If I understand correctly this is what you have:

~/Desktop/freedom-folder:

  freedom.jar

  <other files>

And you want to run freedom.jar as root.

If you want to do it via the terminal

Just open the terminal (Ctrl+Alt+T) then

cd ~/Desktop/freedom-folder

sudo java -jar freedom.jar

If you want to have a launcher for yourfreedom in the Dash

1: Open a terminal

Run the following commands:

mkdir  ~/bin

cp  ~/Desktop/freedom-folder/freedom.jar  ~/bin

sudo  apt-get  install  gksu

The first two lines will create a folder called bin in your home folder and
move your .jar file into it. The last line is to install gksu a GUI frontend for su.

2: Open GEdit Text Editor

Write the following script:

#!/bin/sh



gksudo  java  -jar  ~/bin/freedom.jar

Save it to the bin folder you've created in your home folder. I will assume you've named this script as freedom-as-root without any file extensions.

Now, still in GEdit, click File -> Open... (or click the folder icon). In the file selection dialog, navigate to your home folder and type Ctrl+H to make the hidden files visible. Open .bashrc. Go to the last line of this file and add the following new line:

PATH="$PATH:$HOME/bin"

Save it. (This line in ~/.bashrc adds ~/bin to the search path for executables.)

Create a new file and add the following to it:

[Desktop Entry]

Name=Your Freedom (with root privileges)

Icon=/home/your-username/.icons/freedom.svg

Exec=/home/your-username/bin/freedom-as-root

Type=Application

Terminal=false

StartupNotify=true

Categories=Network;

Save it in your home folder as freedom-as-root.desktop. (Instead of your-username make sure to type your actual username!)

3: Open a terminal again

Before, opening the terminal download this icon, by clicking the image and Save as... or the like. Save it as freedom.svg to your home folder.

(If you wish you can get some other free/libre icon from the internet, Wikipedia is a good source for these.)

Go to a terminal again and type:

chmod  +x  ~/bin/freedom-as-root

mkdir  ~/.icons

mv  ~/freedom.svg  ~/.icons

mkdir ~/.local/share/applications

mv  ~/freedom-as-root.desktop  ~/.local/share/applications

4: See if this worked

Just open the Dash and type your freedom to see if there were any problems.
The icon should appear in the Dash, and when you click it gksu should ask for your password.

Due to an extra step in part (2), now you can also type freedom-as-root in the terminal and it will be enough to run yourfreedom with privileges.

Hope it helps.