How to configure logging when running a JAR?

You can't specify JVM arguments into the MANIFEST.MF file so you have to specify the logging properties at the command line or with a shortcut :

java -Djava.util.logging.config.file=logging.properties -jar yourjar.jar

Otherwise you could package a properties file(logging.properties in your case) in the JAR, read that at startup and put those settings into the system properties.

The javadoc says:

In addition, the LogManager uses two optional system properties that allow more control over reading the initial configuration:

"java.util.logging.config.class"
"java.util.logging.config.file" 

These two properties may be set via the Preferences API, or as command line property definitions to the "java" command, or as system property definitions passed to JNI_CreateJavaVM.

If the "java.util.logging.config.class" property is set, then the property value is treated as a class name. The given class will be loaded, an object will be instantiated, and that object's constructor is responsible for reading in the initial configuration. (That object may use other system properties to control its configuration.) The alternate configuration class can use readConfiguration(InputStream) to define properties in the LogManager.

So, either use the java.util.logging.config.file system property, and store the config file out of the jar file (which is probably a good idea if you want to be able to customize the logging properties in order to debug or analyze some weird behavior), or store the config file wherever you want (in the jar file, for example), and use the java.util.logging.config.class system property to load and instantiate a class that will read the file in the jar file (Using Class.getResourceAsStream()).