Each AgileJ StructureViews diagram is stored in its own resource file with the extension .ajsv. There is no central registry of diagram files, they are each a free standing entity. You are free to make diagram files anywhere within any Eclipse project. They appear in the Package Explorer tree with the
symbol. You can re-locate diagram files without affecting their behavior.
If you want to keep AgileJ StructureViews files entirely separate from your other project resource files you can create a separate project and keep all of your diagram files there. Diagrams you make in the new project will still accept classes dragged in from other projects. This also works well where your diagrams contain a collection of types declared across a number of projects.
However you choose to organize your diagrams, you can always search to find which diagrams contain a given type.