In most circumstances you can take the drag-and. Having good sharing & (scriptable) export options to output PDFs with annotations included can help to satisfy the different needs. Most Mac apps are self-contained, and the trash-to-delete option works on all versions of Mac OS X and later. Storing them in the PDF severely limits your options to develop advanced features, and can make things like sync hard to impossible. While I understand users desiring annotations being stored in the PDF, as an app developer I can fully sympathize with the decision for Zotero 6 to store annotations in the database. When you are in the app, click on the Edit tab, select Preferences from the drop-down menu (if you are on a Mac, select Preferences from the drop-down menu under the Zotero tab in the menu bar), then click on the Advanced tab. Zotero 6 also offers various ways to export its PDFs with the annotations included in the PDF. This allows for fast, conflict-free syncing, including in groups, and enables advanced functionality that wouldn’t be possible otherwise. To enable this tight integration, Zotero stores annotations in the Zotero database, not in the PDF file. The new PDF reader in Zotero 6 makes PDF reading and annotation a first-class part of the Zotero experience. From the article (which has further details): Why does Zotero store PDF annotations in its database instead of in the PDF file?
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