There are many options
1. if you want to do it from command prompt then you would need to set the classpath and then either create a list of java files with package name and use it for compiling, something like this
# Linux
$ find -name "*.java" > source.txt
$ javac -classpath "${CLASSPATH}" @source.txt
:: Windows
> dir /s /B *.java > source.txt
> javac -classpath %{CLASSPATH}% @source.txt
or use build tool like Ant.
Once you have the .class files, you can use "jar" command to create a jar of the .class files
2. Use IDE - you can use any of these IDEs - eclipe, intellij, netbeans.
You need to setup a project with the java files and compile project and export as jar using class files.
I think it would work out better for you to use an IDE.