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File Handling Issues
Unexpected behavior (wrong action, gibberish ("%PDF..."), etc.) when opening files from Zotero
Deleting mimeTypes.rdf from the Firefox profile directory and restarting Firefox is generally what's needed to fix file handling issues. mimeTypes.rdf stores file handling associations and will be recreated automatically the next time you restart Firefox.
Zotero itself doesn't tell Firefox how to handle a file—it simply checks if a file can be handled within Firefox (natively or via a plugin) and then either sends it to Firefox if so or otherwise launches it via the OS. Problems in mimeTypes.rdf can prevent this from working properly, however.
PDFs opening in wrong application on GNU/Linux systems
If you find that PDFs open in eg. Gimp even though you've set the file handler to be Okular in Dolphin/Nautilus/Firefox/what-have-you, this tip might help: open the file
~/.local/share/applications/defaults.list
in your favorite plain text editor and look for the line “application/pdf=…”, change it to
application/pdf=kde4-okularApplication_pdf.desktop
If the file does not exist, just create it and enter the following content:
[Default Applications] application/pdf=kde4-okularApplication_pdf.desktop
Note: on some systems, you might need to use
application/pdf=kde-okularApplication_pdf.desktop
instead.
If you want Evince or Adobe Acrobat instead of Okular, use
application/pdf=evince.desktop
or
application/pdf=acroread.desktop