You should put them in your classpath, for example
java -classpath someJar.jar YourMainClass
And of course you can do the same for javac.
If you need to have more than one jar or directory in your classpath, you need to use your default separator. For example, on Windows,
java -classpath someJar.jar;myJar.jar YourMainClass
On the other hand, it might be easier for you to use the IDE to manage things like this. I personally used only my script editor and did a great job. But it's good to know how to do this using the command line.
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