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The new flexible projects structure is a great step forward in the Eclipse platform. Excellent work. One use of such a structure is in a web application development model. In this model, it is desirable to target the web application'w WEB-INF/classes directory as the output directory. In addition, it is desirable to target this directory for multiple projects. Although the new flexible projects structure allows for this, the Java Builder breaks this by cleaning the output folder on many builds. By cleaning the output folder, the result of one project's build will be lost when a different project is built. It would be helpful if the Java Builder was not quite so controlling of the output folder.
There is an option to control this... it was added in the M4 build. The workspace wide option is found at Windows -> Preferences -> Java -> Compiler -> Other : 'Allow to clean output folders for a full build' A per project option can be found by examining any project's Properties -> Java Compiler -> Other : 'Allow to clean output folders for a full build'