Comments
Notes attached to a passage, in three colours, which travel with the document and never print.
A comment is a note attached to a few words: a doubt, something to check, a reminder for the next draft. The words are highlighted in the colour of the comment, and the note shows when you click them. Comments are not part of the text: they do not count as words and they are not printed.
Adding one
Select the words and press Ctrl+Alt+C⌥⌘C, or click the comment button on the toolbar. A small panel opens with three colours, a box for the note and Apply.

The colour is up to you: green, yellow and red, perhaps for three kinds of note, or three readers. The app remembers the colour you used last and offers it first the next time.
Editing and removing
Click the highlighted words to open the panel again, change the note or the colour, and apply. The bin icon in the panel removes the comment and leaves the words as they were.
Where comments can go
A comment covers words inside a paragraph, a list item, a heading or a table cell. It cannot be put on a code block or on inline code, and a comment goes on one passage at a time: a selection that spans several blocks is asked to be narrowed.
In the files
Comments are kept in the .calmly format, which is the one to use for documents with comments; see Formats. Saving as Markdown, plain text or HTML keeps the words and drops the notes. Exporting to Word turns them into Word comments, with their colour, so a reader with Word or LibreOffice sees them in the margin.
More in Writing
The Markdown shortcuts that turn into headings, lists and emphasis while you type, and the ones you can turn off.
The small toolbar that appears over selected text, and the reminder of shortcuts that shows when you hold Ctrl or Cmd.
Six levels of heading, the panel that lists them, and the keys that move through it without touching the mouse.
Bulleted, numbered and checklist items, nesting them with Tab, and turning one kind of list into another.
Links to web pages, to other documents on your disk and to headings in the same document, and how to follow them.
Four ways to put a picture in a document, the difference between embedding and linking one, and what the editor does not do with images.
The slash menu that inserts blocks, the toolbar that edits tables, and the rules that keep them compatible with Markdown.
Curly quotes, dashes, ellipses and arrows written for you as you type, the quotation marks of your language, and how to turn each one off.
The spell checker and its languages on each system, adding words to the dictionary, and the language of the app itself.
Right-to-left writing for Arabic, Hebrew, Persian and other scripts, per document or for every new document.
Searching the document or every open tab, and a replace that keeps the capitals of what it finds.
What happens to formatting when text comes in from elsewhere or goes out, and the two ways to copy a document as code.
Calmly Writer