I had this problem once before and was able to get it corrected. Looks like it’s back after the upgrade. Running MyEclipse 5.0.1 and Eclipse 3.2 on Win2000. Since this is a legacy project, the structure doesn’t follow standard practices, in that the source folder is the same as the deployment folder. The ‘Allow output folders for source folders’ box is checked in the ‘Java Build Path’ screen.
When I deploy the project as a war file, all of the .java files are mixed in with all of the .class files. I did try adding .java files to the Excluded section under the source tab even though this seemed to be associated with building rather than deployment, but the .java files are still in the .war file, after a clean, rebuild, deploy. The Deployment tab in MyEclipse->J2EE project->Web Project only allows adjusting .jar deployment.
Can you point me to the place where I can exclude files from a deployment?