If this is a console-based application, then merely opening the executable JAR file should make it run in a Command Prompt. This can be done by typing
java -jar "<drive>:\path\to\JAR.jar"
into a CMD window. The program will now run as if it were in the Eclipse console, except in CMD. Using a batch file, you can alter the CMD with
COLOR 0A
as an example.
If you are looking for more of a user-friendly console-based application, you can get the name of the executable JAR and have it run in a ProcessBuilder inside the source code itself. This allows the JAR to open up itself in a CMD.
If I have not specified correctly, do let me know.