Notes about a passage, anchored to the words rather than to a position.
A comment is a note to yourself about a passage, kept off the passage. Select the text, press Comment in the toolbar that appears, and the thread opens beside the note; the passage carries a mark for as long as the thread is open.
A thread holds as many messages as you like, and is closed by resolving it rather than by deleting it.
A comment is anchored to the words it was made on — the quote, the text either side of it, and which occurrence of that quote it is — not to an offset in the file. Editing the paragraph above does not slide a comment onto the wrong sentence, and the same phrase twice in one note can carry two different threads.
If the quoted passage is deleted outright, the thread is not. It is marked orphaned and stays in the sidebar, because what you wrote about a sentence usually outlives the sentence.
.mindex/comments/, one file per note, inside the vault. Nothing is written
into the Markdown, so a note opened in another editor is unchanged — and since
Mindex git-ignores that folder, comments stay on your machine rather than
travelling to a shared repository.
See also File layout.