If you copy files to a project folder using Finder (or Windows Explorer), by default you need to update Eclipse to synchronize it with the underlying file system. In addition, you can avoid copying files to a project outside of Eclipse and instead use Eclipse Navigator (similar to Finder) or Package Explorer views - you can drag and drop from the file system and, for example, drag it to the Navigator view.
In Eclipse> Preferences> General> Workspace, there are several Refresh options that can help automatically synchronize things.
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