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For the record: we noted this workaround in the plugin development thread where we posted the info about how to make sure plugins were compatible with the new plugin framework that will be a part of Sigil 1.0.
It was always our plan that all plugins would still function correctly so long as epubs had the traditional Sigil structure. We wanted to make sure users wouldn't have to do without their favorite plugins, and that plugin-devs didn't have to scramble madly to fix their suddenly broken plugins.
The Sigil 0.9.991 pre-release was also intended as a means for plugin devs to test their plugins to see if they were able to work with alternatively structured epubs (which Sigil 1.0 will support), or if there were modifications needed to be made.
The manual conversion to Sigil's traditional structure will provide a workaround for those plugins that may need tweaking in the interim.
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