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When web module is mounted it creates a shadow node in a project tab. This shadow has children that represent components of web application. This node doesn't have the same (or similar) set of properties as other shadows (original filesystem, original name and properties of original node). Also when the link is corrupted it is not handled in the same way. It means marked with '(Broken link)' text and special icon. Another difference is behaviour during unmounting of original filesystem. Web module tries to remove this link too although other shadows remains on project tab in this situation.
fix is probable impossible will be fixed with new projects
Set target milestone to TBD
Fixed by the new Projects infrastructure.