I was looking for a way to create permanent bookmarks in Atom that would not disappear after the given document is closed. From what I read on official forums, I understand that Atom team do not have plans to include this feature in the standard Bookmarks package. E. g., these 2014 and 2015 topics:
I also haven’t been able to find an add-on package which would do the trick. Maybe someone has found a way to make permanent bookmarks?