http://java.sun.com/developer/Books/javaprogramming/JAR/basics/manifest.html
What does a manifest file do? What is the purpose of it?
Manifest-Version: 1
Manifest file provides the meta data for a file. The meta data is in form of name-value pairs. In your above example they have provided the MD5 hash of the class file which is calculated without the manifest file. This is a security measure so that if someone modifies the file and adds some hackish code, you can detect it with the signatures.
It plays no role in updating the file.