Bookmarks & notes
Line bookmarks (gutter markers, cross-file jump, per-project), plus Personal Notes attached to a word/line/range, stored outside the file, surviving renames, with Markdown bodies.
Two ways to mark up code.
Bookmarks toggle on a line (C-c m) with a gutter marker and an optional note; the Bookmarks tool window lists them across files, C-c ] / C-c [ cycle within a file, and M-g b is a cross-file picker, reorderable and scoped per project.
Personal Notes attach an annotation to a word, line, or range, stored outside the file (great for read-only or generated code). They survive edits and renames via content-hash identity and text anchoring, render Markdown, and have their own tool window and M-g n picker. See the deep-dive.