The problem this solves. You have a few thousand papers, and they already live somewhere — in a reference manager, in a folder you have curated for years, on a drive. Bringing them in the ordinary way would copy every one of them into your wiki: a second copy of everything, and from that moment two versions that drift apart.
File ▸ Files on This Mac ▸ Read a Library… does the other thing. Point MojoPad at the folder and it makes a page for each paper that says where the paper is — never a copy. It reads the words out of each one, so a paper turns up in search, among related pages, and in answers, exactly like a page you wrote. The papers never move, never change, and the program that manages them never notices.
Sub-folders come too, and the pages are filed under a folder named for the library.
What you are agreeing to. You grant a folder, not a list of files: everything inside it, however deep. That permission stays on this Mac and never travels inside the document — send the wiki to somebody else and they get pages that know a paper's name and nothing they can read, until they point MojoPad at their own copy. Each time a paper is opened, MojoPad checks again that it is really still inside the folder you shared; a shortcut pointing somewhere else is refused, however it got there.
A document with a password can't read a library. The papers would sit unprotected on disk while the pages looked locked, which would be a hole in the protection that you could not see. So it is refused outright rather than half-done.
Highlights are the one thing missing. A highlight remembers a place on a page, and a paper you do not own can be re-downloaded, re-scanned or replaced at any moment — a highlight that quietly slid onto the wrong paragraph is worse than none. So papers read in place can be read, searched, found and quoted, but not yet marked up. Papers brought in the ordinary way still highlight as before.
Stop Reading a Library… withdraws the permission. The pages stay and say they can no longer be read; nothing of yours is deleted, and pointing MojoPad at the folder again brings them straight back. Help ▸ Save Diagnostic Report… lists which folders are shared and whether every paper is still where its page says.
Plenty of people arrive at MojoPad already living in something else — a document manager holding years of PDFs, a folder of markdown, a reference library. You don't have to move any of it. The most comfortable arrangement is usually a division of labour: the other app holds the documents; MojoPad holds the thinking and the links between them.
Most Mac apps can hand you a permanent link to one of their items — DEVONthink calls it an item
link, and other apps offer something similar. Copy that link, then in MojoPad select the words you
want to link and choose Make Custom URL Link… (⌥⌘U). Now the sentence in your notes
points straight at the source document, and one click reopens it in the app that owns it — at the
right item, every time.
You don't have to select anything first. If the phrase isn't written yet, put the
cursor where the reference belongs and run the command anyway: type the words and the address,
and MojoPad writes the phrase into your page and links it there. Worth knowing what you've
actually made, because it's more than one link — you've registered a rule, so that phrase
becomes that link everywhere it appears in this document, now and in anything you write later.
For a document you refer to constantly that's far less typing than linking each mention. For a
one-off mention, type [the words](the address) in the sentence instead — that makes
a single link, there and nowhere else.
The first time you click a link like that, MojoPad asks before handing it to another app, and offers to always allow that kind of link. Nothing leaves your Mac; the question is just so a link in a document you imported can't quietly launch something.
If a PDF or book is worth keeping in MojoPad, import it and read it here: highlight passages, and drag a selection onto the page you're writing to land it as a quote with a ↩ backlink to the exact spot. See Importing for the whole reading and excerpting flow.
If it belongs in the other app, keep it there and link to it. Many people annotate PDFs in their document manager and keep MojoPad for what the annotations mean — the argument, the connections, the writing that comes out of them.
Nothing here is a one-way door. A MojoPad document is a folder: right-click it in the Finder and choose Show Package Contents and you'll find one plain file per page, plus your attachments as ordinary files. On top of that, File ▸ Export Document writes the whole wiki out as a folder of Markdown, plain text or Word files, as a website, or as a PDF or ePub — and any single page exports on its own from Export Page As.
Your folders come with you. Exporting to Markdown, plain text or Word writes your Folders as real folders on disk, and each page's file sits inside the one you filed it under, nested as deeply as you nested it — including a folder you have not filled yet, which comes out empty rather than not at all. A page you never filed sits at the top, beside the folders — so a wiki with no folders still comes out as one flat folder of files, though the file names in it are tidied and numbered the same way the nested ones are. A page filed in two places is written once, in the first. Names your disk will not accept are adjusted rather than dropped: a folder called Reading/Writing stays one folder, two folders whose names differ only in capitals stay two, and two pages of the same name in the same folder both survive with the second numbered. Nothing is left out to make the shape work. If you would rather have one flat folder — because something you have written reads that folder and expects every file at the top of it — turn off Keep your folders when exporting to a folder of files in Settings ▸ Exporting.
Word files keep their links to each other across the folders: a link from a page in one folder to a page in another still opens it. Markdown files link by page name, so they are unaffected by where the files sit. A website export is deliberately left flat — its file names are web addresses rather than filing, and nesting them would change every link you had already shared.
A page can be a file on your disk, and a whole folder can be followed so its files arrive as pages and stay in step. That has a chapter of its own: see Linked Files and Folders.