here is related issue to the problem: https://jira.springsource.org/browse/SPR-9208
which causes multiple 404, and slows down startup of application every run.
If maintaining (reindexing) file name in index.list is overwhelming, can you consider giving up creating this index file when packaging ??
According to http://docs.oracle.com/javase/6/docs/technotes/guides/jar/jar.html#JARIndex it seems that you gain benefit of indexing, only when you index.list for multiple jars and put it to the single "main" jar
"The existing jar tool is enhanced to be able to examine a list of jar files and generate directory information as to which classes and resources reside in which jar file. This directory information is stored in a simple text file named INDEX.LIST in the META-INF directory of the root jar file. When the classloader loads the root jar file, it reads the INDEX.LIST file and uses it to construct a hash table of mappings from file and package names to lists of jar file names. In order to find a class or a resource, the class loader queries the hashtable to find the proper jar file and then downloads it if necessary"