Extracting data from an arbitrary combination of layers?

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I'm working on an application with a large number of layers. The goal is for a user to have an arbitrary combination of layers being displayed, with custom layering. One of the requested features is that a user should be able to extract this data into a .shp file or other format. The geoprocessing tools I've seen that do similar extractions seem to do so only from predefined groups of layers... with the number of layers I'm working with that is not feasible. What is the best solution?



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