class not found error referencing invalid package name - maven

Question

I have created a JavaFX Maven project in NetBeans 8.2. When I created the initial starter project, it would run without error. I then generated entity classes from a database with the plan to bind the database tables to various views in the application. I am not using any of the generated entity classes yet but when I try to run the application it now fails. I can Clean and Build the project with a Build Success. However, when I try to us the Run option the build fails and the application does not launch.
I think I have two problems but cannot figure out how to correct them.
"Caused by: java.lang.ClassNotFoundException: com.mycompany.synergyixs.ingestor.FXMLController" - There is no com.mycompany.synergyixs.ingestor package, FXMLController is in com.IXS.synergyixs.ingestor
"Caused by: javafx.fxml.LoadException:
file:/Users/eugenefallon/NetBeansProjects/SynergyIXS-Ingestor/target/SynergyIXS-Ingestor-1.0-SNAPSHOT.jar!/fxml/Scene.fxml:9" - I do not understand why this is not found. I have tried /fxml/Scene.fxml as well as fxml/Scene.fxml
Any help is greatly appreciated. I am fairly new to NetBeans and am probably missing something obvious.
Here is the console output when I try to run:
> cd /Users/eugenefallon/NetBeansProjects/SynergyIXS-Ingestor; JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_51.jdk/Contents/Home "/Applications/NetBeans/NetBeans 8.2.app/Contents/Resources/NetBeans/java/maven/bin/mvn" "-Drunfx.args=-jar '${project.build.directory}/${project.build.finalName}.jar'" org.codehaus.mojo:exec-maven-plugin:1.2.1:exec
Running NetBeans Compile On Save execution. Phase execution is skipped and output directories of dependency projects (with Compile on Save turned on) will be used instead of their jar artifacts.
Scanning for projects...
------------------------------------------------------------------------
Building SynergyIXS-Ingestor 1.0-SNAPSHOT
------------------------------------------------------------------------
--- exec-maven-plugin:1.2.1:exec (default-cli) # SynergyIXS-Ingestor ---
Exception in Application start method
java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
at com.sun.javafx.application.LauncherImpl.launchApplicationWithArgs(LauncherImpl.java:389)
at com.sun.javafx.application.LauncherImpl.launchApplication(LauncherImpl.java:328)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
at sun.launcher.LauncherHelper$FXHelper.main(LauncherHelper.java:767)
Caused by: java.lang.RuntimeException: Exception in Application start method
at com.sun.javafx.application.LauncherImpl.launchApplication1(LauncherImpl.java:917)
at com.sun.javafx.application.LauncherImpl.lambda$launchApplication$152(LauncherImpl.java:182)
at com.sun.javafx.application.LauncherImpl$$Lambda$51/326549596.run(Unknown Source)
at java.lang.Thread.run(Thread.java:745)
Caused by: javafx.fxml.LoadException:
file:/Users/eugenefallon/NetBeansProjects/SynergyIXS-Ingestor/target/SynergyIXS-Ingestor-1.0-SNAPSHOT.jar!/fxml/Scene.fxml:9
at javafx.fxml.FXMLLoader.constructLoadException(FXMLLoader.java:2605)
at javafx.fxml.FXMLLoader.access$700(FXMLLoader.java:104)
at javafx.fxml.FXMLLoader$ValueElement.processAttribute(FXMLLoader.java:918)
at javafx.fxml.FXMLLoader$InstanceDeclarationElement.processAttribute(FXMLLoader.java:967)
at javafx.fxml.FXMLLoader$Element.processStartElement(FXMLLoader.java:216)
at javafx.fxml.FXMLLoader$ValueElement.processStartElement(FXMLLoader.java:740)
at javafx.fxml.FXMLLoader.processStartElement(FXMLLoader.java:2711)
at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:2531)
at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:2445)
at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:3218)
at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:3179)
at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:3152)
at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:3128)
at javafx.fxml.FXMLLoader.loadImpl(FXMLLoader.java:3108)
at javafx.fxml.FXMLLoader.load(FXMLLoader.java:3101)
at com.IXS.synergyixs.ingestor.MainApp.start(MainApp.java:15)
at com.sun.javafx.application.LauncherImpl.lambda$launchApplication1$159(LauncherImpl.java:863)
at com.sun.javafx.application.LauncherImpl$$Lambda$54/1753339148.run(Unknown Source)
at com.sun.javafx.application.PlatformImpl.lambda$runAndWait$172(PlatformImpl.java:326)
at com.sun.javafx.application.PlatformImpl$$Lambda$47/1915503092.run(Unknown Source)
at com.sun.javafx.application.PlatformImpl.lambda$null$170(PlatformImpl.java:295)
at com.sun.javafx.application.PlatformImpl$$Lambda$49/305815329.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at com.sun.javafx.application.PlatformImpl.lambda$runLater$171(PlatformImpl.java:294)
at com.sun.javafx.application.PlatformImpl$$Lambda$48/1567581361.run(Unknown Source)
at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:95)
Caused by: java.lang.ClassNotFoundException: com.mycompany.synergyixs.ingestor.FXMLController
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at javafx.fxml.FXMLLoader$ValueElement.processAttribute(FXMLLoader.java:916)
... 23 more
Exception running application com.IXS.synergyixs.ingestor.MainApp
------------------------------------------------------------------------
BUILD FAILURE
------------------------------------------------------------------------
Total time: 1.340s
Finished at: Mon Feb 06 22:02:30 EST 2017
Final Memory: 6M/245M
------------------------------------------------------------------------
Failed to execute goal org.codehaus.mojo:exec-maven-plugin:1.2.1:exec (default-cli) on project SynergyIXS-Ingestor: Command execution failed. Process exited with an error: 1 (Exit value: 1) -> [Help 1]
To see the full stack trace of the errors, re-run Maven with the -e switch.
Re-run Maven using the -X switch to enable full debug logging.
For more information about the errors and possible solutions, please read the following articles:
[Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
Here 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>com.IXS</groupId>
<artifactId>SynergyIXS-Ingestor</artifactId>
<version>1.0-SNAPSHOT</version>
<packaging>jar</packaging>
<name>SynergyIXS-Ingestor</name>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<mainClass>com.IXS.synergyixs.ingestor.MainApp</mainClass>
</properties>
<organization>
<!-- Used as the 'Vendor' for JNLP generation -->
<name>SynergyIXS</name>
</organization>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>2.6</version>
<executions>
<execution>
<id>unpack-dependencies</id>
<phase>package</phase>
<goals>
<goal>unpack-dependencies</goal>
</goals>
<configuration>
<excludeScope>system</excludeScope>
<excludes>META-INF/*.SF</excludes>
<excludes>META-INF/*.DSA</excludes>
<excludes>META-INF/*.RSA</excludes>
<excludeGroupIds>junit,org.mockito,org.hamcrest</excludeGroupIds>
<outputDirectory>${project.build.directory}/classes</outputDirectory>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>exec-maven-plugin</artifactId>
<version>1.2.1</version>
<executions>
<execution>
<id>unpack-dependencies</id>
<phase>package</phase>
<goals>
<goal>exec</goal>
</goals>
<configuration>
<executable>${java.home}/../bin/javapackager</executable>
<arguments>
<argument>-createjar</argument>
<argument>-nocss2bin</argument>
<argument>-appclass</argument>
<argument>${mainClass}</argument>
<argument>-srcdir</argument>
<argument>${project.build.directory}/classes</argument>
<argument>-outdir</argument>
<argument>${project.build.directory}</argument>
<argument>-outfile</argument>
<argument>${project.build.finalName}.jar</argument>
</arguments>
</configuration>
</execution>
<execution>
<id>default-cli</id>
<goals>
<goal>exec</goal>
</goals>
<configuration>
<executable>${java.home}/bin/java</executable>
<commandlineArgs>${runfx.args}</commandlineArgs>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
<compilerArguments>
<bootclasspath>${sun.boot.class.path}${path.separator}${java.home}/lib/jfxrt.jar</bootclasspath>
</compilerArguments>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.16</version>
<configuration>
<additionalClasspathElements>
<additionalClasspathElement>${java.home}/lib/jfxrt.jar</additionalClasspathElement>
</additionalClasspathElements>
</configuration>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>org.eclipse.persistence</groupId>
<artifactId>eclipselink</artifactId>
<version>2.5.2</version>
</dependency>
<dependency>
<groupId>org.eclipse.persistence</groupId>
<artifactId>org.eclipse.persistence.jpa.modelgen.processor</artifactId>
<version>2.5.2</version>
<scope>provided</scope>
</dependency>
</dependencies>
<reporting>
<plugins>
</plugins>
</reporting>
</project>