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Bookmarks are saved per session, so, if you open the same file in different sessions (workspace) the extension will handle them as different bookmarks. That's the reason why you need to add those central files on each workspace. Also, bookmarks are accessible only if the folder containing that file is opened, even on a multi-root workspace.
I think #287 may fit your needs, as the bookmarks wouldn't be saved per session anymore, so whenever you have the file available on the workspace, the bookmark will be available as well.
Otherwise, if all your central files are stored in the same folder, currently, as the extension works, you could try combining two concepts:
Define the saveBookmarksInProject setting as true, in order to make the bookmarks to be stored within the folder
I have bookmarks eg. to my .zshrc or other central files to quickly adapt them when needed.
Currently I have to add them to every new workspace.
I would love to have the possibility to add specific bookmarks for all workspaces
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