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This should be done in core.jar. During the IDE startup just after the SFS was initialized the FileSystemContextFactory.createContext(SFSRoot) must be called and created root context must be added into lookup. (TBD how it will look after merged context is implemented) At the moment it is in core/registry (see comments in ResettableRootContextImpl), but it should not be "hardcoded" there. core/registry is just a library and how it is used depends on the application.
Reassigning to new module owner jskrivanek.
Registry module is obsolete.