Does jpa replace the need to consume sf web services in a java app, or do i still need to do that to access operations like convertlead?
JPA will only replace the part of the web services API that represent CRUD and query operations on SFDC entities. Special operations like login and convertlead does not map well to JPA. However, you will not have to deal with the low-level SOAP web services. VMforce comes with a SFDC Java connector that exposes all Web Services calls in Java. This is based on the WSC library which is available today.