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Ralph,
If you go to Windows > Preferences > MyEclipse > Jav Enterprise Project > Web Project > Deployment, you can set the Dependent Java Project Deployment Policy to “Use Smart Deployment for Dependent java project”. You can go through section 10 of the following document get get details on how that would affect the deployment:- http://www.myeclipseide.com/documentation/quickstarts/webprojects/#dependent_projects