Comments

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.

Reading, and catching the thought the page just gave you

This is what it is for as often as drafting is. You are reading a paper you brought into your wiki and a sentence sets something off — this contradicts chapter three, ask Sara whether the 2019 figures were revised, this is the paragraph the whole argument turns on. The thought is too small to deserve a page of its own, and writing it down anywhere else means losing the sentence that prompted it.

So put it where the sentence is. Type %%, the thought, then %% again, and it becomes a note the instant you close it — no dialog, no mouse, nothing to select first. Four keystrokes around a thought you were going to lose. Reading continues.

Later, the Notes section of the Context pane lists every one of them on the page in front of you, in the order they appear, each with the sentence it sits in underneath. That is where you come back and decide: develop it, or delete it. See Finding them again below.

Writing one

Three doors, and they make the same note:

• Type it. %%, the thought, %% — the fastest, and the one to learn.
• Right-click where the note belongs and choose Add Note Here…. It is there on a bare cursor as well as on selected words, because catching a thought is something you do at a place, not to words you picked out first. The same command is in Edit ▸ Add Note Here…, in the command palette, and under Blocks in the / menu as Comment.
• Give it a key. Settings ▸ Shortcuts ▸ Editing lists Add Note Here… and Copy Link to Selected Words; neither has one out of the box.

The menu item opens a small box; write the note and press OK. The box takes as many lines as you like — press Return for a new line, and ⌘Return when you are done.

All of this works the same on rich-text pages and on Markdown pages shown formatted. On a Markdown page you are reading as source, typing %% either side of a thought works exactly as it does anywhere else — that is the file's own way of writing one, and it is read back as a note the next time the page is drawn. The dialog and the menu item want the formatted view, and say so rather than making a marker the source view cannot show you.

One thing a code block cannot hold is a note or a marked passage, on a Markdown page. A fenced block is written back to the file as its code and nothing else, so anything tucked inside one would be removed by the next save — MojoPad refuses out loud instead, and the writing around the block takes both.

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.
%%

Typing it works the same way **bold** becomes bold when you close it, 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.

Finding them again

A thought you cannot get back to is a thought you lost more slowly. Open the Context pane — it is pinned to the sidebar, so it is already there — and its Notes section lists everything noted on the page you are reading, in the order it appears in the page:

• Every note you have pinned, its own words on the first line and the sentence it sits in dimmed beneath, so you can tell two of them apart without leaving the pane.
• Every passage you have marked with Copy Link to Selected Words or Format ▸ Add Page Anchor… — the places on this page that other pages can link to.

Click a row and the page scrolls to it and flashes it. That is the "return later" half: read down the list, jump to the two that still matter, delete the rest by clicking each one and clearing its box.

Make a page on a row turns that one note into a page of its own — named from its first words, or from its opening clause in a language written without spaces between words — and carrying a link straight back to the paragraph you wrote it against. The note stays where it is. That is deliberate: your notes are outside the writing on purpose, and turning one into visible prose in the middle of a paper would change the paper. Develop the new page, then delete the note when it has done its job.

The pane reads the page as it is drawn, so a Markdown page you have switched to source shows none — the notes are in the text in front of you, but there is nothing drawn for the pane to list. Switch back to Formatted (⌃⌘P) and they are all there; the pane says as much rather than telling you the page holds none.

The Anchors pane does the same for marked passages across the whole wiki rather than this page — reach it from the command palette by typing Anchors.

What a comment is not

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.

Reading the page without 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.

Changing one

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.

On a rich-text page

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.

Percent signs inside a comment

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.