A note that is in the writing but not part of it. The paragraph you are not sure about, and why. The source you still need to check. A reminder to yourself about the argument you were making at 2am. The half-thought you want to keep near the sentence it belongs to, without it becoming part of what anyone else reads.
Put the cursor where the note belongs, type /, and choose Comment (it is under Blocks). A small box opens; write the note and press OK. That is the way to make one, on both Markdown and rich-text pages.
The box takes as many lines as you like — press Return for a new line, and ⌘Return when you are done.
In the file, a comment is written between double percent signs, which is what you will see if you
open the page's Markdown source (⌃⌘P) or the file in another editor:
The quarterly figures held up. %% check this against the revised numbers %%A whole passage is fenced by %% on a line of its own:
%%
Not sure this section earns its place.
Come back to it after the interview.
%%You can also just type it. Write %%, the note, then %% again,
and it becomes a comment the moment you close it — the same way **bold** becomes bold
when you close it. Nothing to select first, and one undo puts the percent signs back if you meant
to write about percentages.
So if you write your pages in another editor as well, type them the same way there and MojoPad reads them as comments when the page opens.
A comment is never part of what leaves this app. It does not appear in a PDF, an ePub, a Word file, an exported web page, a published site, a page you share over your network, or the feed. It is not counted in the page's word count, it is not found by search, it is not part of what "search by meaning" reads, and it is not shown to the AI — asking a question about your wiki never puts your own asides in front of the model, and an outside assistant connected over MCP does not receive them either.
The one exception is deliberate: exporting your wiki as Markdown files keeps them, because that export exists to hand your writing to another editor, and losing your own notes on the way would make it the one export that quietly threw something away. Every other export strips them.
Comments are drawn quietly — dimmed, in italics, behind a small %% — so you can
see them without them competing with the writing. To read the page as anyone else would see it,
run Hide / Show Comments from the command palette. Run it again to bring them back.
Click a comment to edit it. You cannot type inside one directly — that is the price of its words being kept out of everything above — so it opens a small box instead. Clear the box and press OK to remove the comment entirely.
Comments work the same way on rich-text pages. The / menu and clicking to edit behave identically; only the Markdown shorthand is particular to Markdown pages.
Write what you like in one — "margins were 50%", "down to 45% before the write-down" — and it is kept exactly. The percent signs that fence a comment in the file are written differently from the ones you type, so a note about a percentage cannot accidentally end itself half way through and spill the rest into the page.
The one thing you cannot type inside a comment is another %%, because that is
what ends one — the note would stop there. If you need a doubled percent sign in a note, make the
comment from / ▸ Comment and paste it into the box, where nothing is watching for the fence.
A stray %% in your prose — in a formula, say — stays text. Only a
matched pair makes a comment, and an unmatched one is left exactly as you wrote it. A single
percent sign is never touched, so margins were 50% is safe.