When you add a PDF from another directory, Zotero copies it into its own internal structure, which is confusing and involves folders with random letter names.
I am guessing this has something to do with Zotero running as a FireFox plug-in. You can tell Zotero where the file is, but you would have to do this for every file in the database. If you sync your database to a second computer, it shows the links as still being there, but if you try to click on a file to open it within Zotero you get an error message saying Zotero cannot find it. I love being able to sync my Zotero database between my personal Mac and school PC, but the syncing breaks the file links. Otherwise, they would have it, wouldn't they?
This again makes me think that the way Zotero is written, relative links are not possible. I should also point out that on Zotero's website, there are numerous posts from users requesting relative links, but with absolutely no reply from Zotero. Update: I edited the following paragraph to clear up some confusion pointed out in a posted comment.
There is one problem with Zotero, however, that I just cannot move past: its inability to use relative links for linking to files. If you know the academic me, you know I love, and regularly tout, using Zotero to manage my ever-growing bibliography.
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