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How can I get class files from Maven dependency into the target\classes folder

Is there any sort of Maven plugin that allows me to copy the class files for a dependency into the target\classes folder for my project? Currently I have to manually open the jar file that has the dependencies extract the package that I need to copy over and then copy it into the target\class folder for my project.
I need a way to do those ideally within the pom.xml file but I haven't been able to find a solution that works. Any help would be appreciated, Thanks.

This sounds like a terrible idea. If you want to include unpacked dependencies into your project, use the maven assembly plugin or the maven shade plugin.

Use the maven-dependency-plugin. Here is an example of how you can extract the content of a dependency JAR:
<project>
[...]
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>3.1.2</version>
<executions>
<execution>
<id>unpack</id>
<phase>package</phase>
<goals>
<goal>unpack</goal>
</goals>
<configuration>
<artifactItems>
<artifactItem>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>3.8.1</version>
<type>jar</type>
<overWrite>false</overWrite>
<outputDirectory>${project.build.directory}/alternateLocation</outputDirectory>
<destFileName>optional-new-name.jar</destFileName>
<includes>**/*.class,**/*.xml</includes>
<excludes>**/*test.class</excludes>
</artifactItem>
</artifactItems>
<includes>**/*.java</includes>
<excludes>**/*.properties</excludes>
<outputDirectory>${project.build.directory}/wars</outputDirectory>
<overWriteReleases>false</overWriteReleases>
<overWriteSnapshots>true</overWriteSnapshots>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
[...]
</project>

below is the example to use of assembly pulgin and it works for me
below is the child pom plugin
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>3.4.2</version>
<configuration>
<archive>
<manifest>
<mainClass>my parent package statup class</mainClass>
</manifest>
</archive>
</configuration>
<executions>
<execution>
<id>make-assembly</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
Parent pom plugin
<build>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
</plugin>
</plugins>
</pluginManagement>
</build>

Jar is not creating for spring boot

I am adding pluginManagement to avoid
Failed to execute goal org.apache.openjpa:openjpa-maven-plugin:3.0.0:enhance (enhancer) on project Execution enhancer of goal org.apache.openjpa:openjpa-maven-plugin:3.0.0:enhance failed:
Error. but when I add pluginManagement it stops creating jar for my project.
<build>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
<configuration>
<mainClass>com.test.testApplication</mainClass>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
</plugin>
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>0.7.6.201602180812</version>
<configuration>
<destFile>${sonar.jacoco.reportPath}</destFile>
<append>true</append>
</configuration>
<executions>
<execution>
<id>agent</id>
<goals>
<goal>prepare-agent</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.openjpa</groupId>
<artifactId>openjpa-maven-plugin</artifactId>
<version>3.0.0</version>
<configuration>
<includes>**/tablemodels/*.class</includes>
<addDefaultConstructor>true</addDefaultConstructor>
<enforcePropertyRestrictions>true</enforcePropertyRestrictions>
<persistenceXmlFile>src/main/resources/META-INF/persistence.xml</persistenceXmlFile>
</configuration>
<executions>
<execution>
<id>enhancer</id>
<phase>process-classes</phase>
<goals>
<goal>enhance</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</pluginManagement>
</build>
If I remove pluginManagement from pom then Jar is getting created.

My guess is that you just wrapped your <plugins> tag in a <pluginManagement> tag, which does not do what you want. I suggest you read the documentation to understand the relationship between plugin and pluginManagement. See also another post on StackOverflow.
As to your underlying problem: I guess the error you mention is an Eclipse error. It is emitted by the m2e plugin which requires a connector for each maven plugin in your pom.
You can usually come up with a connector (if it is not found on the Eclipse Marketplace) by typing " m2e connector" into your favorite search engine.
In this case you might want to install this: https://github.com/beskow/openjpa-maven-connector

How do I make IntelliJ IDEA automatically extract a dependency to the artifact jar?

Let's say I'm adding the following dependency to my pom.xml:
<dependency>
<groupId>org.ini4j</groupId>
<artifactId>ini4j</artifactId>
<version>0.5.4</version>
</dependency>
I can now use the Ini class as expected, but if I try to build the jar and run it, it will give me a "noclassdeffounderror" error. When I check the content of the jar, it does not contain org/ini4j.
I was able to fix this by going into File -> Project Structure -> Artifacts
If I want to add another dependency, I'll have to do this every time, which is quite tedious (I didn't need to do this on NetBeans). I then tried to use the following plugins (which I used on NetBeans) to have Maven create a jar with dependencies automatically.
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>3.0.2</version>
<configuration>
<archive>
<manifest>
<mainClass>main.Main</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>1.7.1</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
On NetBeans, this automatically adds all dependencies to the jar file, but it doesn't do anything on IntelliJ IDEA. I have no idea what I'm doing anymore; nothing works. How can I make IntelliJ IDEA automatically extract a dependency into the output root?

Dose your intellij use the same version on maven that your Netbeans uses? if it checks fine, try another plugin for making a fat jar such as the folowing:
<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>

maven javafx plugin: generate MANIFEST

I want to access ${version} property of my pom.xml at runtime, using code like this:
primaryStage.setTitle("MyApp v" + Main.class.getPackage().getImplementationVersion());
I am using the javafx-maven-plugin to build the executable jar.
Knowing that this code only works when MANIFEST file with version property is found, I looked in the documentation of the plugin but found nothing to let it generate the MANIFEST file.
So next I tried to use the maven-jar-plugin which should do the job as posted here.
But I still get MyApp vnull from the above code.
From my pom.xml:
<build>
<plugins>
<!-- Set a compiler level -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.3</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<configuration>
<archive>
<addMavenDescriptor>false</addMavenDescriptor>
<manifest>
<addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
<addDefaultImplementationEntries>true</addDefaultImplementationEntries>
</manifest>
</archive>
</configuration>
</plugin>
<plugin>
<groupId>com.zenjava</groupId>
<artifactId>javafx-maven-plugin</artifactId>
<version>8.1.4</version>
<configuration>
<mainClass>de.tools.Main</mainClass>
<identifier>${project.artifactId}</identifier>
<vendor>Me</vendor>
<bundler>EXE</bundler>
<nativeReleaseVersion>${project.version}</nativeReleaseVersion>
<needShortcut>true</needShortcut>
<needMenu>true</needMenu>
<appName>${project.artifactId}</appName>
</configuration>
<executions>
<execution>
<!-- required before build-native -->
<id>create-jfxjar</id>
<phase>package</phase>
<goals>
<goal>build-jar</goal>
</goals>
</execution>
<execution>
<id>create-native</id>
<phase>package</phase>
<goals>
<goal>build-native</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
What am I doing wrong?

The maven-jar-plugin configuration has nothing to do with the jfx-plugin configuration. In fact they create two distinct jars at two distinct locations (default config).
You have to add the following configuration to your jfx-plugin config:
<manifestAttributes>
<Specification-Title>${project.name}</Specification-Title>
<Specification-Version>${project.version}</Specification-Version>
<Specification-Vendor>${project.organization.name}</Specification-Vendor>
<Implementation-Title>${project.name}</Implementation-Title>
<Implementation-Version>${project.version}</Implementation-Version>
<Implementation-Vendor-Id>${project.groupId}</Implementation-Vendor-Id>
<Implementation-Vendor>${project.organization.name</Implementation-Vendor>
</manifestAttributes>
You can check these values by accessing the-final-jar.jar/META-INF/MANIFEST.MF.
I will create an issue/ticket on the plugins repo to add support for these flags by default similar to the maven-jar-plugin:
javafx-maven-plugin #220

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.