But then which version (the one inside Sigil Prefs) or the one inside the app folder would take precedence?
I am thinking you are very right in that this would have to be thought through very very carefully. How exactly could updates be done?
If we had a github repo for just the "official" plugins, we could create symlinks to individual developers github pages for plugins (similar to how you set up the libxml fix).
I guess we could add an update checker of some sort to Sigil to examine just those linked github sites for new releases and then some internal installer to put them inside the right place in the app folder itself.
Needless to say this is not easy.
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