You can filter your Workspace or Projects display to show only files or markups of a certain type.
To filter the display to show only one file type
From Workspace or Projects, click View by Type... and select the markup or file type you want to display. You are given eight choices: All Markups, Bookshelf Items, Highlights, Bookmarks, Notes, Cited Publications, Cited Pages, Bibliographies.
Select the markup or file type you want to display. The Workspace page refreshes to show only that file or markup type.
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