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I am not sure what the issue is. FolderIn is an input plugin and so you get the warning on Windows and Linux (Macs just open a new window in the current instance.). FolderOut or any output plugin has no impact on the saved/written epub, it is only given the state of the files inside Sigil. As FolderOut does not create a .epub file, only a folder, it can never lose or overwrite what was saved as .epub.
In PluginRunner **before** any plugin is started all state including any changes are written to files in Sigil's temp folder. In other words all tabs are flushed. This also happens before splitting and merging files, making reports, creating navs, etc. So all the plugin sees is the current state of the epub book inside Sigil. It never sees or knows about what is actually written to (saved) to the epub file.
All the dirty flag inside Sigil does is use the fact that something has changed rom the last save to alert them to do a save if they want to a .epub file.
So I guess I don't understand the issue. All plugins and all of Sigil itself only work on what is inside Sigil's temp folders. A Save-as or Save is needed to actually write these to a .epub file and the user determines if that happens or not.
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