It is common practice, and it's a good thing, to keep your source files in one directory and your class files in another. Typically, when you start a project you do something like this:
/application root dir /application root dir/src /application root dir/classes
You create two directories under the root of your application. Put all of your source files under the src directory and compile such that your classes go into the classes directory. Then you can use the JAR archiving tool to package just your classes and deploy those when your application is done.
By default, the javac tool compiles your classes into the same directory that the source file is in. So, you need to pass a command ...