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Jorge kindly pointed me in the correct direction on how to do various things, and I'm now a lot more understanding of the "way" that fusion electronics currently behaves.
But, I've ended up with a slight mess where stuff was all over the place and I didn't know what was current, what wasn't and just a real all round mess.
I've moved my libraries into their own project, although currently, only the latest revision of my project uses the libraries from the correct place, those libraries have the fusion 3D model projects stored in a sub folder below where the libraries are and it's how Jorge has recommended stuff be laid out.
All good so far, I know where I went wrong, and going forward things will be a lot easier.
I went through the library manager, and removed all of the duplicate libraries that are referenced in other earlier revisions (each revision has a clean copy in a totally different folder of the previous version which is then modified) and now all I see in the library manager in the current revisions "in use" page is the list of my current libraries, no other third party libraries are used.
All good so far.
These older libraries, that exist in older revisions do not appear anywhere in the library manager windows.
Even better so far!
But...
In my latest revision, where every component is mapped to my master libraries collection (the "My Libraries" project) if I hit update, I am greeted with a list of libraries, including libraries which are not mentioned anywhere in my design, my design only uses the latest libraries from "My Libraries" project.
Here you can see the multiples, and although it doesn't matter if I select all and update because those superfluous libraries are not used, it is a bit irritating for them to be there, I'd prefer to just see the libraries that are actually referenced.
So can I purge these "dead to this project" libraries?