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When a project is added to the source path for a java project, it automatically adds a core project reference. The reverse is not true, adding a project reference does not automatically update the source path. Consider doing this to ensure consistency between the two lists...
Project references are used by the Java tooling to induce a build order consistent with the classpath settings. In case a project had more than the Java nature, other tooling might set further project references to control further the build order. These references would however not be meaningfull for a Java classpath. So I do not think it would make sense to do it this way. But I understand that it would though be practical to directly set project references in the UI and have them be ordered on the classpath afterwards.