If your Main class is in a package called FileManagement, then try:

java -cp . FileManagement.Main

in the parent folder of the FileManagement folder.

If your Main class is not in a package (the default package) then cd to the FileManagement folder and try:

java -cp . Main

More info about the CLASSPATH and how the JRE find classes:

• How Classes are Found
• Setting the class path (Solaris/Linux)
• http://en.wikipedia.org/wiki/Classpath_(Java)

Ideally you should create a service wrapper for your java application and then make this service run on startup example here.

Use
sudo update-rc.d mytestserv defaults to run your service wrapper on startup on Ubuntu

You can spawn a bash root shell inside a mate-terminal instance, change the mate-terminal's working directory to ~/Desktop and execute your jar file inside it at startup by adding this command to Startup Applications:

mate-terminal -e "sudo -H /bin/bash -c \"cd ~/Desktop && java -jar executable.jar; /bin/bash\""

1. Hit the Super key, type "Startup Applications" and hit Enter
2. Name you command, type the name in the "Name" field and type the command in the "Command" field
3. Click on "Save" and click on "Close"

Command breakdown:

• mate-terminal -e "<command1>": opens a mate-terminal instance and runs <command> in it
• sudo -H /bin/bash -c \"<command1.1>\": spawns a bash root shell and runs <command1.1> in it
• cd ~/Desktop && java -jar executable.jar; /bin/bash: changes the mate-terminal's working directory to ~/Desktop, executes java -jar executable.jar and spawns another bash root shell which will be available for further uses

I wrote another simple wrapper here:

#!/bin/sh
SERVICE_NAME=MyService
PATH_TO_JAR=/usr/local/MyProject/MyJar.jar
PID_PATH_NAME=/tmp/MyService-pid
case $1 in
    start)
        echo "Starting $SERVICE_NAME ..."
        if [ ! -f $PID_PATH_NAME ]; then
            nohup java -jar $PATH_TO_JAR /tmp 2>> /dev/null >> /dev/null &
            echo $! > $PID_PATH_NAME
            echo "$SERVICE_NAME started ..."
        else
            echo "$SERVICE_NAME is already running ..."
        fi
    ;;
    stop)
        if [ -f $PID_PATH_NAME ]; then
            PID=$(cat $PID_PATH_NAME);
            echo "$SERVICE_NAME stoping ..."
            kill $PID;
            echo "$SERVICE_NAME stopped ..."
            rm $PID_PATH_NAME
        else
            echo "$SERVICE_NAME is not running ..."
        fi
    ;;
    restart)
        if [ -f $PID_PATH_NAME ]; then
            PID=$(cat $PID_PATH_NAME);
            echo "$SERVICE_NAME stopping ...";
            kill $PID;
            echo "$SERVICE_NAME stopped ...";
            rm $PID_PATH_NAME
            echo "$SERVICE_NAME starting ..."
            nohup java -jar $PATH_TO_JAR /tmp 2>> /dev/null >> /dev/null &
            echo $! > $PID_PATH_NAME
            echo "$SERVICE_NAME started ..."
        else
            echo "$SERVICE_NAME is not running ..."
        fi
    ;;
esac 

You can follow a full tutorial for init.d here and for systemd (ubuntu 16+) here

If you need the output log replace the 2

nohup java -jar $PATH_TO_JAR /tmp 2>> /dev/null >> /dev/null &

lines for

nohup java -jar $PATH_TO_JAR >> myService.out 2>&1&