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jar executable is dysfunctional while it is functional in Netbeans maven project

I have a maven project in Netbeans.
Running it shows a GUI in which you can select and read files using a JFileChooser.
The file chooser has the method getSelectedFiles() which returns a File[] which then I feed into fileProccesing(File[] files) to read them using PDDocument.load(file) from Apache pdfBox depedency.
Debugging has led to the conclusion bellow.
When running in Netbeans it works fine but when it's running as a jar executable it stops at the PDDocument.load(file) command. However no IOException is thrown.
Ether JFileChooser getSelectedFiles() returns some abnormal type of files or my pom.xml is problematic in some way. You can see my pom.xml bellow.
<?xml version="1.0" encoding="UTF-8"?>
4.0.0
<groupId>application</groupId>
<artifactId>toolToManagePdfs</artifactId>
<version>1.0-SNAPSHOT</version>
<packaging>jar</packaging>
<name>toolToManagePdfs</name>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
<maven.compiler.source>11</maven.compiler.source>
<maven.compiler.target>11</maven.compiler.target>
</properties>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.11</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.apache.pdfbox</groupId>
<artifactId>pdfbox</artifactId>
<version>2.0.22</version>
</dependency>
<dependency>
<groupId>org.apache.opennlp</groupId>
<artifactId>opennlp-tools</artifactId>
<version>1.9.3</version>
</dependency>
</dependencies>
<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>
<configuration>
<argLine>-Dfile.encoding=UTF-8</argLine>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<mainClass>
application.App
</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
</plugins>
</pluginManagement>
</build>

A normal JAR does not contain or reference its dependencies at runtime. If you want to run a JAR, you need to either
build an executable JAR with the maven assembly plugin or maven shade plugin.
list the classpath explictly when running the JAR.

Here's what I use to have the jar files in the lib subdir:
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>3.2.0</version>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<classpathPrefix>lib/</classpathPrefix>
<mainClass>application.App</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>3.1.2</version>
<executions>
<execution>
<id>copy-dependencies</id>
<phase>package</phase>
<goals>
<goal>copy-dependencies</goal>
</goals>
<configuration>
<outputDirectory>${project.build.directory}/lib</outputDirectory>
<overWriteReleases>false</overWriteReleases>
<overWriteSnapshots>true</overWriteSnapshots>
</configuration>
</execution>
</executions>
</plugin>

The problem stemmed from having all plugins inside <pluginManagement></pluginManagement>.
Moreover the configuration was incomplete and didn't include the dependencies inside the jar.Using maven-assembly-plugin fixed that.
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
<configuration>
<archive>
<manifest>
<mainClass>
application.App
</mainClass>
</manifest>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
</execution>
</executions>
</plugin>

Packing Source Code and Dependencies

I am trying to build a jar package using Maven with source code and all dependencies. The problem is that Maven is no packing the source code only the dependencies.
Do I need to set a configuration to pack the source code too?
<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>courier-perf-test</groupId>
<artifactId>courier-perf-test</artifactId>
<version>0.0.1-SNAPSHOT</version>
<build>
<plugins>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<archive>
<manifest>
<mainClass>ze.delivery.HTTPRequestClass</mainClass>
</manifest>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</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>
</plugins>
</build>
<dependencies>
<!-- https://mvnrepository.com/artifact/org.json/json -->
<!-- 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>
</dependencies>
</project>

Use src as the descriptorRef in your assembly-plugin configuration to create source archives for your project or it might be better to use the predefined descriptor project:
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
<descriptorRef>src</descriptorRef>
</descriptorRefs>
OR:
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
<descriptorRef>project</descriptorRef>
</descriptorRefs>
Reference: maven-assembly-plugin

NoClassDefFoundError with HikariCP

When trying to compile HikariCP with my application, I'm getting a java.lang.NoClassDefFoundError: com/zaxxer/hikari/HikariConfig error.
It does build into the .jar file, but it seems like at runtime the application can't find it.
<?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>me.MyApp.App</groupId>
<artifactId>App</artifactId>
<version>1.0-SNAPSHOT</version>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<version>3.0.0</version>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<archive>
<manifest>
<mainClass>me.MyApp.App</mainClass>
</manifest>
<manifestEntries>
<Class-Path>.</Class-Path>
</manifestEntries>
</archive>
</configuration>
<executions>
<execution>
<id>make-assembly</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>com.zaxxer</groupId>
<artifactId>HikariCP</artifactId>
<version>2.6.2</version>
<scope>compile</scope>
</dependency>
</dependencies>
</project>
I thought adding the Assembly plugin would fix it, but it didn't. What am I doing wrong?

Because you have this:
<archive>
<manifest>
<mainClass>me.MyApp.App</mainClass>
</manifest>
<manifestEntries>
<Class-Path>.</Class-Path>
</manifestEntries>
</archive>
...I would assume that this means that your Class-Path entry in MANIFEST.MF is just a "." (i.e. the current directory only - no JAR files).
I'd suggest you change it to:
<archive>
<manifest>
<mainClass>me.MyApp.App</mainClass>
<addClasspath>true</addClasspath>
</manifest>
</archive>
Reference Link

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>