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Maven Assembly Plugin : Resources are not copied as expected

I am using maven assembly to build my java application and package it as a JAR file. The resources are located in src/main/resources and they are not copied to the created JAR file.
The POM.XML is like this:
<build>
<pluginManagement><!-- lock down plugins versions to avoid using Maven defaults (may be moved to parent pom) -->
<plugins>
<!-- clean lifecycle, see https://maven.apache.org/ref/current/maven-core/lifecycles.html#clean_Lifecycle -->
<plugin>
<artifactId>maven-clean-plugin</artifactId>
<version>3.1.0</version>
</plugin>
<!-- default lifecycle, jar packaging: see https://maven.apache.org/ref/current/maven-core/default-bindings.html#Plugin_bindings_for_jar_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-jar-plugin</artifactId>
<version>3.0.2</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>
<!-- site lifecycle, see https://maven.apache.org/ref/current/maven-core/lifecycles.html#site_Lifecycle -->
<plugin>
<artifactId>maven-site-plugin</artifactId>
<version>3.7.1</version>
</plugin>
<plugin>
<artifactId>maven-project-info-reports-plugin</artifactId>
<version>3.0.0</version>
</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>com.test.Application</mainClass>
</manifest>
</archive>
</configuration>
<executions>
<execution>
<id>make-assembly</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
Please let me know how can I fix this! I tried to use Resource tag, but it did not work.

Maven Java integration

Here's a simple Java code with SL4J built with maven. Following commands have no issues. All of them work well
mvn compile
mvn package
mvn clean install
mvn exec:java
But when I try any of the following
java -cp target/MaventestApp-1.0-SNAPSHOT.jar com.maven.helloworld.App
jar tf ./target/MaventestApp-1.0-SNAPSHOT.jar
I get the following error
exception in thread "main" java.lang.NoClassDefFoundError: org/slf4j/LoggerFactory
at com.maven.helloworld.App.main(App.java:17)
Caused by: java.lang.ClassNotFoundException: org.slf4j.LoggerFactory
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:338)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
Here is the relevant part of my pom.xml file:
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<maven.compiler.source>1.7</maven.compiler.source>
<maven.compiler.target>1.7</maven.compiler.target>
<slf4jVersion>1.6.1</slf4jVersion>
</properties>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.11</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-simple</artifactId>
<version>${slf4jVersion}</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>${slf4jVersion}</version>
</dependency>
</dependencies>
<build>
<pluginManagement><!-- lock down plugins versions to avoid using Maven defaults (may be moved to parent pom) -->
<plugins>
<plugin>
<artifactId>maven-clean-plugin</artifactId>
<version>3.0.0</version>
</plugin>
<!-- see http://maven.apache.org/ref/current/maven-core/default-bindings.html#Plugin_bindings_for_jar_packaging -->
<plugin>
<artifactId>maven-resources-plugin</artifactId>
<version>3.0.2</version>
</plugin>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.7.0</version>
</plugin>
<plugin>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.20.1</version>
</plugin>
<plugin>
<artifactId>maven-jar-plugin</artifactId>
<version>3.0.2</version>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<mainClass>com.maven.helloworld.App</mainClass>
</manifest>
</archive>
</configuration>
</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>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>exec-maven-plugin</artifactId>
<version>1.2.1</version>
<executions>
<execution>
<goals>
<goal>java</goal>
</goals>
</execution>
</executions>
<configuration>
<mainClass>com.maven.helloworld.App</mainClass>
</configuration>
</plugin>
</plugins>
</pluginManagement>
</build>
Code for this sample is here
Can someone help me understand maven and execution process better? Appreciate your time.

The problem is how you are building your JAR file (dependencies are no included in it). You could use maven-assembly-plugin instead (see the differences between assembly and jar plugin here).
Basically, replace your current build section by the following:
<build>
<plugins>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<archive>
<manifest>
<mainClass>com.maven.helloworld.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>
</build>
Then execute the generated jar-with-dependencies using the following command:
java -jar target/MaventestApp-1.0-SNAPSHOT-jar-with-dependencies.jar
See more about creating executable JARs here.

There is the Exec Maven Plugin that should do the job. Something like
mvn exec:java -Dexec.mainClass=com.maven.helloworld.App
The actual problem is that you only add your jar to the classpath and since you do not have the sl4j-classes inside your own archive but declared them as external dependency they are simple missing (aka NoClassDefFoundError).
The command above links all runtime dependencies to the classpath as configured in the pom.

How to create a fat jar?

With SpringBoot, you have the #SpringBootApplication annotation, but what is the equivalent with the neat Java Spark framework?
IntelliJ creates a Maven project and I added the spark dependency, but running the install goal, I get a 5 KB jar with no manifest. Not an executable jar.
The pom.xml created thus far is as follows:
<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>sparkdemo</groupId>
<artifactId>sparkdemo</artifactId>
<version>1.0 </version>
<packaging>jar</packaging>
<name>sparkdemo</name>
<url>http://maven.apache.org</url>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>3.8.1</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.sparkjava</groupId>
<artifactId>spark-core</artifactId>
<version>2.5.4</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.3</version>
<configuration>
<source>${java.version}</source>
<target>${java.version}</target>
<optimize>true</optimize>
<debug>true</debug>
</configuration>
</plugin>
</plugins>
</build>
</project>
Would appreciate any suggestions....Thanks!

What you need here is an executable jar that will not only contain your classes, but also classes from all your dependencies.
For that you can use the Maven Assembly Plugin.
See the sample code below.
<project>
[...]
<build>
[...]
<plugins>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<version>3.0.0</version>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<archive>
<manifest>
<mainClass>org.sample.App</mainClass> // specify your main class here
</manifest>
</archive>
</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>
[...]
</project>
Then, run mvn package and the executable jar should be located in the folder target (with a name like ProjectName-1.0-SNAPSHOT-jar-with-dependencies.jar).

Looks like you are looking for maven assembly plugin
Add this in the plugin section and run mvn package
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>3.0.0</version>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
<executions>
<execution>
<id>assemble-all</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>

Class Not Found Exception for a Maven Jar

I use maven to manage dependency in my project. This is my pom.xml
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.prasanna</groupId>
<artifactId>fft-java</artifactId>
<version>1.0.0</version>
<packaging>jar</packaging>
<name>fft-java</name>
<url>http://maven.apache.org</url>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.11</version>
</dependency>
<dependency>
<groupId>com.github.wendykierp</groupId>
<artifactId>JTransforms</artifactId>
<version>3.0</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<!-- Build an executable JAR -->
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.4</version>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<classpathPrefix>lib/</classpathPrefix>
<mainClass>com.prasanna.TestFFT</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
</plugins>
</build>
</project>
I have only one java class in my application. When I run my class from my application, it runs as expected. Whereas if I make a mvn package and try to run it from the terminal as java -jar test-fft.jar, I get a java.lang.ClassNotFoundException: org.jtransforms.fft.DoubleFFT_2D
But this DoubleFFT_2D is a part of JTransforms dependency that I have added. How would I run this jar?

<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<executions>
<execution>
<id>copy-dependencies</id>
<phase>prepare-package</phase>
<goals>
<goal>copy-dependencies</goal>
</goals>
<configuration>
<outputDirectory>Mydir/lib</outputDirectory>
<overWriteReleases>false</overWriteReleases>
<overWriteSnapshots>false</overWriteSnapshots>
<overWriteIfNewer>true</overWriteIfNewer>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.4</version>
<configuration>
<outputDirectory>MyDir</outputDirectory>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<classpathPrefix>lib</classpathPrefix>
<mainClass>com.test.entryClassOfJarHavingMainMethod</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
</plugins>
</build>
Use these configuration in pom.xml to create jar with lib folder and package as a jar

use the maven-assembly plugin to build the jar with dependency.
<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>

Error while adding SVN revision in JAR manifest with Maven and maven-bundle-plugin

I am trying to add SVN revision number in the manifest of my projects. To do so, I used Maven build number plugin and added the following lines in my Super POM:
<!-- Gets the SVN revision number -->
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>buildnumber-maven-plugin</artifactId>
<version>1.1</version>
<executions>
<execution>
<phase>validate</phase>
<goals>
<goal>create</goal>
</goals>
</execution>
</executions>
<configuration>
<doCheck>false</doCheck>
<doUpdate>false</doUpdate>
<providerImplementations>
<svn>javasvn</svn>
</providerImplementations>
</configuration>
</plugin>
<!-- Add the SVN revision number in the manifest (works on Hudson only) -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.1</version>
<configuration>
<archive>
<manifest>
<addDefaultImplementationEntries>true</addDefaultImplementationEntries>
</manifest>
<manifestEntries>
<Implementation-Build>${buildNumber}</Implementation-Build>
</manifestEntries>
</archive>
</configuration>
</plugin>
Note the configuration:
<doCheck>false</doCheck>
<doUpdate>false</doUpdate>
I did that on purpose because if I have local modifications "doCheck" will prevent me from compiling (and I want to compile and test BEFORE commiting my work).
The "doUpdate" is also a problem for me as I don't necessarily want to update the code from repository. Same reason than above, I want to test locally before commiting (and potentially solving conflicts).
My problem is that in the manifest, what appears is:
Implementation-Build: ${buildNumber}
Thus the variable is not interpreted. What did I miss?
Thanks
Edit:
The problem is in fact with maven-bundle-plugin. I use it in my projets to generate OSGi bundles.
The POM packaging of the projects is thus:
<packaging>bundle</packaging>
Instead of:
<packaging>jar</packaging>
I guess this messes with the Maven lifecycle.
When I remove the maven-bundle-plugin everything works fine. But I cannot remove it as my applications are OSGi apps.

The problem was mixing maven-bundle-plugin and maven-jar-plugin to manipulate the Jar MANIFEST.
The solution:
In the Super POM:
<build>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.felix</groupId>
<artifactId>maven-bundle-plugin</artifactId>
<version>2.3.7</version>
<extensions>true</extensions>
<configuration>
<instructions>
<Implementation-Build>${buildNumber}</Implementation-Build>
</instructions>
</configuration>
</plugin>
...
</plugins>
</pluginManagement>
<plugins>
<!-- Gets the SVN revision number -->
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>buildnumber-maven-plugin</artifactId>
<version>1.1</version>
<executions>
<execution>
<phase>validate</phase>
<goals>
<goal>create</goal>
</goals>
</execution>
</executions>
<configuration>
<doCheck>false</doCheck>
<doUpdate>false</doUpdate>
<providerImplementations>
<svn>javasvn</svn>
</providerImplementations>
</configuration>
-</plugin>
</plugins>
</build>
And that's it!

Instead of using configuration/archive try using configuration/instructions to add your ${buildNumber}, like this:
<plugin>
<groupId>org.apache.felix</groupId>
<artifactId>maven-bundle-plugin</artifactId>
<extensions>true</extensions>
<configuration>
<instructions>
<Implementation-Build>${buildNumber}</Implementation-Build>
</instructions>
</configuration>
</plugin>
With your approach and Maven 2, it all worked. We switched to Maven 3, the maven-bundle-plugin was not happy (same behavior as yours). This approach did the trick.

You can make use of Maven Plugin Management.
Add your plugin definitions in the super pom under <pluginManagement/> like so:
<project>
...
<build>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>buildnumber-maven-plugin</artifactId>
<version>1.1</version>
<executions>
<execution>
<phase>validate</phase>
<goals>
<goal>create</goal>
</goals>
</execution>
</executions>
<configuration>
<doCheck>false</doCheck>
<doUpdate>false</doUpdate>
<providerImplementations>
<svn>javasvn</svn>
</providerImplementations>
</configuration>
</plugin>
<!-- Add the SVN revision number in the manifest (works on Hudson only) -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.1</version>
<configuration>
<archive>
<manifest>
<addDefaultImplementationEntries>true</addDefaultImplementationEntries>
</manifest>
<manifestEntries>
<Implementation-Build>${buildNumber}</Implementation-Build>
</manifestEntries>
</archive>
</configuration>
</plugin>
</plugins>
</pluginManagement>
</build>
...
</project>
And then in the project where you want to use these now configured plugins you add this to the poms:
<project>
...
<build>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>buildnumber-maven-plugin</artifactId>
</plugin>
<plugin>
<artifactId>maven-jar-plugin</artifactId>
</plugin>
</plugins>
</build>
...
</project>
That should sort it out for you.