Bluemix is great because you can simply push your Java EE application (WAR or EAR) and select what services your application needs. You don't have to worry about the server configuration because it's generated for you by the Liberty buildpack. Ideally, you should write your application in such a way that the generated configuration works for your application. But if you need to enable a Liberty <feature>, set a JVM argument in jvm.options, or provide a shared library that resides outside the WAR, this video explains how to modify server.xml, package your server, and deploy it to Bluemix.
The BluemixBoutique sample demonstrates a very basic online store application built by consuming cloud services. The core of the application is written using Java EE with a few different RESTful patterns to access the backend data stored in two different types of databases
If you are looking for a super quick outline of using Eclipse and the Bluemix plugin to deploy apps, here it is!
CloudTrader is a Java EE application that simulates an online stock trading system. This application enables users to log in, view their portfolio, lookup stock quotes, and buy or sell stock shares. It is built primarily with Java Servlets, JSPs, and JavaBeans. CloudTrader was created by making changes on top of a ten year old DayTrader benchmark application to showcase how you can migrate an existing application to BlueMix and revitalize it with services in Bluemix.
My favorite thing about the BlueMix platform is how quick and easy it is to stand up services and start using them. Let me show you what I mean by outlining a java web application which inserts some data into a DB2 database service. If you’re familiar with creating a servlet, you can do this with me in less than 10 minutes.
While most of your applications should work just fine in the cloud, remember: Don't write to disk. The file system is a resource that isn't persisted. As you application instance gets restarted, updated, scaled or recreated, the file system it sits on changes. Using the disk for temporary or cache purposes is OK, if you need persistent storage, create a database.