The Main-Class property in a manifest file makes that JAR file a runnable JAR. You then can invoke that JAR with the command:
java -jar <jar-file>
But you also can directly invoke the main class with the traditional way:
java -cp <jar-file> your.pkg.MainClass
Notice, that you must include your JAR file in the class path, so that Java can find the classes inside it. An additional note: If you don't have a Class-Path property in the JAR's manifest file but your classes depend on other classes in other JARs, you must include all those JARs in the class path:
java -cp <jar-file>;<lib1>;<lib2>;... your.pkg.MainClass
Note, in Linux systems the path separator is a colon, not semicolon.