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Error: Unable to initialize main class Caused by: java.lang.NoClassDefFoundError: org/bson/conversions/Bson

https://github.com/Gjonathan252/AutoPart-Java-Database-w-MongoDB
Its my first time using maven and I am trying to run the .jar of my program but I keep getting this error in the command prompt when I run.
java -jar autopartsjavamongodb-1.0-SNAPSHOT.jar
result:
Error: Unable to initialize main class com.example.autopartsjavamongodb.main
Caused by: java.lang.NoClassDefFoundError: org/bson/conversions/Bson
The Java program uses mongodb dependencies and they all seem to be working when I run the program on the IDE or using this long command on the command prompt.
"C:\Program Files\Java\jdk-16.0.2\bin\java.exe" "-javaagent:C:\Program Files\JetBrains\IntelliJ IDEA Community Edition 2021.2\lib\idea_rt.jar=63226:C:\Program Files\JetBrains\IntelliJ IDEA Community Edition 2021.2\bin" -Dfile.encoding=UTF-8 -classpath "D:\Computer Science Lessons\AutoPart Java Database w MongoDB\target\classes;C:\Users\gjona\.m2\repository\org\mongodb\mongodb-driver-sync\4.3.1\mongodb-driver-sync-4.3.1.jar;C:\Users\gjona\.m2\repository\org\mongodb\bson\4.3.1\bson-4.3.1.jar;C:\Users\gjona\.m2\repository\org\mongodb\mongodb-driver-core\4.3.1\mongodb-driver-core-4.3.1.jar" com.example.autopartsjavamongodb.main
This is what the pom.xml file looks like. I dont think I am missing any depencacies as I am able to run it on the IDE.
<modelVersion>4.0.0</modelVersion>
<groupId>com.example</groupId>
<artifactId>autopartsjavamongodb</artifactId>
<version>1.0-SNAPSHOT</version>
<packaging>jar</packaging>
<properties>
<maven.compiler.release>11</maven.compiler.release>
<maven.compiler.source>16</maven.compiler.source>
<maven.compiler.target>16</maven.compiler.target>
</properties>
<dependencies>
<dependency>
<groupId>org.mongodb</groupId>
<artifactId>mongodb-driver-sync</artifactId>
<version>4.0.5</version>
</dependency>
<dependency>
<groupId>org.mongodb</groupId>
<artifactId>mongodb-driver-sync</artifactId>
<version>4.3.1</version>
</dependency>
<dependency>
<groupId>org.mongodb</groupId>
<artifactId>bson</artifactId>
<version>4.0.5</version>
</dependency>
</dependencies>
<build>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.1</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<configuration>
<archive>
<manifest>
<mainClass>com.example.autopartsjavamongodb.main</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
</plugins>
</pluginManagement>
</build>

Normally, when we package a project into a jar file, the jar file doesn't contain its dependencies, so the dependency jar files would need to be included in the classpath.
One way to achieve that is by using maven-assembly-plugin
As a result, all the dependency jars would be packaged in one jar.
pom.xml example
`<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>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<classpathPrefix>libs/</classpathPrefix>
<mainClass>com.example.autopartsjavamongodb.main</mainClass>
</manifest>
</archive>
</configuration>
</plugin>`
Also please note pluginManagement tag is used to define the plugin version in your parent POM, in your case you shouldn't include pluginManagement tag

Maven clean install not including sqlite dependency for executable jar file

After using
mvn clean install
and then
java -jar executable.jar
I get this error:
java.lang.ClassNotFoundException: org.sqlite.JDBC
This is my 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/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>****</groupId>
<artifactId>****</artifactId>
<version>0.7-SNAPSHOT</version>
<packaging>jar</packaging>
<name>****</name>
<description>****</description>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
<java.version>1.8</java.version>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
<dependencies>
<dependency>
<groupId>org.xerial</groupId>
<artifactId>sqlite-jdbc</artifactId>
<version>3.23.1</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.junit/junit5-engine -->
<dependency>
<groupId>org.junit</groupId>
<artifactId>junit5-engine</artifactId>
<version>5.0.0-ALPHA</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.tinyjee.jgraphx/jgraphx -->
<dependency>
<groupId>org.tinyjee.jgraphx</groupId>
<artifactId>jgraphx</artifactId>
<version>3.4.1.3</version>
</dependency>
</dependencies>
<build>
<sourceDirectory>******</sourceDirectory>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>exec-maven-plugin</artifactId>
<version>1.2.1</version>
<configuration>
<mainClass>*****</mainClass>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>3.1.1</version>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<classpathPrefix>lib/</classpathPrefix>
<mainClass>******</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.3</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
</plugins>
</build>
Running the program inside intelliJ works without problems. I included it there from the project structure.
I replaced names and directories with ****. This is a school project and I don't want my prof accusing me of providing solutions to other groups in case they find this stackoverflow entry.

Probably you are getting this only when you are running your jar because the dependencies are not available/packaged inside of it.
Try generating a "fat jar" (also known as uber-jar), it will package all your dependencies inside the jar:
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
</execution>
</executions>
<configuration>
<finalName>YOUR_JAR_FINAL_NAME</finalName>
</configuration>
</plugin>
</plugins>
</build>
Documentation related to the maven-shade-plugin can be found in here
Since you are using a runnable jar file, you can follow this section of the documentation related to Executable Jars

Some background.
Maven install never installs dependencies;
it only installs the project that is build via the POM.
The installation of dependencies are a task that you must also perform
if you don't use either a "fat jar" (which I can't recommend) or use
the new spring boot executable jar implementation.
The classic "fat jar" is an amazingly terrible
(but often the only option)
solution for a problem like this.
Consider using Spring-Boot;
they have developed a new,
sane,
version of an executable jar file that includes the dependencies within the executable jar and adds them to the classpath at startup.
This functionality is similar to the functionality of a "war" file when it is added to
a JEE container.
Caveat: I don't work for Pivotal,
I just like much of their work (the Spring Framework).
Edit:
Here is a link to the
Executable Jar Section in the Spring Boot Reference.
It contains some details.

Execution of Scala and Maven project

I have created a simple maven project of Scala in eclipse's scala ide using below details -
Artifact Id - scala-archetype-simple
Group Id - net.alchim31.maven
After created the project I have modified the pom.xml file.
<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>
<groupId>com.test</groupId>
<artifactId>scalapoc</artifactId>
<version>0.0.1</version>
<name>${project.artifactId}</name>
<description>Test scala app</description>
<properties>
<maven.compiler.source>1.6</maven.compiler.source>
<maven.compiler.target>1.6</maven.compiler.target>
<encoding>UTF-8</encoding>
<scala.version>2.11.5</scala.version>
<scala.compat.version>2.11</scala.compat.version>
</properties>
<dependencies>
<dependency>
<groupId>org.scala-lang</groupId>
<artifactId>scala-library</artifactId>
<version>${scala.version}</version>
</dependency>
<!-- Test -->
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.11</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.specs2</groupId>
<artifactId>specs2-core_${scala.compat.version}</artifactId>
<version>2.4.16</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.specs2</groupId>
<artifactId>specs2-junit_${scala.compat.version}</artifactId>
<version>2.4.16</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.scalatest</groupId>
<artifactId>scalatest_${scala.compat.version}</artifactId>
<version>2.2.4</version>
<scope>test</scope>
</dependency>
</dependencies>
<build>
<sourceDirectory>src/main/scala</sourceDirectory>
<testSourceDirectory>src/test/scala</testSourceDirectory>
<plugins>
<plugin>
<!-- see http://davidb.github.com/scala-maven-plugin -->
<groupId>net.alchim31.maven</groupId>
<artifactId>scala-maven-plugin</artifactId>
<version>3.2.0</version>
<executions>
<execution>
<goals>
<goal>compile</goal>
<goal>testCompile</goal>
</goals>
<configuration>
<args>
<!-- <arg>-make:transitive</arg> -->
<arg>-dependencyfile</arg>
<arg>${project.build.directory}/.scala_dependencies</arg>
</args>
<archive>
<manifest>
<mainClass>App.scala</mainClass>
</manifest>
</archive>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.18.1</version>
<configuration>
<useFile>false</useFile>
<disableXmlReport>true</disableXmlReport>
<!-- If you have classpath issue like NoDefClassError,... -->
<!-- useManifestOnlyJar>false</useManifestOnlyJar -->
<includes>
<include>**/*Test.*</include>
<include>**/*Suite.*</include>
</includes>
</configuration>
</plugin>
</plugins>
</build>
</project>
I have also added manifest entry inside plugin tag.
<archive>
<manifest>
<mainClass>App.scala</mainClass>
</manifest>
</archive>
I have only one App.scala file and one test file available in project. Build was successful. But when trying to execute the jar using java -jar <jar_name> getting below error -
no main manifest attribute, in scalapoc-0.0.1.jar
When trying to execute the command java -cp scalapoc-0.0.1.jar com.test.scalapoc.App.scala getting below error -
Error: Could not find or load main class com.test.scalapoc.App.scala
Please suggest what to be needed to execute the jar.

try
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<configuration>
<archive>
<manifest>
<mainClass>com.test.scalapoc.App</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
.scala is for source only, source is not executable
archive tag is part of the configuration of a plugin
see https://maven.apache.org/shared/maven-archiver/examples/classpath.html#Make
UPDATE 2018-06-05:
To create a standalone jar (without need to defined a classpath with scala-library and other dependencies on command line), you should create a jar that included other classes/jar.
see:
Apache Maven Shade Plugin – Executable JAR and the rest of the doc of the plugin for tuning & configuration
or the old one-jar tool Deliver Your Java Application in One-JAR™ !

Maven dependencies doesn't get exported into the jar

I have a project which I want to export as jar (for some reasons it's impossible to export it as a runnable jar). I have 3 maven dependencies, gson, io and junit, but when I execute the maven built jar in console it says this:
Check my build path:
I export it this way (Eclipse):
Run as -> Maven build...
(mvn) package
And here is my 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>
<groupId>Carlos</groupId>
<artifactId>Buscaminas</artifactId>
<version>0.0.1-SNAPSHOT</version>
<packaging>jar</packaging>
<name>Buscaminas</name>
<url>http://maven.apache.org</url>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
<build>
<plugins>
<plugin>
<!-- Build an executable JAR -->
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>3.0.2</version>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<classpathPrefix>lib/</classpathPrefix>
<mainClass>res.application.Main</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>3.8.1</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.google.code.gson</groupId>
<artifactId>gson</artifactId>
<version>2.8.2</version>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.5</version>
</dependency>
</dependencies>
</project>
Also the maven build result:

My project didn't seem to have the correct project structure so I crated a new (maven) project and migrated my packages to the src/main/java folder and then used 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>
<archive>
<manifest>
<mainClass>res.application.Main</mainClass> <!-- Or wherever is your main method-->
</manifest>
</archive>
</configuration>
</execution>
</executions>
</plugin>
And executed mvn package
That created a "jar-with-dependencies" jar also with all the recources (images, interface fxml files...).

From what I understand what you need might be this one
mvn install dependency:copy-dependencies

The built jar does not contain the dependencies, you must either provide them in classpath when executing the jar or have build process copy them into your jar, creating a so-called uber-jar. Good way to achieve the latter is using maven-shade-plugin.

maven how to include dependencies correctly

I was trying to figuring out how to use maven but I didn't get it.
First I tried sqlite 3.8.7 from :
mvnrepository.com/artifact/org.xerial/sqlite-jdbc/3.8.7
I can compile well but when I try to execute maven doesn't find sqlite jar file, so I try to use :
mvn install:install-file
but It didn't work too, so I just used -cp and I have fixed.
Second I try to use jfreechart from :
http://mvnrepository.com/artifact/jfree/jfreechart/1.0.13
I did same steps below for jfreechart but this time it gives me NoClassDefFoundError.
Both of them works when I compile manually but with maven it's not. What I am missing about it ? If I always add manually like sqlite why should use maven anyway ?
Notes : I compile as :
mvn compile
and I'm packaging as :
mvn package
and finally I try to execute as :
java -cp target/porject.jar org.path.App
Edit :
This is for jfreechart app(pom.xml)
I add dependency tags from mvnrepository.com
<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>org.project</groupId>
<artifactId>ChartTest</artifactId>
<version>1.0-SNAPSHOT</version>
<packaging>jar</packaging>
<name>ChartTest</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>jfree</groupId>
<artifactId>jfreechart</artifactId>
<version>1.0.13</version>
</dependency>
</dependencies>
</project>
Thanks in Advance

All that you need to create your jar executable with your dependencies and launch it as a standalone app:
<build>
<plugins>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<archive>
<manifest>
<mainClass>com.mypackage.main.Main</mainClass>
</manifest>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
</plugin>
</plugins>
</build>
and then run goal :
clean package assembly:single

Your problem is you don't include your dependencies in your target jar.
Add this to your pom.xml:
<build>
<plugins>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<version>2.1</version>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
<executions>
<execution>
<id>make-assembly</id> <!-- this is used for inheritance merges -->
<phase>package</phase> <!-- append to the packaging phase. -->
<goals>
<goal>attached</goal> <!-- goals == mojos -->
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
Then you can start your app using the command line:
java -cp target/ChartTest-1.0-SNAPSHOT-jar-with-dependencies.jar org.path.App

Don't use hyphen in commands, use mvn package and mvn compile