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IIRC, there is some logic in the updater to avoid downloading unnecessary files. E.g.: if a JAR file in jars/ has no plugins which depend on it in plugins/, it may not be flagged for installation in some cases? I have noticed this in the past, at least, but never had time to investigate and understand it.
My speculation is that this feature is somehow involved in the undesirable behavior here.
If I update my update site (Funimage) and add a new file, then run Update fiji, the new files do not appear in the main screen.
However, if I go to Manage update sites, uncheck and recheck the Funimage update site, the new files then appear in the main updater screen.
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