A wiki gets its power from reuse: write something once, see it everywhere it matters. MojoPad takes the page embed further — embed just a section, or just a single block, and open a second page beside the one you're writing. All of it live.
Add a heading's name after the page name and the embed shows just that section — the heading and everything under it, up to the next heading of the same level:
![[Project Plan#Milestones]]Three ways to make one:
![[Page#Heading]] on its own line, on any page that takes text: formatted, Markdown, or plain text./ and choose Embed page; after you pick a page with headings,
MojoPad offers the whole page or any single section.⌃⌘O), hover a heading, and click
the ⧉ that appears. Paste on any page and it becomes the live embed.Plain-text pages embed too — put ![[Page Name]] on a line of its own and it
renders there like anywhere else, whole page or single section. A reader asked for exactly this: a
plain-text page should be able to pull in another plain-text page, and there was no good reason it
couldn't.
What is worth knowing is what the file holds. A plain-text page's whole promise is that the
text is the text, so what is stored is the marker you typed — ![[Page Name]] — and never
the borrowed words. Edit around it, close the page, open it in any other editor: the line is still
five characters and a page name. The embed is a way of seeing the other page, not a copy of
it, so the other page changing changes what you see here and nothing needs re-doing.
The marker has to be alone on its line. ![[Notes]] and more stays as written, on the
same principle: a block that swallowed the words beside it would be taking liberties with a page whose
point is that it doesn't.
And it travels. Export the page — HTML, PDF, Markdown, Word, ePub, a published site — and the
embedded page comes with it as a quoted passage under its own name, the same as on any other page
type. So a plain-text outline of a talk assembled out of ![[Section One]] markers goes
out as the whole talk, not as a page of markers. The same is true of a pane beside it and of a card:
what you see is the other page, wherever you are looking from.
Any paragraph, heading, or list item can carry a small permanent name — a block id — and be embedded anywhere:
⇧⌘P).![[Page#^ab12cd]] becomes a live embed of just that block.On Markdown pages the id is plain text — a trailing marker like Some paragraph. ^ab12cd —
so it travels with your notes and round-trips cleanly (the marker is hidden when the page renders).
You can write your own memorable ids: end a line with ^budget and reference it as
![[Plans#^budget]].
When you export a page — HTML, PDF, Markdown, Word, ePub, a published site — an embedded
page comes with it, as a quoted passage under the name of the page it came from. So a manuscript
assembled out of ![[Chapter One]] embeds exports as the whole manuscript, not as a
page full of holes. Embeds nest three deep and never loop; a live database view names itself
rather than pretending to be a table in a file that can't refresh.
Section and block embeds are live views: edit the source and every embed shows the new content the next time it renders. Click an embed's title to jump to the source, right at that section. Embeds count as connections — they appear in Backlinks and on the Graph.
Some work needs more than one page in view at once. Three cases panes are built for:
There is one command for it: Open Beside. It opens a page in a new pane to the right of the pane you are in, and your caret stays where you were writing.
⌥-click a page link.⌥⌘↩. With the caret in a link, or just after one you have typed, that page opens
beside and your caret stays in the sentence — the quickest way to bring up a source while you write
about it. With the caret anywhere else, it asks which page, as View ▸ Open Beside… does. In a
dialog, a list or a board card being written in, the key is left to them. You can give it another key
in Settings ▸ Shortcuts.Earlier versions had four names for this — Open Beside This Page, Add a Pane on the Right or Left, Open on the Left to Write In and Write here too — plus a reading pane that could only be read and a Side by Side mode that could only hold two. They are one command now, and every pane is the same.
Any pane can show any page, and changing what one shows leaves the others as they are.
⌘J (View ▸ Go to
Page), type a few letters of its name and press Return, or click a link on the page that pane
shows. The page opens in that pane, and only that pane changes. ⌘-click a page in the Pages panel
to open it in a new tab of that pane instead.◀ ▶ in the pane's bar go back and forward through the pages shown in the tab in front.
A link follows your setting. By default, a link opens in the pane you clicked it in
— a link to a PDF or another file in a new tab of that pane, so the page you were reading stays. If under Settings ▸ Links & Pages you chose Open links and results in a new tab, it
opens in a new tab of that pane; if you chose Open Beside the page you are in, it opens in a new
pane to the right instead. The Pages panel and ⌘J always use the pane you are in.
⌘W closes the tab you are in (and the pane, with its last tab), and
⌘1 to ⌘9 pick a tab in the pane you are in. A page that arrives on its own — a web
clip, an import — opens in the pane you are in, in a tab with nothing of its own to show if it has
one, rather than adding another.Every pane can hold a board, a storyboard, a mind map, the graph, Tasks, the Journal, a folder as one Longform document, the gallery or a database view, or search results — and several panes can hold them at once. Some of the ways that helps:
How they behave:
Esc closes the graph or the search
results in the pane you are in, and leaves Find, a search or the graph in another pane as it was.
⌘F in a pane holding the Journal filters that Journal; in the pane beside it, it finds in that
page. The arrow keys and a paste in a paper or a page stay there, never reaching a board in another
pane.Esc there, never stops this one.⌘Z there takes back the last change made to it, wherever that was made. Opened beside your page, a
board leaves you where you were and opens the Card panel with it.Say your draft is on the left and three papers stand beside it: a steroid trial, a splinting study and a surgical cohort. As you write, you want the two you are comparing right now side by side, the third out of the way but one click from coming back, and the page you just looked up kept behind the paper it belongs with. Panes are arranged for that in three ways, and none of them happens unless you do it.
Esc while dragging to put it back where it was.⇧⌘P) moves the page you are in, chosen with the arrow keys and Return.Tab and press Return or the space bar — and it opens where it
stood. Unfold All Panes opens every strip at once. Asking for a page that is in a folded pane (a
link, Go there) opens its pane too. The last open pane cannot be folded.A page behind another in a pane's tabs keeps its own color, shown along the top of its tab, and a thread from a sentence that mentions it ends on that tab. So the splinting study, filed behind the steroid trial, is still tied to the words that cite it; click its tab to bring it forward.
With more than one pane open, each has a bar across its top: ◀ ▶, the pane's thread dot ● (or ✎ on the pane the threads start from), its number, its tabs and ＋, ⋯ and ✕. While a board is open for excerpts to land on, a pane showing a page or a paper also has ✂ for Excerpt Mode. A pane with one tab gives that tab the whole bar, so its page's name reads in full, and its ✕ is the pane's own. In a pane too narrow for all of it — three panes in a laptop window, say — ◀ ▶ and ＋ move into the ⋯ menu as Back, Forward and New Tab, and the toolbar's own ◀ ▶ still act on the pane you are in. The ⋯ holds:
View ▸ Next Pane (⌥⌘O) and View ▸ Previous Pane move the keyboard from pane to
pane and put the caret back where you left it in each; with only one pane open, ⌥⌘O asks which page
to open beside. ⌥⌘↩ opens the link at your caret beside, or asks which page when the caret is not in
one. View ▸ Close Pane closes the pane you are in. The same commands, and the ones on
⋯, are in the command palette (⇧⌘P), with Move to Pane…, Fold Pane and
Unfold All Panes — so moving a page to another pane, folding and unfolding need no mouse. Next Pane and
Previous Pane step over a folded pane rather than opening it.
Panes share the width equally — the page you are writing too — so four papers and a draft on a large display, or a draft and two papers on a laptop, each get the same room. Drag the line between two panes to give one more room; a pane you have dragged keeps its width while the others make room around it — folding and unfolding a pane beside it included — and a double-click on the line shares the room equally again.
Panes narrow as you open more. When there is no longer room for all of them, the page you are writing keeps a width prose is comfortable at, the others stop at the narrowest a pane is drawn, and the row scrolls sideways rather than squeezing anything further: scroll it to reach any pane, and every pane's buttons come with it. The first time that happens, the status line suggests folding the panes you are not reading (⋯ ▸ Fold Pane). Nothing folds, moves or resizes by itself. A narrow pane lays a paper or a book out more tightly, so it stays readable there.
Quit with panes open and they are there the next time you open the wiki, each with its tabs, in its color, at the width you dragged it to, and folded if you folded it. A desk (View ▸ Desks) keeps them too, widths and folds included. A desk saved on a larger display fits a smaller one: the widths you dragged shrink together, keeping their shape, until every pane has room. A desk or a session saved by an earlier version comes back as panes: the reading pane, the columns and both halves of Side by Side each become a pane, in the order they stood, sharing the width equally. No two papers beside the page you are writing wear the same color as long as there are colors left.
Help ▸ Save Diagnostic Report… has a line in its Rendering section beginning Panes:. It says how many panes are open and how many tabs each holds, how many are folded, which pane has the keyboard, which the threads start from, which view each pane shows (the graph, Tasks, the Journal and the like), how many page colors are worn, and whether every pane carries the same editing safeguards as the first. It is counts only, never a page's name or a word of it.
A small window is a card: one page, floating, for glancing at. Sometimes what you want is a second workspace — two real windows on one wiki, so a long document can sit open on one screen while you write against it on another, each with its own tabs.
Window ▶ New Window for This Wiki opens one, and so does Open in a New Window
on any page list, which opens the second window straight onto the page you picked. It is in the
command palette (⇧⌘P) too, and Settings ▶ Shortcuts will give it a key of your
own — it ships without one, because every combination a hand reaches for is already taken.
Asking for it from a second window does nothing and says so: a new window comes from the one
you opened the wiki in. It is a full
window: its own tab bar, its own Pages panel, the toolbar, find, the outline and the format bar.
Pages you write in it are saved exactly as they are anywhere else, and both windows stay in
step — save in one and the other has it a moment later, with the same warning bar as always if you
were both editing the same page. If your cursor is in that page when the other window saves it, the
words under your cursor stay put until you leave the page, and then change where they are — in any
pane or a day of the Journal as much as on a page of its own. If you were in the other
window when it saved, the change is already showing when you come back. Type there first, and the bar
asks which to keep — Use theirs or Keep mine — before anything is saved. That goes for
a storyboard, a mind map and a canvas too, a thought you are still writing on one included, and the answer
always goes to the page the bar names, even if you have clicked into another pane since. While the bar is
asking, a rename, a tag, a property or a line an assistant adds goes onto both versions, so whichever you
choose keeps it; and closing the window or quitting before you choose asks first. A page locked with a
password of its own works the same way in both windows. If it locks again while the bar is asking —
after the time set in Settings ▶ Security — your version and theirs are locked away with it,
and neither stays on screen; unlock it and the bar is still asking, with both. Keep mine also works
while it is locked. Writing in a property
that holds prose asks nothing: it is not the page's words, so what you write there and the other window's
change are both kept — and so is a thought typed on a mind map in the pane beside your page. A rename
from the other window asks nothing either: what you type is saved under the new name, and every pane and
stack shows it.
A password put on a page in the other window protects it here too, at once. If the page is open in this window, it locks: its lock screen takes the page's place, wherever the page was showing — any pane or a small window as much as the page on its own. If you were writing in it at that moment, nothing you wrote is lost, and nothing is saved without the password. Your words stay in this window, and a bar says a password was put on the page, with two ways on: Unlock… opens the page with its password and then asks, as above, whether to keep your version or theirs — whichever you keep is saved with that password — and Export my changes… saves your words to a file you choose, outside the wiki, for when you don't know the password. There is no Keep mine on that bar: it would save your words without the password. The same happens when the password is changed in the other window. When it is taken off there while you are writing, the bar offers Use theirs, which shows the page as it now is, with no password, and Export my changes…: your words were written while the page had a password, and they are not saved without one. In case MojoPad closes unexpectedly while your words wait, it keeps a copy of them on this Mac, locked with the page’s password — the one you last unlocked it with — and offers it back the next time it starts (see Two Macs and a password). While either bar is up, closing the window or quitting asks first, and after the time set in Settings ▶ Security the page is covered by a lock screen with the same two ways on — when the password was changed or taken off, Export my changes… there first asks for the password your words were written with. While the bar is up, your words in that window are kept from everything that leaves it, as any page with a password is: a connected assistant, search, exports and a page that shows this one inside itself. A password put on, changed or taken off on another device is handled the same way, and a password taken off there is said when it arrives. And Encrypt Page… on a page that is locked here asks you to unlock it first, rather than offering to take its password off.
What the second window does not do is rearrange the wiki. Folders, pins, properties, kinds, saved views, page styles, desks, the sort order and your flashcard reviews are all kept in the window you opened the wiki in — saving a desk says so before it asks you for a name. Try one of them in the second window and it says so; the rest of the time a quiet Second window chip in the status bar is there to be hovered or clicked for the whole explanation.
There are two kinds of gesture here, and they behave differently. The ones that are only a change to the arrangement — a pin, a folder dragged somewhere, a rename — go through on the screen in front of you and are not kept: reopen the window and the arrangement is as it was. A sentence says so the first time and then not again for half a minute, so a run of them can look entirely successful. Make those in the window you opened the wiki in, where they hold.
The ones that would change your pages as well are declined before they start. Deleting a property, changing a property's type, importing kinds or references, merging another document into this one, making a new page type, and the two commands on a followed folder all say no and do nothing at all. That is the more important half, because those gestures write the wiki and your pages, and a second window is allowed to write pages. Deleting a property here took its answer off every page, which cannot be undone, and left the property itself standing — empty — the next time you opened the wiki. Choosing to stop following a folder sent its pages to Recently Deleted while the folder went on being followed, so every file arrived as a page again on the next open. Each of those commands now refuses at the door, before anything is touched, and names the window to do it in.
Importing files is not on that list, because importing is writing pages and that is what a second window is for. The one part of it that cannot land is a field a file brings that this wiki has no property for yet: those fields are left rather than written somewhere nothing could find them, and the import names them when it finishes. A field the wiki already has a property for is filled as usual, here or anywhere.
Nor is filing them — and the notice says which of the two happened. Drop files on a folder here and the pages arrive, unfiled, and it tells you so rather than naming a folder they are not in. File them yourself in the window you opened the wiki in, whenever you like; the pages are already saved and waiting.
That holds for every way something can land in a folder, not only the obvious one: a folder of notes that arrives arranged in folders of its own, File ▶ Import's part-by-part plan, a paper handed to MojoPad from outside, an emailed page and the files it brought, the export Table of Contents, and the folders MojoPad makes without being asked — for pages born on the task surface, for today's note, for a kind. None of them draws a folder here that the next open will not have. A day in the Journal is the one that still lands: what puts an entry on its date is a mark on the page, which is the page's own, not the wiki's arrangement.
Following a folder is done in the window you opened the wiki in, too: Link a Folder says so here before it asks you for one. A folder you already follow keeps working while the second window is open — the wiki's own window takes in what arrives, and the new pages turn up in both — and if that window closes, the second one takes the following over along with everything else.
Why that limit exists, because it is worth knowing rather than guessing at: a wiki's arrangement is kept as one thing, and each window holds its own copy of it while it is open. If both windows could write it, the one that saved last would quietly replace everything the other had done — a folder you made, a page you pinned — with no sign that anything had gone. Pages are different: each is its own, so two windows can write different pages all day without touching each other's work. Making the arrangement behave like the pages is the next piece of this, and until it is built the second window is honest about what it keeps.
Close the wiki's own window and the second one takes over. It becomes the window that keeps the folders and the rest, its chip goes, and it says so — so you are never left with a window that can only point at one that has closed.
It reads the wiki before it writes it. While both windows were open, the other one was the only one keeping the folders, pins and properties — so the moment it closes, this window catches up with everything that was done there, and only then starts keeping them itself. That order matters: before it, the window took over still holding the wiki as it had been when it opened, and the next pin wrote that back over everything the other window had done in between. The folders you had open here are drawn from the wiki as it now stands, which is the small price of catching up.
If the wiki cannot be read at that moment — it moved, or it is still coming down from a sync — the window stays as it was and says so, rather than taking over with a copy it cannot trust. Reopen the wiki and it takes over cleanly.
A few smaller things follow from the same rule. The second window opens on the page you sent it to rather than restoring your tabs, and it does not remember its own tabs when it closes — your places belong to the wiki's own window. It does not run the wiki's page scripts, which the first window has already run. It does not take clips from the web clipper, because filing one is a change to the arrangement. And Open Recent in it opens that wiki in a window of its own rather than taking this one somewhere else. Close it whenever you like; nothing depends on it.
Sometimes the reference you keep glancing at deserves its own little window — checklist, style guide, the page of numbers you're writing against. Right-click any page and choose Open in Small Window: the page opens as a compact card that floats above your other windows, so it stays in view while you write anywhere else — even in another app.
Any page, from any list. Not only the sidebar: search results, the Context, Backlinks, Related and Rediscover panes, the Pages pane, and the list you check sources from all offer the same right-click — Open, Open Beside, Open in Small Window and Open in a New Window. Comparing two results no longer means opening one, going back, and running the search again.
If you would rather it behaved like any other window and went behind whatever you switch to, turn off Keep small windows in front of other windows in Settings ▶ Links & Pages. Cards already open change the moment you do.
The card opens as a live reading view: edit the page in the main window and the
card updates the moment it saves. Links inside it work. Close it like any window
(⌘W), or click Open in Main Window to continue in the full app — it arrives
as a new tab, so the page you were working on is still there when you come back, and the
card closes behind you. If that page is already open in a tab, you land on that one rather than
getting a second copy of it.
And you can write in it. Click the ✎ pen in the card's header and the page becomes editable right there, with the same formatting controls and the same Find and Replace as the main window — jot the thought, check the box, rewrite the paragraph. The pen becomes 👓 eyeglasses; click again to go back to reading (your edit saves as you go, and the main window mirrors it the moment it lands). If the same page ever has unsaved changes in two windows at once, MojoPad never guesses: a small bar appears — Use theirs / Keep mine — and nothing is overwritten until you choose.
Open as many cards as you like: each is its own window, so you can draft in one, keep a source open in another, and work on a translation in a third, sized and placed however suits you.
Every PDF and ePub's toolbar has a 📓 Book Notes button. Click it and MojoPad assembles your reading room: it opens (creating it the first time) a page named <Book> — Notes, opens the book in a pane beside it, and files the pair under Books ▸ that book — each book on its own shelf. Nothing you've already filed is moved. From there the excerpt loop below does the rest: drag a passage across and it arrives quoted, linked back to the exact spot — notes that argue with the book, page by page.
Writing with the keyboard and want to scroll the book without reaching for the mouse?
View ▸ Next Pane (⌥⌘O) hops the keyboard between the two. While the book's pane
holds the keyboard it wears a quiet ring, and the arrow, space, and page keys scroll the reading —
press ⌥⌘O again and you're back in your sentence, where you left the caret.
Your layout comes back. The two panes are remembered for the wiki — reading on one side, notes on the other. Quit MojoPad, reopen the wiki later, and the book is back in its pane beside your notes, so you pick up exactly where you were. Close the pane and it stays closed next time.
And the book remembers your place. A PDF or EPUB you're reading resumes where you left off next time you open it — a PDF at the same page, an EPUB at the same spot in the same chapter (anchored to the chapter, so it holds even if you resize the pane or change the reading font). This works in the first pane too, not just the one beside it. EPUBs are reflowable and have no fixed page numbers, so the place is remembered as a position within the book rather than a page count.
Zoom a PDF with the small − 100% + pill at the reader's lower right — or ⌘+ /
⌘− while your pointer is over the pages, ⌘0 to snap back to fit width, or a trackpad
pinch. Pages re-render sharp at any size (never a blurry stretch), your highlights stay exactly on
their words, and each document remembers its zoom along with your reading place.
PDFs and books read fully in the pane — real pages, selectable text, and the excerpt loop below.
The book's pane is a pane like any other, with its own tabs in the bar across its top, and any page
can stand in it: a page link clicked there opens in that pane — or beside it, if that is what you
chose under Settings ▸ Links & Pages — and ⌥-click always opens it beside. To put the
book on the other side, choose ⋯ ▸ Swap with Pane on the Left in its bar;
✕ in the bar closes it, and dragging the line between the two panes resizes them — the
width comes back next time. All of what a pane can do is in Panes: several pages side by side, each
with its own tabs, earlier in this chapter.
Reading a PDF or book in the pane, pull the good bits straight into the page you're writing:
drag a selection onto the note (or ⌘C it, then ⌘V on the page) and it lands as a
quote — dropped as its own block, never split into the line you were on — with a ↩ backlink
to the source and its own highlight left in the document. With ⌘C and ⌘V, paste within half
a minute of the copy: after that, or if you copy something else in MojoPad first, you get the words alone,
with no quote around them. The quote is made only in the page itself: pasted or dropped into a property, a
plain text page or a Markdown page in the raw source view, the words arrive as they are. In the Journal,
the quote goes into the day you are writing in: click into another day to quote into it. Click the ↩ and the source opens in a
pane beside your page at that exact spot — or, if a pane already shows it, that pane goes to
the spot — with a thread drawing from your quote to the highlight. The same gesture
works on a rich-text page, a Markdown page, or a canvas card, so an idea always leads back to where you
found it.
Drag a selection right away. In a paper kept in your wiki, press anywhere on the words you
selected and move: the drag starts at once, with no need to hold the pointer still first, and a slip of the
hand as you press doesn't lose your selection. Everything else you do on the selected words works as it
always has — a click clears them, a double-click selects a word and a triple-click a line, ⇧-click
extends the selection, and right-click opens its menu. To start a new selection that begins inside the
selected words, click once to clear them, then drag. Dropped into another app, the
passage arrives as the same text it always did. A paper read in place from a folder works as before: hold
the pointer still for a moment, then drag.
A passage that runs over a word the paper split at the end of a line — tin- on one line, gling on the next — is quoted and highlighted like any other, and the quote writes the word without a gap.
Each excerpt owns a separate highlight, so quoting the same passage in two places never tangles them. Highlights are permanent marks: right-click one in the reader to remove it, or clear them all at once with the button on the bar above the paper or book that says how many there are — Clear 3 highlights, say — in whichever pane it is open. It asks first.
What you highlight is the most considered thing on the page. Somebody decided, one passage at a time, that this mattered — and a connected assistant can now read exactly that, rather than being handed the whole document and left to guess. It gets the passages in the order you read them, each with the place it sits in the work (page 7, chapter 3) and the day you made it. A highlight in a paper also comes with the color you chose for it, when you chose one. A highlight in a book carries no color of its own — MojoPad marks a book in one shade, with none to choose — so none comes with it. Each one also comes with a link that opens the paper or the book at that mark, the kind of link your own excerpts carry, so a page an assistant writes from your marks can link each passage, not only the paper it is in.
So you can ask for a timeline built only from what you marked across twenty papers, with every line citable back to the page it came from. There is a ready-made way to ask — from-what-i-marked under AI Agents — and it is told not to fill the gaps from the papers themselves, so where your marks run out it says so instead of writing something that reads the same and is not yours.
What a color means is yours, and nothing guesses at it. If yellow means evidence to you and pink means I do not believe this, that is worth saying out loud when you ask; a paper's colors come back by name and no meaning is assumed.
A page with a password gives no marks at all. What you highlighted is part of what the password covers — a mark holds the passage itself — so it is sealed with everything else, and an assistant is told the password is the reason rather than being handed an empty list.
If you encrypted a page before this, its marks were written beside the ciphertext rather than inside it — a page already on disk is not changed by MojoPad learning better. Nothing in MojoPad will read them, but they are in the file. Help ▸ Diagnostic Report has a line under What you have marked while reading that says how many pages are like that, and on almost every Mac it says none. Unlock such a page once and it is re-sealed with your marks inside.
A link can carry the words of a passage in one of your PDFs, not just the paper. Click it and MojoPad opens the paper at that page, finds the words, marks them, and draws a line from the link to the mark. Three ways people use it:
On a page full of these links, choose Edit ▸ Links ▸ Mark the Quoted Passages (also in the command palette, and on the right-click of any such link). MojoPad reads each paper out of sight, marks every quoted passage it finds, and ends with one sheet: Marked 12 passages in 4 papers; 2 quotes weren’t found, the quotes it could not find with the page each was looked for on, and any paper it left alone and why. Remove the marks this made on that sheet takes back exactly those marks and nothing you marked since. A passage that is already marked is not marked again, and neither is one you mark, or reach by clicking its link, while MojoPad is still working. If a paper is locked, or the wiki locks, before MojoPad finishes, the sheet lists each paper it didn’t finish and how many quotes are left in it. A paper whose password was changed on another device while MojoPad was marking it is listed too: answer the bar at the top about it first, then mark its passages again.
The link names a page, and MojoPad looks there first, then on the page after, the page before, and two pages either way — never further. A link names the page by the PDF’s own count, starting at one, and the numbers printed on a paper’s pages are often different: a page or two later when the PDF adds a cover sheet, and a journal’s own numbers, which run through the whole volume, can be in the hundreds or thousands. A quote at the foot of a page is often counted as the next. Past two pages, the same words are more likely a different passage than a miscount, so MojoPad stops rather than mark the wrong one. A link that names no page, or a page past the paper’s last one, is looked for through the whole paper.
A quote that runs from the foot of one page onto the top of the next is found too, past the page number and the heading printed between the two halves. A mark is on one page, so MojoPad marks the part on the page that holds more of it.
Only letters and digits are compared, in any language. Spaces, line breaks, punctuation, curly or straight quotation marks, the different dashes, a word broken across a line with a hyphen, the invisible hyphens some papers carry, and letters a font joins together (the fi in finding) are all taken as the page has them. Capitals are compared as written first, and only if that finds nothing are they ignored. A quote of fewer than eight letters is not looked for at all, because it would match on every page.
A manuscript with numbered lines. A paper under review prints a number beside each line, and in the paper’s text that number stands between the last word of one line and the first word of the next. MojoPad recognizes a column of line numbers in the left or right margin and reads the lines without them, so a quote that runs from one line onto the next is found whether or not it repeats the number, and a word broken at the end of a line — inter- on one line, vention on the next — is found written as intervention, inter-vention or inter- vention. The mark covers the quoted words only, not the number beside them. Numbers that are part of the text — a count, a figure’s number, a footnote — are read as the words they are. A table whose rows are numbered 1, 2, 3 down the very edge of its page, with nothing further out, can look like a numbered margin: a quote of one of its rows is still found, though its mark may leave out the row’s number.
And a link to a mark that has since been removed — a citation from an excerpt, or a link you made with Copy Link to Selected Words — no longer opens the paper in silence: it says MojoPad couldn’t find the marked passage this link points to, and, for a citation that names a page, which page it opened instead.
No assistant can mark your papers: there is no tool for it. An assistant writes the link, and your click makes the mark. When an assistant later reads what you marked, a mark made from a link comes back labeled as one, so it is not reported as a passage you chose. The words a link quotes are never written to MojoPad’s log, and the diagnostic report counts these marks — reading highlights: 40 (12 made from a link) — without saying what they say.
The link is written mojoref:, the paper’s page id, then the parts it needs, each
after a semicolon:
mojoref:<page id>;pdf=4;q=the%20cohort%20was%20smallpdf= is the page, counted the way the PDF counts. q= is the words,
written the way a web address writes them — a space as %20, and most punctuation
the same way — at most 500 characters. Add c=green (or amber, pink or blue) for a
color other than yellow. A link that also names a mark, with hl=, goes to that mark while
it is there and uses the words when it is not. The words survive a Markdown page, a Markdown export
and a Word file; in Word the link still opens MojoPad at the passage. A part MojoPad doesn’t
recognize is skipped and the rest of the link still works, and a color it doesn’t have is
yellow — though a Word export leaves a link like that out and lists it with the links it
couldn’t keep. An assistant connected to MojoPad is told all of this; you only need it to write
one yourself.