The header line tells you how many topics there are and how many need attention, for example “48 topics to explore · 2 need attention”. Below the look-up field, the home page lists:

• Pinned: topics you pinned, so the ones you care about stay at the top.
• Recently changed: the last few pages you opened or Atlas wrote, with when each was written.
• Needs attention: topics with statements to re-check, written as a sentence such as “Bridge Retrofit has 3 claims to re-check”.
• Browse by type: counts of the statements Atlas has recorded, by kind (Fact, Decision, Question, Interpretation, Status).
• Browse topics: the topics Atlas found, with how many notes mention each.
• Vault overview: a one-page front page for the whole vault (see below).

Inside a page, the breadcrumb at the top lets you step back along the topics you followed, and All Topics returns home. Click Done to go back to your notes.

Type a word or phrase into Look up anything in your vault…. As you type, Atlas shows matching topics and three choices under Choose what you mean:

• Open existing page, when Atlas already wrote one.
• Ask this question, which hands the phrase to Ask Header with the whole vault as scope.
• Generate new page, which writes a page about the phrase.

Before generating, Atlas checks that at least one note mentions the phrase. If none does, it says “No notes mention … yet” and makes no AI call. Atlas only writes pages it can ground in your vault.

The first time you open a topic, Atlas writes its page; you'll see “Synthesizing from your notes…” while it works. After that the page opens from what Atlas saved, with no new AI call, even after you edit the notes behind it. A page shows:

• Grounded in 7 notes: how many notes the page was written from.
• Generated synthesis: the AI-written text, with citations like [2]. Topic names in the text are links to their own pages.
• Key facts, Decisions timeline, Needs review and Open questions: the page's statements sorted by kind. Click one to see the exact excerpt it came from and a link such as Open Site visit 2026-09-12, lines 14–18, with a line like “Direct evidence · verified Oct 20, 2026” (or “Inferred evidence” when the note supports it less directly).
• Sources: the notes behind the citations, numbered [1], [2] and so on. Click one to open it.
• Related: other topics the page mentions.

Header checks each statement on a page against the note it cites. When the cited note doesn't contain it, the statement is marked Unverified: the cited note doesn't contain this (or …is no longer in this vault if the note is gone), its citation turns into [2, unverified], and it moves to Needs review instead of Key facts. Treat it as a lead to check, not a fact.

When your notes disagree with each other (two dates for the same deadline, say), the page shows a count such as 2 conflicts and a Contradictions in your notes box listing them. Atlas keeps only conflicts it can trace back to the source text. Open both notes and decide which is right; Atlas doesn't pick for you.

When you edit, add or remove notes behind a page, the page shows Sources changed. It keeps showing the version you already have until you choose to update it. Click Review updates and Atlas writes a fresh draft from the current notes, then lists only what changed, each with a link to the source lines:

• New Claim: something the notes now say that the page didn't.
• Changed Status: a statement whose kind, backing or disputed state changed.
• Lost Evidence: a statement whose cited passage changed, or whose note is gone.
• Conflict Introduced: a new disagreement between notes.

For each item, click Accept, Dismiss or Edit (edit the wording, then Accept edit). Nothing replaces the current page until every item is decided. Then click Apply reviewed updates. Accepting a Lost Evidence item removes that statement from the page. If nothing needs review, Atlas says “No evidence-backed Atlas updates need review.” Close the panel to keep the page as it was.

On a topic page, the … menu next to the title holds:

• Pin / Unpin: keep the topic under Pinned on the home page.
• Rename…: change the name Atlas shows. Your notes and their filenames stay as they are.
• Merge into: fold this topic into another one, for example “ACME Corp” into “Acme”. Its recorded statements move to the other topic, and it no longer appears on its own.
• Lock manual section: choose Overview, Key Facts, Decisions or Open Questions. When you later apply reviewed updates, a locked section keeps the text it had.
• Mute topic: hide a topic you don't want, such as a word that keeps showing up in templates.

Each entry in the Sources list has its own … menu. Mark authoritative puts that note first in the list of notes Atlas writes the page from, which is useful for a contract or a spec that should outrank meeting chatter. Exclude from this topic leaves the note out of this topic (Include in Atlas brings it back). These take effect the next time the page is written or reviewed.

Your curation choices are saved inside the vault, in .header/atlas-curation-v1.json, so they travel with the vault to your other Macs.

At the bottom of the home page, open Vault overview and click Write my vault's overview. Atlas makes one AI call over a small sample of notes from your most connected topics and writes a front page: what the vault is about, the main themes as links, and threads worth revisiting, with citations. When those notes change, the overview shows Notes changed; click Regenerate overview when you want a new one. A vault with only a few connected topics may not have enough for an overview yet.

Atlas pages live inside Atlas until you publish one. Click Publish as Markdown on a page to save it as an editable note in an Atlas Pages folder in your vault, named after the topic. If a note with that name exists, Header adds a number rather than overwriting it. The note keeps its [[links]], marks unverified citations as [n, unverified], lists any verified contradictions, and ends with a Sources list linking each note.

Its frontmatter says it was generated (generated: true) and sets exclude_from_atlas_sources: true, so Atlas won't read it back as a source. It's a snapshot: later updates in Atlas don't change the published note.

Health Check looks over the pages Atlas has written, without any AI, and lists Stale pages (sources changed since they were written), Orphans (pages no other page links to) and Missing links (a page names another topic without linking it). Click a topic to open it. From the same panel, Scan all pages for conflicts uses AI to compare your pages with each other and lists contradictions that span topics; it needs at least two pages.

Export Index writes two files into Atlas Pages: index.md, a catalog of the pages Atlas has written, and log.md, a record of Atlas activity. Both are replaced each time you export. Refresh rescans the vault for new or changed notes; Atlas also does this on its own while it's open.

Atlas doesn't edit the notes it reads. Here is everything it stores:

Ask Header answers from your notes. If you also want it to read Atlas pages, tick Include Atlas pages under Context & routing in the Ask Header panel. It's off by default, and Atlas pages are labelled in the answer as AI-generated summaries rather than original notes.