is it possible to have either different metadata templates for different types of store elements (let's say PageRefs in the SiteStore vs. Pages in the PageStore) or can I write a "dynamic" template which will allow the editor to fill in different elements depending on the type of element the metadata is attached to?
There's only metadata template for all stores, but with FirstSpirit 5 it will be possible to write "dynamic" forms so that you can just display the form elements suitable for the current store. See Formulare mit Prรคsentationslogik for futher information.
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