I have only read about jar-indexing but never used it. It is supposed to speed up classloading when using several JARs. I can certainly tell you it speeded up my program since it went from working to failing very fast.
Let me explain. I have a Swing-application that uses hivemind as IoC-container. Hivemind is sweet, it discovers injection information automatically from all jar-files on the classpath. It uses a pretty simple getResource to get all files called META-INF/hivemodule.xml regardless of hte JAR-file they live in.
So I have an executable jar-file (you know, with the main-class attribute in the manifest file). It has a Class-Path attribute that points to some other JAR-files. This has always worked before I started converting my build scripts to maven.
Since I mindlessly copied the example from the jar-plugin page (http://maven.apache.org/plugins/maven-jar-plugin/examples/manifest-customization.html) the maven JAR-plugin created the jar-index file INDEX.LST.
With this index file in the jar hivemind failes almost directly.
I guess it is because the index file did not contain the dynamically loaded resources, at least that is the spec for INDEX.LST. If it exists it is trusted to contain everything needed. Since the jar-plugin did not index my dynamically loaded resources they simply do not exist as far as the classloader goes.
You learn something new every day.