Make Zotero be able to link own folders on personal computers rather than create a new folder
I realized that Zotero would make its own contents folder which makes it hard to track down PDF's moved into the Zotero app. Unlike the app -PDF Expert and Documents app, Zotero would make duplicates of PDFs from our personal to the "Zotero" file/folder and Zotero would name them on their own accord. I want the option to have my PDF documents connected to my folders where I have them set and not have to chase down the annotated "Zotero file" of the same work/PDF. This separation of from my own files into Zotero's folder that Zotero creates on my Macbook is unnecessary. I can just allow access to my folders and that's it. There would be times I would look for my PDF where I saved it, only to realize that all of the annotations are not there because Zotero took that file, placed in a different folder, (their own) created somewhere on my mac, and those annotations are a different file altogether. I place my PDFs in Zotero app for work, I should not have to manage my own PDF folders and Zotero's folder on my mac .
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See Stored Files and Linked Files for more.
https://www.zotero.org/support/attaching_files#stored_files_and_linked_files
The rationale for the way annotations made in the Zotero PDF viewer are stored in the Zotero database is described below . But there is nothing stopping you adding annotations to linked PDFs in other PDF viewers outside Zotero, and also having those annotations appear in the Zotero reader (albeit locked, unless imported).
https://www.zotero.org/support/kb/annotations_in_database
You can even open PDFs in an external viewer from within Zotero using this plugin ...
https://github.com/retorquere/zotero-open-pdf