass>
</configuration>
</execution>
</executions>
</plugin>

Maven - How to include single java files as sources/depedencies

I have created a multi-module project in maven which is as follows:
root/pom.xml
|________client/pom.xml
|________/src/main/java
|________/src/main/resources
|________common/pom.xml
|________/src/main/java
|________tools/pom.xml
|________/src/main/java
|________server/pom.xml
|________/src/main/java
|________/src/main/resources
I would like to compile the "client" module code which depends on ALL java classes in "common" module but on SOME java classes in the "tools" module.
Using the build-helper-maven-plugin as below, I was able to add all java source files under common/ path, but I need a way to define individual java files as sources which are under tools/.
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<version>3.2.0</version>
<executions>
<execution>
<phase>generate-sources</phase>
<goals>
<goal>add-source</goal>
</goals>
<configuration>
<sources>
<source>../common/src/main/java</source>
<!-- Adding single java files as below does not work -->
<source>../tools/log/Log.java</source>
<source>../tools/socket/SocketClient.java</source>
<!----------------------------------------------------->
</sources>
</configuration>
</execution>
</executions>

You should include module "common" and "tools" as dependency in "client"
Then you can run build in the root of project: mvn clean install - it will build all modules.

Don't try to use parts of a module as dependency. Maven does not support this and it results in brittle and hard to maintain constructions.
If you only need parts of tools, then this is a clear signal that tools is too large and you need to split it up into two modules.

Ok, based on the comments received it seems that the ideal solution is to break the modules into sub-modules and use those as dependencies. However, as this is currently a time consuming task, I am posting a quick and dirty solution on how you can include one or more java files into your build by copying the files under a new source directory, src/main/external, and then add this directory as part of your sources.
<build>
<plugins>
<plugin>
<artifactId>maven-resources-plugin</artifactId>
<version>3.2.0</version>
<executions>
<execution>
<id>copy-source-java-files</id>
<phase>generate-resources</phase>
<goals>
<goal>copy-resources</goal>
</goals>
<configuration>
<outputDirectory>src/main/external</outputDirectory>
<overwrite>true</overwrite>
<resources>
<resource>
<!-- External source directory -->
<directory>../tools/src/main/java/</directory>
<includes>
<!-- Files to be copied along with their directory paths -->
<include>tools/log/Log.java</include>
<include>tools/socket/SocketClient.java</include>
<include>tools/client/reader/**</include>
</includes>
</resource>
</resources>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<version>3.2.0</version>
<executions>
<execution>
<phase>generate-sources</phase>
<goals>
<goal>add-source</goal>
</goals>
<configuration>
<sources>
<source>src/main/java</source>
<source>src/main/resources</source>
<source>../common/src/main/java</source>
<!-- Here we add the source with the files copied -->
<source>src/main/external</source>
</sources>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
The output after compilation would be as follows:
root/pom.xml
|________client/pom.xml
|________/src/main/java
|________/src/main/resources
|________/src/main/external <----- This contains all external java files.

How to make Eclipse recognize folders as "code folders" when a project is imported?

I have a Maven Java project in which I added to the pom:
<build>
....
<plugin>
<!-- adding second test source directory (just for integration tests) -->
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<version>${plugin.build-helper-maven-plugin.version}</version>
<executions>
<execution>
<id>add-integration-test-source</id>
<phase>generate-test-sources</phase>
<goals>
<goal>add-test-source</goal>
</goals>
<configuration>
<sources>
<source>src/integration-test/java</source>
</sources>
</configuration>
</execution>
<execution>
<id>add-integration-test-resource</id>
<phase>generate-test-resources</phase>
<goals>
<goal>add-test-resource</goal>
</goals>
<configuration>
<resources>
<resource>
<directory>src/integration-test/resources</directory>
</resource>
</resources>
</configuration>
</execution>
</executions>
</plugin>
</build>
InteliJ recognized my java and resource folders under integration-test as a code folder, but Eclipse doesn't.
Is there any way that eclipse adds these folders as code folders when the project is imported?

Try to right click on your folder in Project Explorer select Build Path option in context menu and later click Use as Source Folder in menu which appears after choosing Build Path.

I suggest not using your own directory layout with Maven since this will cause many problems and you always have to configure around it. Just stick to the standard.
Separate integration tests and unit tests not by their source folders, but by their name.
Put all tests in src/test/java. You don't have to configure anything at this point, this path is taken by default.
Call integration tests IT*.java and unit tests UT*.java.
They can be run separately because maven-surefire-plugin executes unit tests and maven-failsafe-plugin executed integration tests. You can define filename patterns for identifying the test classes.
You could also create profiles for running only UTs or only ITs.
<project>
<!-- ... -->
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.13</version>
<configuration>
<includes>
<include>**/UT*.java</include>
</includes>
<excludes>
<exclude>**/IT*.java</exclude>
</excludes>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<version>2.18</version>
<configuration>
<includes>
<include>**/IT*.java</include>
</includes>
</configuration>
<executions>
<execution>
<id>failsafe-integration-tests</id>
<phase>integration-test</phase>
<goals>
<goal>integration-test</goal>
</goals>
</execution>
</executions>
</plugin>
Further reading: http://tomaszdziurko.pl/2013/01/running-unit-tests-integration-tests-separately-maven-testng/
There is also a interesting article about the correct usage of integration tests here: http://zeroturnaround.com/rebellabs/the-correct-way-to-use-integration-tests-in-your-build-process/

Maven Source Plugin - How do I generate the source jar for ONLY the classes I want included

Currently, the project I am working on has all of the code for the web service in a single and is creating a war and a jar file.
The Jar file only contains the bare minimum of classes shared by other projects.
I don't have the option to split the shared classes out into a separate core project at this time. (Though I would prefer that)
I'm trying to put only the necessary java files in the source jar:
Common_Model-1.1.2.jar
Common_Model-1.1.2.jar-sources
I have something like this in my POM:
<plugin>
<artifactId>maven-jar-plugin</artifactId>
<version>2.3.2</version>
<executions>
<execution>
<goals>
<goal>jar</goal>
</goals>
<configuration>
<includes>
<include>gov/app/api/common/models/**</include>
<include>gov/app/api/intra/models/**</include>
<include>gov/app/api/models/**</include>
</includes>
<finalName>Common_Model-1.1.2</finalName>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-source-plugin</artifactId>
<executions>
<execution>
<goals>
<goal>jar</goal>
</goals>
<configuration>
<includes>
<include>gov/app/api/common/models/**</include>
<include>gov/app/api/intra/models/**</include>
<include>gov/app/api/models/**</include>
</includes>
<finalName>Common_Model-1.1.2</finalName>
</configuration>
</execution>
</executions>
</plugin>
While this does create the sources jar, it ignores the includes configuration and adds all of the .java files from the entire project.
I've also tried using <excludes>, but that too is ignored.

I tried this in my project:
<include>com/sandbox/**/Permutations*</include>
And the resulting Common_Model-1.1.2-sources.jar only had this one file in it named Permutations.java When I tried
<include>com/sandbox/Permutations*</include>
<include>com/sandbox/Sandbox*</include>
The jar had only those two files. So what you've got should work. I suspect your patterns are too broad.

Including dependencies in a jar with Maven

Is there a way to force maven(2.0.9) to include all the dependencies in a single jar file?
I have a project the builds into a single jar file. I want the classes from dependencies to be copied into the jar as well.
Update: I know that I cant just include a jar file in a jar file. I'm searching for a way to unpack the jars that are specified as dependencies, and package the class files into my jar.

You can do this using the maven-assembly plugin with the "jar-with-dependencies" descriptor. Here's the relevant chunk from one of our pom.xml's that does this:
<build>
<plugins>
<!-- any other plugins -->
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
</plugin>
</plugins>
</build>

With Maven 2, the right way to do this is to use the Maven2 Assembly Plugin which has a pre-defined descriptor file for this purpose and that you could just use on the command line:
mvn assembly:assembly -DdescriptorId=jar-with-dependencies
If you want to make this jar executable, just add the main class to be run to the plugin configuration:
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<archive>
<manifest>
<mainClass>my.package.to.my.MainClass</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
If you want to create that assembly as part of the normal build process, you should bind the single or directory-single goal (the assembly goal should ONLY be run from the command line) to a lifecycle phase (package makes sense), something like this:
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<executions>
<execution>
<id>create-my-bundle</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
...
</configuration>
</execution>
</executions>
</plugin>
Adapt the configuration element to suit your needs (for example with the manifest stuff as spoken).

If you want to do an executable jar file, them need set the main class too. So the full configuration should be.
<plugins>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
<configuration>
<!-- ... -->
<archive>
<manifest>
<mainClass>fully.qualified.MainClass</mainClass>
</manifest>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
</plugin>
</plugins>

Method 1: Copy the dependencies' JAR files into target/lib and then add them to the JAR's classpath in MANIFEST:
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<configuration>
<outputDirectory>${project.build.directory}/lib</outputDirectory>
<excludeTransitive>false</excludeTransitive>
<stripVersion>false</stripVersion>
</configuration>
<executions>
<execution>
<id>copy-dependencies</id>
<phase>package</phase>
<goals>
<goal>copy-dependencies</goal>
</goals>
</execution>
</executions>
</plugin>
<!-- Add LIB folder to classPath -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.4</version>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<classpathPrefix>lib/</classpathPrefix>
</manifest>
</archive>
</configuration>
</plugin>
Method 2: Unpack all dependencies and repack their classes and resources into one flat JAR. Note: The overlapping resources will be randomly lost!
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<executions>
<execution>
<phase>package</phase>
<goals><goal>single</goal></goals>
</execution>
</executions>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
</plugin>

There's the shade maven plugin. It can be used to package and rename dependencies (to omit dependency problems on the classpath).

You can use the newly created jar using a <classifier> tag.
<dependencies>
<dependency>
<groupId>your.group.id</groupId>
<artifactId>your.artifact.id</artifactId>
<version>1.0</version>
<type>jar</type>
<classifier>jar-with-dependencies</classifier>
</dependency>
</dependencies>

If you (like me) dont particularly like the jar-with-dependencies approach described above,
the maven-solution I prefer is to simply build a WAR-project,
even if it is only a stand-alone java application you are building:
Make a normal maven jar-project, that will build your jar-file (without the dependencies).
Also, setup a maven war-project (with only an empty src/main/webapp/WEB-INF/web.xml file, which will avoid a warning/error in the maven-build), that only has your jar-project as a dependency, and make your jar-project a <module> under your war-project. (This war-project is only a simple trick to wrap all your jar-file dependencies into a zip-file.)
Build the war-project to produce the war-file.
In the deployment-step, simply rename your .war-file to *.zip and unzip it.
You should now have a lib-directory (which you can move where you want it) with your jar and all the dependencies you need to run your application:
java -cp 'path/lib/*' MainClass
(The wildcard in classpath works in Java-6 or higher)
I think this is both simpler to setup in maven (no need to mess around with the assembly plugin) and also gives you a clearer view of the application-structure (you will see the version-numbers of all dependent jars in plain view, and avoid clogging everything into a single jar-file).

http://fiji.sc/Uber-JAR provides an excellent explanation of the alternatives:
There are three common methods for constructing an uber-JAR:
Unshaded. Unpack all JAR files, then repack them into a single JAR.
Pro: Works with Java's default class loader.
Con: Files present in multiple JAR files with the same path (e.g.,
META-INF/services/javax.script.ScriptEngineFactory) will overwrite one
another, resulting in faulty behavior.
Tools: Maven Assembly
Plugin, Classworlds Uberjar
Shaded. Same as unshaded, but rename (i.e., "shade") all packages of all dependencies.
Pro: Works with Java's default class loader.
Avoids some (not all) dependency version clashes.
Con: Files
present in multiple JAR files with the same path (e.g.,
META-INF/services/javax.script.ScriptEngineFactory) will overwrite one
another, resulting in faulty behavior.
Tools: Maven Shade Plugin
JAR of JARs. The final JAR file contains the other JAR files embedded within.
Pro: Avoids dependency version clashes. All
resource files are preserved.
Con: Needs to bundle a special
"bootstrap" classloader to enable Java to load classes from the
wrapped JAR files. Debugging class loader issues becomes more complex.
Tools: Eclipse JAR File Exporter, One-JAR.

My definitive solution on Eclipse Luna and m2eclipse:
Custom Classloader (download and add to your project, 5 classes only)
:http://git.eclipse.org/c/jdt/eclipse.jdt.ui.git/plain/org.eclipse.jdt.ui/jar%20in%20jar%20loader/org/eclipse/jdt/internal/jarinjarloader/;
this classloader is very best of one-jar classloader and very fast;
<project.mainClass>org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader</project.mainClass>
<project.realMainClass>my.Class</project.realMainClass>
Edit in JIJConstants "Rsrc-Class-Path" to "Class-Path"
mvn clean dependency:copy-dependencies package
is created a jar with dependencies in lib folder with a thin classloader
<build>
<resources>
<resource>
<directory>src/main/java</directory>
<includes>
<include>**/*.java</include>
<include>**/*.properties</include>
</includes>
</resource>
<resource>
<directory>src/main/resources</directory>
<filtering>true</filtering>
<includes>
<include>**/*</include>
</includes>
<targetPath>META-INF/</targetPath>
</resource>
<resource>
<directory>${project.build.directory}/dependency/</directory>
<includes>
<include>*.jar</include>
</includes>
<targetPath>lib/</targetPath>
</resource>
</resources>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<mainClass>${project.mainClass}</mainClass>
<classpathPrefix>lib/</classpathPrefix>
</manifest>
<manifestEntries>
<Rsrc-Main-Class>${project.realMainClass} </Rsrc-Main-Class>
<Class-Path>./</Class-Path>
</manifestEntries>
</archive>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<executions>
<execution>
<id>copy-dependencies</id>
<phase>package</phase>
<goals>
<goal>copy-dependencies</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</pluginManagement>
</build>

Putting Maven aside, you can put JAR libraries inside the Main Jar but you will need to use your own classloader.
Check this project: One-JAR link text

I was trying to do sth similar, but I didn't want all jars to be included. I wanted to include some specific directories from the given dependency. In addition classifier tag was already occupied, so I couldn't do:
<dependencies>
<dependency>
<groupId>your.group.id</groupId>
<artifactId>your.artifact.id</artifactId>
<version>1.0</version>
<type>jar</type>
<classifier>jar-with-dependencies</classifier>
</dependency>
</dependencies>
I used maven-dependency-plugin and unpack goal
And unpacked what I wanted to the ${project.build.directory}/classes, otherwise it will be omitted
Because it was in the classes directory, maven finally placed it in the jar
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<executions>
<execution>
<id>unpack</id>
<phase>prepare-package</phase>
<goals>
<goal>unpack</goal>
</goals>
<configuration>
<artifactItems>
<artifactItem>
<groupId>my.group</groupId>
<artifactId>my.artifact</artifactId>
<classifier>occupied</classifier>
<version>1.0</version>
<type>jar</type>
</artifactItem>
</artifactItems>
<outputDirectory>${project.build.directory}/classes</outputDirectory>
<includes>aaa/**, bbb/**, ccc/**</includes>
</configuration>
</execution>
</executions>
</plugin>

This post may be a bit old, but I also had the same problem recently. The first solution proposed by John Stauffer is a good one, but I had some problems as I am working this spring. The spring's dependency-jars I use have some property files and xml-schemas declaration which share the same paths and names. Although these jars come from the same versions, the jar-with-dependencies maven-goal was overwriting theses file with the last file found.
In the end, the application was not able to start as the spring jars could not find the correct properties files. In this case the solution propose by Rop have solved my problem.
Also since then, the spring-boot project now exist. It has a very cool way to manage this problem by providing a maven goal which overload the package goal and provide its own class loader. See spring-boots Reference Guide

Have a look at this answer:
I am creating an installer that runs as a Java JAR file and it needs to unpack WAR and JAR files into appropriate places in the installation directory. The dependency plugin can be used in the package phase with the copy goal and it will download any file in the Maven repository (including WAR files) and write them where ever you need them. I changed the output directory to ${project.build.directory}/classes and then end result is that the normal JAR task includes my files just fine. I can then extract them and write them into the installation directory.
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<executions>
<execution>
<id>getWar</id>
<phase>package</phase>
<goals>
<goal>copy</goal>
</goals>
<configuration>
<artifactItems>
<artifactItem>
<groupId>the.group.I.use</groupId>
<artifactId>MyServerServer</artifactId>
<version>${env.JAVA_SERVER_REL_VER}</version>
<type>war</type>
<destFileName>myWar.war</destFileName>
</artifactItem>
</artifactItems>
<outputDirectory>${project.build.directory}/classes</outputDirectory>
</configuration>
</execution>
</executions>

Thanks
I have added below snippet in POM.xml file and Mp problem resolved and
create fat jar file that include all dependent jars.
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
<configuration>
<descriptorRefs>
<descriptorRef>dependencies</descriptorRef>
</descriptorRefs>
</configuration>
</plugin>
</plugins>

I found this to be the clearest answer; other answers here were missing things that weren't obvious to me such as mvn clean package command for example, and adding the plugin separately as a dependancy also. All of which are probably obvious to more habitual maven users.
https://howtodoinjava.com/maven/executable-jar-with-dependencies/

To make it more simple, You can use the below plugin.
<plugin>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
<executions>
<execution>
<goals>
<goal>repackage</goal>
</goals>
<configuration>
<classifier>spring-boot</classifier>
<mainClass>
com.nirav.certificate.CertificateUtility
</mainClass>
</configuration>
</execution>
</executions>
</plugin>