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Looks like a regression caused by commit into WebProjectProperties 1.39 by pfiala. If you add a project in Packaging Project dialog it will be added into project.xml but when you open the dialog second time it will not be visible. WebProjectProperties.get returns empty list for this.
This is not a primary functionality so I marked it only as P3 but it makes the Packaging Project unusable so it needs to be fixed in 40.
Fixed
v