The Tools menu

The wrench icon in the editor toolbar, top to bottom. Analysis and import/export already have their own pages — this one covers the rest, including three commands that reset the Story Bible and are easy to mix up.

Formatting

Prose Formatting…

Opens the style editor — fonts, sizes, line spacing, margins and colour for both body text and headings, with a live preview beside the controls. This is what the manuscript preview and PDF/EPUB exports actually use; nothing here touches your prose, only how it is typeset.

A Presets menu holds "Standard Manuscript Format" plus any you save yourself, and an Import Style menu can pull a look from elsewhere: a Vellum EPUB, a .ulstyle file from Ulysses, or a book.json folder. Every import lands as a new named preset rather than overwriting your current style, so trying one out costs nothing.

Style Check Word Lists…

Adds your own words and phrases to the style check's lists from a CSV file, one list at a time, and resets any list back to the built-in words. The same sheet opens from Word Lists… in the inspector's Style tab. See Your own word lists.

AI Analysis

Analyze Manuscript with AI…, the two re-analyze commands, and Propose Scene Splits… have their own page — see Reading the manuscript with AI. The Engine: line beneath them is not a command; it names whichever of Claude or on-device Apple Intelligence is about to do the reading.

Story Bible

Scan Manuscripts for Entity Links

A retroactive sweep, not a preview. It reads every chapter and scene in the active manuscript (or, when a project has more than one, an additional Scan All Manuscripts for Entity Links covers every book at once) for plain-text mentions of names already in the Story Bible, and rewrites each free-standing one into a real link — the same link the wikilink autocomplete would have made if you had typed it. A summary reports how many mentions were linked.

Look Up Wikipedia References

The bulk sibling of the "Import from Wikipedia" option on a single record. This one walks every character, location, event, object and organization in the project that does not already have a reference and searches for each in turn. An exact-title match is linked automatically; a genuinely ambiguous search is left for you, and the summary afterward tells you how many need a decision — open each in its own inspector to choose among the candidates.

Continuity Check…

Reads for eleven kinds of inconsistency: plot items set up but never paid off (and the reverse), a character appearing in a scene before the event where they should have learned something, participation in an event dated outside a character's own lifespan, a character double-booked in two overlapping events, physically impossible travel between two dated locations, conflicting birth or death dates, a stub entity linked from the manuscript but never filled in, prose describing a character's eyes or hair in a colour that contradicts their record, and — in a series, once a Character State is tagged to a specific book — a character recorded dead at the end of one book and alive again at the start of the next.

That last one — the alive-again rule — only fires once a Character State's Book field is set — left unset, a state applies everywhere and nothing compares against it. It reads each book's own boundary state (last recorded in one, first in the next) and flags only the hard-edged case: deceased, then alive again, across that seam. Softer differences — occupation, address, condition — are common and legitimate across a series, so they're left for your own eye; see Series Continuity in The analysis tools for a side-by-side view built for exactly that reading.

Scoped to whichever manuscript the toolbar's "Working on" picker names, the same as Scan for Entity Links above — a check on one book's plot structure doesn't need every other manuscript in the project pulled in to answer it. With more than one manuscript open, a second command appears to check every one of them at once, and a third — Compare Specific Manuscripts… — lets you pick two or more by hand: useful for catching a character double-booked, or a date that contradicts, between book one and book three of a trilogy while skipping the volume in between. The results sheet's title names whichever manuscripts were actually checked, and each conflict is labelled with its own manuscript when comparing more than one.

The sheet this command opens lists every open issue it found — a setup with no payoff and vice versa, a stub entity, a date or timeline conflict — alongside every date on file, sorted chronologically. Each issue also appears on the entity's own record, in its Continuity Issues section, which is where Resolve and Ignore actually live. Re-running the check does not raise an issue twice — an ignored one stays ignored until the thing that caused it changes.

Link Integrity Report…

A different kind of broken from Continuity Check. That tool compares the Story Bible against the manuscript and reports disagreements. This one never reads your prose at all — it walks the project's own cross-references, every field on a record that points at another record, and reports the ones that no longer hold up.

Three things count as broken:

• The target is gone. A field still points at a record that was deleted or merged away. "linked record no longer exists."
• The target is the wrong kind. The record is there, but it is not a type this field accepts — an owner field pointing at a Location. "linked to a Location; expects Character or Organization."
• A containment is recorded on one side only. A location claims a parent that does not list it as a child, or the reverse.

A clean project reports No broken links found under a checkmark seal. One with issues gets a title that counts them — Link Integrity (N) — and a row per issue explaining what broke and what the field expected instead.

You do not have to run the report to know it would find something. When the project has broken links, a red capsule sits in the editor's top-trailing corner carrying the count, with the tooltip "N broken links — click to review." It stacks directly below Continuity Check's own badge when both have something to say, and it is absent entirely when there is nothing to report — so seeing it at all is the finding.

Statistics…

One dashboard, read-only, scoped by the menu at the top — All Manuscripts by default, or check off just the ones you want the numbers to cover. Everything below it follows that scope: total entities, connections and tags; word count written against target, with an Earned Value Analysis underneath it for anyone who wants to track a manuscript the way a project schedule would — a Schedule Index comparing how much of the book is actually finished against how much word-count credit that should represent, and a Writing Index comparing words written to words earned, so a chapter that's technically "on target" by word count but still mostly drafted rather than revised doesn't read as further along than it is.

Below that: every chapter's word count against its own target, scenes grouped by status, each story arc's completion percentage, a count of unresolved continuity issues by severity, upcoming Writing Reminders if you've created any, and a full breakdown of every record type in the project. Nothing here is editable — it's a single place to see the shape of the whole project at a glance, without opening each tool that tracks a piece of it separately.

An AI-Assisted Content section, when the scoped manuscript(s) have any AI marks at all, shows the same figures the AI Provenance Report is built from — total words carrying a mark, as a percentage, broken down by where each one came from — live, without exporting anything. See Writing aids in the editor for how a passage gets marked in the first place, and for the exportable report that lists the marked passages themselves rather than just totalling them.

Research Highlights…

Browses whatever's been read into the project from your Apple Books library via the Highlights app — see Research Highlights for the full path in, browsing, and inserting a quote into the manuscript or a note.

Import / Export

Importing and exporting live on the toolbar's own Import and Export menus and the windows their More Imports… and More Exports… open — covered in full at Importing and exporting.

Apple Books Highlights, in the Import window, is covered separately at Research Highlights instead — it reads from the Highlights app's own backup file rather than a document you pick each time.

Anonymization

Apply Pseudonyms to Prose… and Restore Real Names in Prose… work from the mapping kept in the Name Registry — see The analysis tools for how the registry itself is built and edited.

Works & Data

A submenu at the foot of the Tools menu, so these less-used commands are out of the way. When something needs tidying (empty manuscripts, unused pictures, oversized portraits or duplicated records), the matching command appears inside it.

Manage Works (add / delete)…

The general-purpose list for every manuscript in the project — rename in place, drag to reorder, add a new one, and delete. The binder toolbar's New Manuscript button is the fast path for starting one; this sheet is where you go to rename several, reorder the list, or remove one. Deleting here uses the exact same cascade as deleting a manuscript from its own context menu in the binder — see The binder — chapters and scenes exclusive to that manuscript go with it, and anything shared with another manuscript is kept and simply un-scoped.

Document Health…

Runs every check for trailing data at once and lists what each one found, with its fix beside it. Six checks: manuscript shells (manuscripts nothing points at), empty manuscripts that still hold Story Bible records, records scoped only to manuscripts that no longer exist, unused pictures, duplicated records, and broken links. A check that finds nothing says so.

Each fix asks first, writes a backup, and touches only what its own check listed, so removing shells doesn't also delete the stranded records shown further down. The commands below it, and Link Integrity Report…, still work on their own. This is the place to look when you don't yet know what to suspect.

Show Automatic Backups…

Opens the backups folder in the Finder — this command does not restore anything itself. A full project backup is written automatically immediately before every bulk rewrite or deletion in the app, the most recent twenty are kept, and File ▸ Import Project Backup… is where you actually restore one. There is no separate timed or autosave-driven backup; every one in that folder was taken right before something specific was about to change.

Compact Document…

Two housekeeping passes in one command. First, old automatic snapshots of your prose — the copies the app keeps of what a section looked like before each bulk rewrite — are trimmed to the five most recent per chapter or scene; anything you saved as a snapshot yourself is never touched. Second, the document's own database is repacked without the empty space that deleting records, pruning snapshots and editing prose leave inside it, which is where the size on disk actually shrinks; the alert gives the size before and after. Safe to run at any time. If something else in the app is writing at that moment, the repack is skipped and the alert says to try again.

The three Story Bible reset commands

These look similar and are not. Read the scope column before choosing — none of these is undoable from the Edit menu, though a backup is written automatically first in every case.

A fourth, narrower command — Remove Empty Manuscript(s)… — only appears when the project actually has one: a work with no chapters or scenes at all, left over from an import or an abandoned start. It lists each empty manuscript by name and notes that any Story Bible record appearing only in them goes too. It carries none of the risk of the three above, because by definition there is no prose to lose.