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I've made some more updates to the layout file but also have some more ideas and think it'll get confusing if I keep posting small updates, so I'll just explain what I have done and intend to do.
I've now changed python script created by the layout file (but not posted it yet) so that it will determine for each selected entry if the PDF is file or a directory. If it is a file it will create the container directory, etc as above. If it is a directory (i.e. it has already been opened on the iliad) it will only create a new manifest file and will leave the existing scribble file. I've added this because I decided I want to be able to use jabref to quickly update how all of my articles appear on the iliad.
If neither a file or directory exists that matches it does nothing (i.e. no longer crashes).
The thing that I am thinking about adding is support for images. I'm thinking that if there is an image (in a user-specified image directory) that matches the journal field then it will add a line to the manifest and copy in that image. So if I have an image called bmj.png and I have a journal entry bmj then it will copy in the image. That way I will be able to have journal covers for each article.
I think this could easily be used to manage non-academic content as well, e.g. PDF books. There's no journal field for book types by default but it is easy to add that and set its value to a name that would map to a cover image.
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