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Reference management software: Zotero 7

Cloud storage

You should not store your Zotero library in cloud storage, for reasons given at the following link: https://www.zotero.org/support/kb/data_directory_in_cloud_storage_folder.

If you are using a Mac that syncs to iCloud, be sure to store your Zotero library in a folder that is not part of the synchronisation. For instance, the Applications folder is usually safe.

Can you delete PDF files without removing the reference itself?

Yes, you can, click the arrow to the left of the icon so that the PDF file is visible, right-click on the PDF field and select "Move item to trash..." in the menu.
 
 

Zotero space is starting to fill up.

To save space in Zotero, you can choose not to sync your attachments. You can sync as many references as you want, but the free space in a Zotero account cannot contain more than 300 MB of PDFs.
 
In Zotero → Edit → Settings → Sync → you can uncheck File Sync to save space.