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In ArcGIS 10.3.1 Models I have set my workspace paramters to save intermediate data in a scratch database. When I run the model out of the Modelbuilder Editing window the intermediate stage data is saved. If I however simply double click the model in ArcCatalog only the finished results are saved and no intermediatary data is saved in my scratch database.
Can anyone explain to me why this is, and how I can change it?
The behaviour you describe sounds correct. The outputs of tools in your model are automatically intermediate, you need to right click on the green blobs and untick intermediate.
These intermediate outputs persist when you run your model from within modelbuilder as modelbuilder needs this to happen so the "ready to run" state can be established. This does not happen when you run the model directly.
If you have unticked the intermediate property of an output then it will exist after the model has executed if you had run it directly from ArcCatalog.
