You're able to replicate project tree view with only those files you're temporarily interested in. Bookmarked files tree loads on the right side (currently the only option), and has shortcuts for quickly showing/hiding both bookmark tree and regular file tree.
It is also able to quickly load bookmarks from git repository, adding new and modified files in the current branch.
** To suggest a feature/improvement, open an issue on github repo: *** https://github.com/akalajzi/atom-file-bookmark/issues
Good catch. Let us know what about this package looks wrong to you, and we'll investigate right away.