The Story Read markers (Green dots) mark a story as read or not. If the dot is green, you haven't accessed the story yet. If the dot is grey, it's read.
The flags are a site-wide selection tool. You can have them mean whatever you want. Maybe a flagged story is a story you like so much, or not like at all, maybe a flagged story has a particular kink that you like.
You can filter search results by read/unread (green or grey dot) and by flagged or unflagged. You can also batch bookmark flagged stories.
If a story has a green arrow next to it, that means you have downloaded a copy (Zip, txt or EPUB or Kindle). A green arrow will disappear if a story's text gets updated telling you that there is a new version.
We created the following video demo for the green dots: