Research Mode (Cafes)

Overview

Research Mode ("Cafes") is a standalone research feature where you create independent research workspaces, gather material from multiple sources, and curate findings for use in your Scribes. Available to every signed-in user — token balance is the only limit.

Getting Started

1. Click Research in the navigation bar
2. Click + New Cafe to create a research workspace
3. Name your Cafe (e.g., "Climate Research", "AI Startups")
4. Start searching and gathering research

The Workspace: Three Zones (W1.13)

Opening a Cafe now shows three zones side by side, redesigned in W1.13 so nothing renders full-content in the side columns anymore:

• Sources rail (left) — a dense, scannable list of rows (not cards). Each row shows a type icon, truncated title, status dots (credibility, verify, DOI), and a scope checkbox (see Ask-Your-Cafe Scope below). Group by question, type, used/unused, detail, or verify status; filter by title/text; toggle compact or comfortable row density (your choice persists). The rail is drag-resizable at its edge.
• Reading pane (centre) — the single place anything gets read: a source, a Serving Tray item, or a research report. Click any row in either rail and it opens here, with one action toolbar on top (no more per-row button rows). When nothing is open, the pane's home view is the Ask Your Cafe chat — see below.
• Tray rail (right) — your Serving Tray, defaulting to a slim collapsible strip so it doesn't eat width. Expand it to drag-reorder items; click any item to read/edit it in the pane.

Reading is URL-addressable. Whatever is open in the pane is reflected in the address bar (?read=...) — refresh the page, use browser Back/Forward, or share the exact URL and the same source/report/tray item opens back up. A "← Ask your Cafe" back button in the pane returns you to the chat home view.

On mobile (narrow screens), the rail is full-width and tapping a row drills into a full-screen reader with a Back button; the tray becomes a slide-in drawer opened from a "Tray (N)" button.

Ask-AI Popover: Highlighting Anywhere in a Cafe

Wherever you're reading in a Cafe — a source card, a Q&A reply, the Serving Tray, an Auto-Write report, or the full-screen report reader — you can act on any piece of text without hunting for a per-surface button.

Opening the popover

• Highlight text (drag-select 3 or more characters) anywhere in the Cafe → a small popover appears near your selection.
• Right-click a source card → the popover opens scoped to the whole source (not just a snippet). Add to Tray and Save to Notebook carry that source's citation reference along, so attribution is never lost.

The four actions

A fifth action: Dictionary

Highlight a single word instead of a phrase and a Dictionary action appears — click it for an instant AI-generated definition, the same dictionary popup used in book Reading Mode. You can save the definition straight to your notebook from the popup.

Where it works

Anything open in the reading pane (a source, a report, or a tray item), Q&A chat replies, and the full-screen report reader (/cafe/[cafeId]/artefact/[artefactId]) all support the popover — it's the same selection handler regardless of which zone you're highlighting in. On the full-screen report reader, Ask AI answers in place — you get an inline answer grounded in that report's sources without leaving the page. Save to notebook and Add to tray also work there; Verify is not available on the standalone reader. On a shared report link, the popover shows only the read-only subset (no Verify, no owner-only actions).

It knows where the highlight came from

Highlight text inside a specific source or report and Ask AI automatically threads that source/report's title into your question — so the answer accounts for which piece of research the passage came from, even if you don't mention it yourself.

Cafe Settings (Citation Style, Filters, Reference Count, and More)

Each Cafe has a Settings panel, accessible via the gear icon in the Cafe toolbar. Settings are saved per Cafe and take effect on all subsequent searches in that workspace.

Citation Style

Choose from five citation formats: APA 7 (default), APA 6, MLA 9, Chicago Notes-Bibliography, and Harvard Cite Them Right 2025. Enriched source cards in the Cafe show a formatted citation in the style you pick. The style affects how references appear in the card — authors, title, journal, volume, issue, pages, DOI.

Source Tier Filter

Filter results to show only sources from specific tiers: Academic Journal/Paper, Government Source, News Article, Web Article, Social Post, or Wiki Summary. Leave the filter empty (default) to see all tiers. Enable Academic Sources Only as a quick toggle to restrict results to academic-tier sources.

Reference Count

Set how many sources each search returns. Options: Auto (default, resolves to 7), or a fixed count from 1 to 25 — the same ceiling for every signed-in user, no account tier involved.

Enriched Sources Only

When on, search routes hide sources where metadata enrichment returned only a bare URL (no title, author, or date). Useful when you need citable academic sources rather than raw web results.

Web Search

Toggle web search on or off for this Cafe. When off, the Web search mode disappears from the search bar — only Academic search and identifier paste remain available. Default is on.

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Identifier Paste (every signed-in user)

Instead of searching, you can paste a known identifier. Click the small "Add by identifier" chip in the search bar's info row (next to the model picker) to open a drawer containing the identifier-paste input — along with Cafe Settings and Providers. Paste the identifier into that input and CoffeeScribe auto-detects the type as you type, showing a pill:

The Enrich button is disabled if the type is unrecognised. On submission, the enrichment pipeline resolves the identifier against the appropriate database (Crossref, OpenAlex, PubMed, Open Library, Google Books, or the Crossref Journals API for ISSNs) and adds an enriched source card to your Cafe.

After the metadata enrichment returns, CoffeeScribe automatically attempts to scrape the full article body from the source URL in the background. This is best-effort:

• Open-access articles — full readable body is usually retrieved and stored in the source card.
• Paywalled publishers (Nature, Science, Elsevier, etc.) — the scrape is blocked by a challenge page; the abstract from the enrichment metadata is kept as the content.
• Either way, the 200 response arrives immediately — the body scrape happens in the background and doesn't slow down the identifier flow.

Identifier paste is available to every signed-in user. Cost: a small token charge applies when OpenAlex is reached during enrichment (other resolvers such as Crossref, PubMed, arXiv, Open Library, and Google Books are platform-absorbed at no per-use cost to you). The background body scrape uses the same URL-scrape path as the URL Scraping feature and is charged at the same rate.

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Source Cards — Enrichment Surface

Every source card in the Cafe now shows enrichment metadata when available:

Metadata Health Badge

A small pill in the card header indicates how complete the enrichment is:

• Full (green) — author, year, journal/publisher, volume, issue, pages, and DOI all present
• Partial (amber) — some fields present; others missing
• URL only (grey) — no structured metadata; bare URL or failed enrichment

Source Tier Label

A small pill shows the source's classified tier: Academic Journal/Paper, Government Source, News Article, Web Article, Social Post, or Wiki Summary. This reflects the source's type, not its quality.

Academic Provider Label

Academic source cards from Auto-Research show an additional provider label — arXiv, PubMed, OpenAlex, or Scholar — so you can tell at a glance which database the source came from, rather than seeing only the generic "Academic" type.

Freshness Badge

A year pill colour-coded by age:

• Green — published within the last 2 years
• Amber — published 3-5 years ago
• Grey — published more than 5 years ago

Hover the badge to see the full publication month and year.

Source-detail Badge

A small badge showing Well-documented, Some research, Limited research, or No details — a quick read of how much we know about a source, shown on every source card. It is not a judgement of whether the source is true, and the weak end is grey, never red — "Limited research" means we've only captured a little about it (often just a link), not that it's fake. It's a cheap, automatic, structural check — no claim verification happens. The read looks at:

• Academic identifier — a DOI, PMID, or arXiv id (even just in the URL, e.g. a PubMed link) marks a peer-reviewed work as authoritative, even before it's fully enriched
• Source tier — academic journal / government source scores higher than a social post
• Author / date presence — a named author and a publication date are positive signals
• Domain reputation — known reputable domains (.gov, .edu, established publishers, doi.org, arxiv.org, PubMed) score higher
• Metadata completeness — richer enrichment reads as more documented

Important: this badge is not the same as "Verified." "Well-documented" means we have a lot of detail about the source — it does not mean a claim in it has been fact-checked. Whether a claim checks out is the separate Verify flow: every source card has a working "Verify claim" button that runs a real cross-reference loop against other sources and returns a verdict (see Verify Claim below). Hover the badge for the reasons behind the rating.

Use the source-detail badge as a quick first-pass signal; always read the source (and Verify important claims) before citing it.

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Sources Rail — Finding, Organising, Trusting, and Scoping Your Sources

The Sources rail (left side of the Cafe, redesigned again in W1.13 on top of the W1.4 foundation) renders every source as a dense row rather than an expanded card, so it stays scannable at hundreds or thousands of sources. Click a row to read the source's full detail — enrichment, citation, evidence, everything the old expanded card showed — in the central reading pane. Key capabilities:

Grouping ("Group")

The Group control at the top of the rail groups sources five ways:

• Question (default when your research used fan-out sub-questions) — by the sub-question that produced each source; sources with no sub-question fall into a "General research" bucket
• Type — by source type (Web, Academic, YouTube, Reddit, …) — the default when no sub-questions exist
• Used — splits sources into "Used in reports or Tray" vs "Unused" so you can quickly see what contributed to your output
• Detail — groups by Well-documented / Some research / Limited research / No details
• Verify — groups by verification status
• None — a flat list with no grouping

Groups render as collapsible headers in the rail (large groups — more than 50 rows — start collapsed so the rail stays scannable). Your group-by choice is remembered per Cafe. Grouping is purely a view preference — it doesn't change or delete anything.

Narrowing to one type ("Show")

Beside Group is a Show dropdown that narrows the rail to exactly one category — a single source type, Reports, Conflicts, or Earlier research — restoring the old at-a-glance category-isolation the previous pill row gave you. Pick "All types" to see everything again.

Density Toggle

Two icon buttons switch every row between compact (denser, more rows visible at once) and comfortable (larger touch targets, better for mobile). Your choice persists across sessions.

Filter and Search Box

A text input above the rail filters visible rows by title, query, or body text. Results update as you type. Beside it are two toggles and a reset:

• Well-researched only — narrows the rail to Well-documented + Some research sources — useful when writing a report that needs citable, well-detailed references.
• Verified — narrows the rail to sources you've run Verify on, regardless of verdict (Verified / Contradicted / Mixed / No-evidence).
• Clear filters — resets the search box and both toggles in one click.

Ask-Your-Cafe Scope (Persistent Checkboxes)

Every source row (including "Earlier research" legacy rows — see below) has a checkbox that controls whether that source is included when you ask a question in Ask Your Cafe. Uncheck a source to keep it in your Cafe but leave it out of grounded Q&A answers.

• The rail header shows "N of M in scope" at a glance.
• Every group has its own toggle-all control so you can scope a whole batch (e.g. every source from one sub-question) at once.
• Your choice is saved to your account — it's a persistent setting on the source, not a per-session filter. Come back tomorrow and the same sources are still scoped the way you left them.
• Explicit "ask about THIS source" selections (from the Ask-AI popover) still override the checkboxes for that one question — checkbox scope is the default audience, not an absolute lock.
• In shared/read-only Cafes, viewers see the checkbox state but cannot change it.

If you uncheck every source, Ask Your Cafe still tries to answer from your Serving Tray items — see Filtering and Scoping Sources below for the full behaviour.

"Used in Reports" — Passages from Your Generated Reports

Open any source in the reading pane and look for a "Used in reports" section. This shows the exact passage(s) a generated report cited from that source, tagged with the report that used them. This fixes the "blank reference" problem — a source your report cited is never content-empty; you can always see what the report took from it.

Provenance Link (Clickable ↗)

Every source shows a ↗ (open-in-new-tab) link next to the title, both on the rail row and in the reading pane. Click it to open the original URL — the primary source — in a new tab. This is the canonical provenance link for citations.

Earlier Research

Sources created by the older AI web-search path (before W1.4) — where the AI combined multiple results into a single synthesized response — are grouped under "Earlier research" (read-only) in the rail, or via Show → Earlier research. Their content is preserved exactly as gathered and they do not show a Credibility badge, Verify button, or full reading-pane detail beyond the raw response. The "Well-researched only" filter hides them.

Legacy rows get scope checkboxes too (W1.13). Even though their content is read-only, "Earlier research" rows are counted in your "N of M in scope" total and can be checked/unchecked like any other source — since they can still ground Q&A answers, you need full control over whether they're included.

Verify Claim — Live, with auto-produced cited report

Every source has a "Verify claim" button in the reading pane's toolbar. Clicking it opens a dialog where you pick the claims to verify and set a token ceiling, then the loop runs in the background. You can also trigger it by highlighting a passage (or right-clicking a source) and choosing Verify claim from the Ask-AI popover — it verifies the enclosing source's main claim.

• The source resolves to a verdict badge (visible both on the rail row's status dot and in the pane): Verified / Contradicted / Mixed / Couldn't verify.
• The evidence panel in the pane shows the underlying source, supporting evidence, and opposing evidence for each claim.
• A cited report is automatically created in the Reports rail group when the loop completes — one section per claim, with inline [N] citations and a References list containing only the sources cited in the body.

The loop runs in the background — you can close the pane and come back later. See Verify Claim & Cited Report for the full walkthrough.

Find the Truth & Claim Evidence Matrix (W1.11)

Two related features go a step further than Verify claim — instead of checking a claim already sitting in a source, they let you type any claim (or question) and get a probability that it's true, plus a claim-centric view across everything you've checked in the Cafe.

• Find the Truth (every signed-in user, costs tokens) — the toolbar button next to Claims. Type a claim, the system researches it (and separately hunts for the best evidence against it), then returns a probability (clamped 5–95%, never absolute certainty), a plain-language finding, a credibility-tier-weighted evidence breakdown, the strongest counter-evidence found, and a cited report. Runs in the background and survives closing the tab, with a re-openable "Past truth checks" list.
• Claim Evidence Matrix (every signed-in user, free to view) — the Claims chip opens /research/[cafeId]/claims, a table of every claim checked in the Cafe (by Find the Truth or Verify claim) with supporting / contradicting / silent sources grouped by credibility tier and deduped to independent roots (so ten articles quoting one wire story count as one root, not ten).

See Find the Truth & Claim Evidence Matrix for the full walkthrough, including how to read the probability, the "Overall reading" anchor row, and why a Wikipedia-only basis can't push a claim's score much past the mid-80s.

On-Demand Full-Body Fetch

On any source card, a "Fetch full article" action pulls the entire body of the page on demand and stores it in the card for in-column reading. This is optional and gated (it costs a URL scrape). A fetch state indicator shows:

• Not fetched (default) — only the excerpt/abstract is stored
• Fetched — full body available
• Failed — scrape was blocked (e.g. paywall) — the excerpt and metadata are preserved; the card does not regress to a bare reference

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Source Download

Click the download icon in the reading pane's toolbar for a dropdown with four formats:

• Download as .txt — structured plain text (title, authors, date, journal, DOI, URL, summary)
• Download as .json — full enrichment data as JSON
• Download as .md — the same structured content as Markdown
• Download as .pdf — the same structured content as a formatted PDF

The filename includes the Cafe name and a short source ID. All four formats carry the full body content (title, authors, date, journal, DOI, URL, and summary/body) — not just metadata.

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Provider Picker (every signed-in user)

The Provider Picker lets you choose which search tools are active for a Cafe. Click the Providers chip row to expand the picker. Provider toggles here control the manual search bar and Auto-Write; the Auto-Research modal has its own per-run tool toggles that work alongside these settings.

Free providers (available to every signed-in user, always on):

• Web Search — AI-powered web search
• Academic Search — OpenAlex, arXiv, PubMed

Apify Actors (every signed-in user, token-billed — each requires a one-time consent per Cafe):

• Google Scholar — Academic paper search via the Google Scholar actor
• Twitter / X — Recent posts on a topic
• Reddit — Community discussions and threads
• LinkedIn — Professional profiles and posts
• Instagram — Posts and profiles
• TikTok — Video posts
• YouTube Search — Video results (distinct from the YouTube Transcript extractor)

Enabling an Apify Actor

Toggle any Apify Actor chip. If you haven't consented to that Actor for this Cafe, a consent modal opens first. The modal shows:

• The platform's terms of service implications (e.g., LinkedIn's scraping policy)
• The approximate per-result token cost for that Actor
• Consent and Cancel buttons

Consenting is recorded per Cafe per Actor — you only see the modal once per Actor per Cafe. On subsequent uses, the Actor is available directly.

Apify Actors are available to every signed-in user — each one still requires the one-time per-Cafe consent above, and each result costs tokens.

Per-Actor Cost

Each Apify Actor charges a small per-result token cost (higher than the free academic databases). The consent modal shows the exact cost estimate before you enable an Actor.

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Research Sources

AI Web Search

Type a search query with the AI Web toggle selected. The AI searches the web, synthesizes findings, and presents a formatted response with inline citation links and a numbered Sources section at the bottom. Cost: a small portion of your allowance per search (varies by model). The per-action estimate is shown before you confirm.

Web search works with all models — not just Perplexity Sonar. The AI receives real-time web results regardless of which model you select.

Academic Papers

Click the Academic dropdown to choose from three academic search sources:

• OpenAlex — Search 250M+ works across all disciplines. Includes citation counts. Free, open-access metadata.
• arXiv — Search preprints in physics, mathematics, computer science, and related fields. Includes direct PDF links.
• PubMed — Search 35M+ biomedical and life sciences articles from the NCBI database.

Which database should I use?

Results show paper title, authors, year, citation count (where available), and abstract. Each paper card shows relevant links (DOI, arXiv ID, or PMID). You can:

• Analyze — Send the paper to AI for analysis (Key Findings, Methodology, Compare, ELI5, or custom prompt)
• Add Raw — Save the paper's abstract directly to your Cafe without AI processing
• Dismiss — Remove individual papers from results

The Analyze and Add Raw flows work identically regardless of which academic source you use.

YouTube Transcripts

Paste a YouTube URL and the search bar auto-detects it, showing a "YouTube Transcript" badge. Before extraction, a modal lets you choose:

• Content only — Extract just the transcript
• Summarize, Key Points, Fact Check, Topics & Structure — Extract and analyze in one step
• Custom prompt — Ask anything about the video

You can select multiple options at once.

URL Scraping

Paste any article URL (including www. addresses) and the search bar auto-detects it, showing a "Scrape URL" badge. Same modal options as YouTube — extract content only, or extract and analyze.

Add Multiple Sources at Once (Batch Import)

Pasting two or more sources into the search bar at once triggers the batch import modal automatically — no separate button to find. The bar's placeholder reads "AI web search, YouTube URL, article link — or paste multiple sources at once" as a reminder.

How it works:

1. In the search bar, paste a list of links and/or queries — newline-separated, comma-separated, or just whitespace-separated.
2. As soon as the parser detects 2+ items, the "Add multiple sources at once" modal opens, pre-populated with what you pasted.
3. Each item shows its detected type (Web Search / YouTube / Article / OpenAlex / arXiv / PubMed) with an icon and a per-item token cost. The footer shows the total source count and total cost estimate.
4. Click Run all — items are dispatched to the correct backends with a concurrency cap of 3 (so we don't burst-rate-limit Apify or OpenRouter) and a 1.5s stagger between launches.
5. Each row updates live: Pending → In progress → Done ✓ / Failed ✗. A retry counter appears next to in-progress rows when transient failures (502/503/timeout/Apify/network) trigger an automatic retry.
6. After the batch completes, a summary banner shows how many succeeded, how many failed, how many tokens were charged. Failed items can be retried with one click; sibling successes are not re-run.

Mixed input examples:

Type-hint prefixes (case-insensitive — useful when you want to force a specific backend instead of relying on auto-detect):

• arxiv: pubmed: openalex: academic: — academic backends
• web: search: — force web search (handy when a query happens to look like a domain)
• youtube: yt: — force YouTube (rarely needed; auto-detect handles the common YouTube URL forms)
• url: scrape: — force URL scraping

A line that starts with one of these prefixes is treated as a single item even if it contains spaces (e.g. arxiv: deep RL for robotics is one query, not three).

Batch limit: up to 50 items per batch, for every signed-in user — no account tier involved. If you paste more than the cap, the extras are dropped and an amber "Capped at N items per batch" hint appears. The modal still runs the items it kept.

Failure isolation and retries:

• One bad URL (404, 502, Apify timeout) does not stop sibling items.
• Each item retries up to 3 attempts automatically on transient failures (5xx, 429, timeout, network, Apify-shaped errors). 4xx errors and "no papers found" fail immediately.
• The summary banner is colour-coded: green (all succeeded), amber (partial), red (none succeeded). Failed items can be re-run via the Retry button — successes are skipped.
• The modal blocks accidental dismiss (Escape, click-outside) only while the run is in flight so you don't lose progress mid-batch. After the run completes, you can close it normally.

Cancelling mid-batch: click Cancel. In-flight items are allowed to complete (the server has already done the work and may have already billed for them); pending items are dropped at no charge.

Cost: the same per-item fees as the single-input bar — see the Token Costs table below. The total at the bottom of the modal is the sum of every parsed item's per-type fee, computed before you click Run all.

Analyze Source (on any saved source)

Every saved research source has an Analyze source button (sparkle icon). Click it to open the analysis modal and run AI analysis on any previously saved content — web search results, transcripts, scraped pages, uploaded documents, or imported notebook entries — with presets (Summarize, Key Points, Fact Check, Topics & Structure) or a custom prompt. You can select multiple presets at once.

This button used to be labelled "Ask AI"; it was renamed to avoid colliding with the new Ask-AI popover's Ask AI action, which opens a quick chat about a highlighted snippet rather than running a structured analysis on the whole source. Same capability, clearer name.

The Serving Tray

The right rail is your Serving Tray — a curated collection of the most useful snippets from your research.

Collapsible Rail (W1.13)

The tray defaults to a slim collapsed strip — a count badge plus the top three item titles — so it doesn't eat width you'd rather give to the sources rail and reading pane. Click the strip to expand it into the full item list; collapse it again the same way. Your collapse/expand choice is remembered.

Adding to the Tray

• Highlight text anywhere (a source open in the pane, a Q&A reply, a report) → the Ask-AI popover appears → "Add to tray"
• Add to tray action in the reading pane's toolbar adds the full content of whatever source is currently open
• Import from Notebooks brings in highlights and notes from your Scribes

Managing Tray Items

• Drag to reorder items (expand the rail first)
• Click any item to open and read/edit it full-length in the reading pane — items no longer expand/collapse in place in the rail
• Edit notes on any item, from the pane
• Delete with undo (5-second window to restore)

Source Provenance

Each tray item shows a small label indicating where it came from — for example, "Web: coffee brewing methods" or "YouTube: How espresso works". Items you created manually show "Manual note". This helps you track the origin of each snippet, especially when combining research from multiple sources. The same labels appear in the Workspace Cafe Trays tab and the import modal.

When you import tray items into a Scribe section, the source attribution line includes the original source query and URL (when available), formatted as: Source: {Cafe name} . {query} . {url}.

Tray Source Attribution (W1.6)

Tray items produced by Auto-Research now show the sources they were synthesised from as clickable chips beneath the item text. Each chip is numbered [1], [2], … and labelled with the source title (or domain / source type as a fallback). Click a chip to open that source in the reading pane — the same behaviour as clicking a [N] in a report.

This applies to the "Key Findings", "Summary", "Best Quotes", "Most Up-to-Date", and "Contradictions & Gaps" items the Auto-Research agent synthesises. Manually added tray items and plain notes do not have source chips (no synthesis happened).

RAG Promotions Preserve Citations (W1.6)

When you Save to Tray, Save as source, or Save to Notebooks from a Q&A answer, the saved item preserves the citations from the answer:

• Save to Tray — the tray item's [N] markers are clickable; click one to open the cited source in the reading pane. The tray item is titled "Cafe chat: {your question}".
• Save as source — the promoted source is saved with the real rag_answer source type (W1.6.1) and grouped under "Saved from Q&A" in the Sources rail. This is a proper source type — not a renamed notebook import.
• Save to Notebooks — the note is saved as a cafe note (W1.6.1) and grouped under this Cafe's name in Notebooks, separate from Free Notes. Open Notebooks and look for the Cafe's title in the left panel to find it.

In all three cases, the citations remain meaningful and clickable in the Cafe. The promotions do not strip or lose the source references.

Editing Tray Item Text

Click any tray item to open it in the reading pane. A textarea there lets you modify the content directly. Press Ctrl+Enter (or Cmd+Enter on Mac) to save, or Escape to cancel without changes. Each tray item supports a generous character limit per note — long enough for substantial excerpts.

Adding Notes

Click the + button in the Serving Tray header to create a blank note. This is useful for pasting in content from external sources that aren't covered by the built-in search and scraping tools, or for writing your own observations and annotations alongside your research.

Combining Items

To merge multiple tray items into one:

1. Click the Select toggle in the Serving Tray header to enter selection mode
2. Use the checkboxes to select two or more items you want to combine
3. Click the Combine button that appears
4. The selected items are merged into a single item, with each constituent prefixed by its source label (e.g. [From source: Smith 2022]: ...) and separated by horizontal rules
5. An Undo option appears for 5 seconds in case you want to reverse the merge

The combined item shows a "Combined from N sources" badge so you can tell at a glance it's a merge. Source provenance is preserved — if all constituent items came from the same source, the combined item inherits that source link; if they came from different sources, the combined item is unlocked from any single citation (useful for tray-mode Auto-Write, where each constituent is labelled individually in the prompt).

Combining is useful for assembling related excerpts from different sources into one consolidated reference.

Using Tray Content

Tray items are ready to use in your Scribes, Notebooks, or Workspace. In the Workspace, the Cafe Trays tab lets you browse and paste tray items directly into sections.

Choosing a Model

The model selector appears in the search bar's info row, next to the "Add by identifier" chip. Your selected model is used for all AI operations — web search, paper analysis, and Ask AI.

Every signed-in user gets the full picker — CoffeeScribe Model recommended at the top and pre-selected, ~12 curated alternatives, then a collapsed advanced disclosure for the full 350+ catalogue (at your own risk). Nothing here is tier-gated.

Each result card shows which model was used, how many tokens were charged, and whether web sources were found. Different models produce different quality results — experiment to find what works best for your research topic.

Q&A Chat (Ask Your Cafe)

Ask Your Cafe is the reading pane's home view (W1.13) — it's not a floating bubble anymore. As soon as the pane has nothing else open (no source/tray item/report selected), it shows the chat, ready for a question, with an overview strip (source count, in-scope count, conflicts badge, latest-report link) above the conversation. On mobile, an "Ask" button in the rail-home bar opens the same chat.

How It Works

Your research is automatically processed into searchable chunks using local embeddings — no data leaves the server. When you ask a question, the system finds the most relevant passages from your in-scope sources and tray items (see scope above), then sends them to the AI along with your question to generate a grounded answer.

The chat is ready as soon as you add your first source. While your sources are being processed for search, a spinner indicates that embeddings are in progress. You can still browse your research — the Q&A will be ready in a few seconds.

Asking Questions

1. Open a Cafe — if nothing else is open, you're already looking at the chat
2. Type your question and press Enter (or click Send)
3. The AI answers using only your in-scope Cafe research, citing sources as numbered references like [1], [2]
4. Click any citation badge to open the original source in the reading pane

Grounded vs. General

Above the chat input is a prominent Grounded / General segmented control, with a helper line explaining the current mode:

• Grounded (default, everywhere — including from the Ask-AI popover) — the AI answers strictly from your in-scope Cafe sources and tray items, citing them. If your research doesn't cover the question, it says so rather than guessing.
• General — the AI answers from its own training knowledge. No research context is sent (this mode skips embedding/vector search entirely) and there are no citations. Use this for background questions your Cafe's material doesn't address.

Your choice is remembered per browser and persists across reloads. When a Grounded answer comes back as a refusal ("your sources don't cover this…"), the answer includes an "Ask the AI directly" button — click it to instantly re-run the same question in General mode without retyping it.

Filtering and Scoping Sources

Which sources ground a Grounded answer is controlled by the checkboxes on the sources rail, not by anything inside the chat panel itself (there's no separate in-chat filter icon anymore — scope lives on the rail so it's visible and persistent, not a session-only setting buried in the chat). See Ask-Your-Cafe Scope above for how to check/uncheck sources and groups.

A quirk worth knowing: your Serving Tray is never scope-gated. Even if you uncheck every single source, Ask Your Cafe still answers from whatever is in your Serving Tray — with an honest "Answering from 0 of N sources" banner on the reply so you know exactly what grounded the answer. This is deliberate: tray items are things you've already curated as worth keeping, so they're always available to Q&A regardless of the source checkboxes. If there's genuinely nothing in scope anywhere (no checked sources AND an empty tray), you'll see a friendly "all sources are toggled off" message instead of a fabricated answer.

Explicit "ask about THIS source" requests (from the Ask-AI popover on a specific source) still bypass the checkboxes entirely for that one question, exactly as before.

Conversation Context

The chat maintains conversation history within a session. Follow-up questions can reference earlier answers — for example, "Tell me more about point 3" or "How does that compare to the other study?"

Click Clear Chat to permanently delete all Q&A history and start fresh. This cannot be undone.

Actions on Answers

Each answer has action buttons:

• Copy — Copies the answer with a full reference list appended
• +Tray — Save the answer to your Serving Tray. The tray item is titled "Cafe chat: {your question}" and its [N] markers are clickable — click one to open the cited source in the reading pane. Citations are preserved.
• +Source — Save as a new research source. The promoted source is grouped under "Saved from Q&A" in the Sources rail.
• +Notebook — Save to your Notebooks as a free note with citations preserved. Find it under Free Notes in Notebooks.
• Delete — Remove a single Q&A entry

Editable Source Titles

Double-click any research source title to rename it. This helps you organise your sources when the auto-generated titles aren't descriptive enough. Tray items can also have custom titles.

Embedding Costs

Each research source and tray item is automatically chunked and embedded when created. This is a small one-time cost per item, broken into chunks of a few thousand characters each. The per-action estimate is always shown before you confirm.

Model

Q&A uses Gemini 2.5 Flash — a model chosen specifically for its ability to follow strict instructions and answer only from provided context. This is separate from the model you select for web search and analysis.

Sharing a Cafe

You can share any Cafe with other Coffeescribe users via a read-only link.

Enabling Sharing

1. Open a Cafe and click Share in the toolbar
2. Toggle Enable sharing on
3. A share URL appears — click Copy to copy it to your clipboard
4. Send the link to anyone with a Coffeescribe account

What Viewers Can Do

Viewers who open your shared link can:

• Browse all your research sources and their content
• Read your Serving Tray items
• Ask Q&A questions about your research (using their own tokens, not yours)
• Copy text from sources and tray items

What Viewers Cannot Do

Viewers cannot search, add sources, modify tray items, delete anything, or save Q&A answers to your Cafe. All edit controls are hidden. Read-only access is enforced at the database level.

Q&A on Shared Cafes

Viewers can ask Q&A questions in your shared Cafe. Their questions use their token balance (not yours), and their Q&A history is session-only — it is not saved to your Cafe and disappears when they close the page.

Revoking Access

Toggle sharing off in the Share dialog to immediately disable the link. Anyone with the old link will be redirected away.

Regenerating the Link

Click Regenerate link to create a new share URL. The old link immediately stops working. A confirmation dialog warns you before regenerating.

Share Indicator

Shared Cafes show a small share icon next to the cafe name on the Research listing page, so you can easily see which Cafes are currently shared.

Auto-Research (W1.5b)

Auto-Research is a steerable AI agent that researches a topic for you across a wide range of tools. You control what it uses, how deep it goes, and what it extracts — the agent turns those controls into a plan, executes it step by step, and sends the results into your Sources rail and Serving Tray.

Click the Auto-Research button in your Cafe toolbar to open the control surface.

Runs in the Background — Survives Closing the Tab

Auto-Research runs as a server-side background job. Once you click Start Research, the run continues on the server regardless of what you do in your browser:

• Close the tab, refresh, or navigate away — the run keeps going. Come back to the Cafe and your sources will be there when it finishes.
• Reattach after a refresh — if a run is still in progress when you reload the page, the live progress panel comes back automatically.
• Sources land as the agent works — sources are saved to your Cafe as each step completes. Tray items (your selected extract types) are added once the full run finishes.

Note: Tray items are only produced when the run completes. If you cancel mid-run, sources gathered before you stopped are kept, but no tray items are produced — the synthesis step only runs on completion.

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What to EXTRACT

Choose what the agent synthesizes into your Serving Tray at the end of the run. Select one or more:

• Key Findings — the most important takeaways from the research
• Summary — a concise overview of what was found
• Best Quotes — the most citable or representative passages
• Most Up-to-Date — the most recent information on the topic
• Contradictions & Gaps — conflicting claims and missing evidence

These become Serving Tray items marked with a robot icon when the run completes. You can edit, delete, or build on them like any other tray item.

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Tools

The agent can search across a wide range of sources. Toggle each tool on or off before starting:

Always-free tools (no consent required):

Consent-gated tools (every signed-in user, token-billed):

Each of the following requires a one-time per-Cafe consent the first time you enable it. The consent modal explains the platform's terms, what data is sent, and the approximate cost per result. After consenting, the tool is available immediately for that Cafe.

What consent means: These tools use Apify actors to access social platforms. Your search query is sent to Apify; it runs the actor on its own infrastructure. Your queries are not attributed to your personal account on those platforms. Consent is recorded per Cafe per tool — you only see the modal once per tool per Cafe. See the Privacy Policy and Third-Party Data Sources section for the platforms' terms of service links.

Availability: The six consent-gated tools are available to every signed-in user — enabling one still requires the per-Cafe consent above, and each result costs tokens.

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Research Depth

Important about Deep: The token budget is a hard ceiling, not a target. The agent uses its own judgment and stops when it believes it has gathered enough, which is often well before the budget is exhausted. "Deep" means the agent is instructed to be thorough — it does not mean it will burn your entire budget. The pre-flight cost estimate is shown before you start; a Deep warning appears in the modal when Deep is selected.

Deep can reflect and replan (new). After a Deep run's first research pass, the agent briefly checks its own work: "did this leave any real gaps?" If it did, it runs up to two more focused rounds chasing the specific unanswered facets or contradictions — you'll see a second (or third) "Research plan ready" step appear in the live progress log, which is the agent digging deeper rather than a glitch. If the first pass already answered the topic well, it stops there — a well-covered topic finishing in one round is the correct, expected outcome, not a shortfall. Either way, this stays inside the same token budget you set (extra rounds don't get a fresh ceiling), and there's a hard cap of two extra rounds regardless of how thorough the agent thinks it could still be. This only applies to Deep — Quick and Standard never reflect or replan.

Deep sets Fan-Out to Auto by default. Because fan-out (decomposing your topic into sub-questions — see Fan-Out below) is the natural companion to a thorough run, selecting Deep sets fan-out to Auto (the planner decides); Quick and Standard set it to Off. This is a default, not a lock — change it to On or Off in Advanced, and your explicit choice sticks even if you change depth afterwards. When Auto is active, the pre-flight estimate shows a rough number with a warning, because the agent decides at runtime how many sub-questions to create.

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Results Per Search (Top-k)

The Results per search control (5 / 10 / 20) sets the candidate pool size — how many results each search tool fetches for the agent to consider. This is separate from depth:

• Depth = how many cycles / how hard the agent tries
• Results per search = how wide a net each individual search casts

Higher top-k gives the agent more to choose from per step but increases per-step cost.

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Advanced Controls

Click Advanced — prompt, skills & loop to expand:

Prompt Sections

The agent's behaviour is driven by five editable prompt sections. Each has a sensible default — edit to shape the run, or click Reset to restore the default:

• Role — what kind of researcher the agent acts as
• Method — how it approaches the topic (broad-to-deep, query variation, source routing)
• Evidence & Skepticism — how hard it tries to disprove claims before accepting them
• Source Hierarchy — how to weight different source types (peer-review > preprint > official > news > social)
• Output Contract — what to extract and how to format it

Note: The JSON-plan contract (the machine-readable format the agent uses to structure its plan) is always appended by the system after your text and cannot be overridden. Editing prompt sections changes the agent's strategy, not its ability to produce a parseable plan.

Research Skills

Toggle preset research playbooks on or off:

• Systematic Literature Review — structured, comprehensive, tracks methodology
• Fact-Check Claims — actively seeks disconfirming evidence
• Find Opposing Views — seeks counter-arguments and alternative perspectives

Each skill injects additional instructions into the agent's planner and synthesis steps.

Fan-Out (Sub-Question Decomposition)

Fan-out controls whether the agent decomposes your topic into parallel sub-questions or researches it as a single linear sweep. The control is now a tri-state:

Deep selects Auto by default — because a thorough run naturally benefits from letting the agent decide how to structure the research. Quick and Standard default to Off. These are only defaults: switch to any setting in Advanced, and your explicit choice sticks even if you later change depth.

When Auto is active, the pre-flight cost estimate shows a rough number — because the agent decides at runtime whether to decompose and how many sub-questions to create. A "Rough estimate — the agent decides how deep to go, up to your cap of X tokens" warning appears near the estimate. The executor's hard ceiling is still honoured: the agent always stops at or before your token budget, and billing charges only actual tokens (the estimate is advisory).

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Live Progress and Cancel

While the agent runs, a live progress log shows each step (tool, query, step result), running token cost, and source count. Sources appear in the Sources rail as they're found.

Cancel: Click Stop at any time. The server-side job receives the cancel signal and stops at the next step boundary. Sources gathered before you stopped are kept. Tray items are not produced for a cancelled run.

Per-step timeout: If a tool step hangs (for example, a slow Apify actor cold-start), it automatically times out after 90 seconds, is marked as skipped, and the run continues. You will never see an infinite spinner.

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Ambient Conflict Nudge (new)

After any Auto-Research run completes, CoffeeScribe automatically runs a quick, free, lexical-only check across your Cafe's sources for potential factual disagreements. If it finds any, a calm amber "N potential conflicts" chip appears next to the Detect Conflicts button in the toolbar.

• This check is completely free — no AI model call, no tokens charged, no extra step for you. It just looks at word-overlap between source titles/abstracts to flag pairs worth a closer look.
• The badge is a nudge, not a verdict — it's telling you "these sources might disagree," not "these sources definitely disagree." Click the badge to open the same Detect Conflicts dialog you'd reach from the toolbar button — running the actual AI-powered conflict check (which costs tokens, per Detect Conflicts above) is still something you choose to do.
• The count is capped for display (you'll never see an alarming "47 potential conflicts" — the badge tops out at a small number) and is durable — it's saved with the research run, so it's still there if you come back to the Cafe later, not just while the run was live in front of you.
• No badge appears if the check finds nothing, or on a Cafe without enough overlapping sources to compare.

Budget Control

Set a token budget before starting. This is a hard ceiling — the agent stops before or at this limit and synthesizes with whatever it has gathered. The pre-flight cost estimate is shown in the modal before you commit.

Auto-Research is available to every signed-in user. The CoffeeScribe Model is pre-selected by default, and every user can choose a different model from the picker.

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Third-Party Data Sources

The consent-gated social and scholar tools access content via Apify actors. By enabling them you acknowledge that:

• The data is accessed via third-party actors and is subject to each platform's terms of service.
• Content from these platforms is for use in your own research within those terms.
• Apify is the access layer; see the Apify Privacy Policy.

Relevant platform terms:

Legal note: An AUP / indemnification clause for automated access to third-party platforms is a legal-team follow-up item and is not yet included. Use these tools responsibly and within each platform's terms.

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Availability

Other Features

Notebook Import

Click Import in the Cafe toolbar to bring in highlights and notes from any of your Scribes. Choose to import as Research Material (left panel) or directly to the Tray (right panel).

Document Upload

Click Upload to add PDF, DOCX, TXT, or MD files (up to 5 MB) as research sources.

Deleting Sources

Hover over any research source to see the delete button. Deletion includes a 5-second undo window.

Token Costs

Every action below is available to every signed-in user — availability doesn't vary by account. Cost is deducted from your token balance regardless of account type.

The per-action estimate is always shown before you confirm so you know what you're spending.

Availability

Every feature below is available to every signed-in user — none of it is gated by account tier. Token balance is the only limit, and Apify-backed tools additionally require the one-time per-Cafe consent described above.

Reports (Unified) (W1.6.1, rehomed in W1.13)

The sources rail's Reports group lists all report types together (find it via Group or narrow to it with Show → Reports):

• Auto-Write reports — prose research reports generated by the Auto-Write button
• Verify cited reports — the cited report automatically produced when a Verify claim loop completes
• Conflict reports — factual disagreements detected by Detect Conflicts (these live in a separate Conflicts group)

All report types appear newest-first. Click a row to open it in the reading pane — reports no longer expand inline in the rail. This means a re-verified source never orphans its prior report — every report is listed, so old verify reports stay reachable even as the latest one tops the group.

Reports auto-drop into the Serving Tray. When an Auto-Write or Verify report is created, a tray item is automatically added. Click that tray item and its reading-pane view shows an "Open report" link at the top so you can jump straight to the full-screen artefact viewer without hunting through the rail's Reports group.

Tips

• Create multiple Cafes for different topics — one Cafe per research project
• Use Academic search for scholarly sources — try OpenAlex for broad coverage, arXiv for preprints, or PubMed for biomedical literature
• YouTube transcripts are great for extracting key points from lectures and interviews
• Combine sources — search the web, find papers, scrape articles, then curate the best bits on your Tray
• Analyze anything — the Analyze source button works on every saved source, so you can re-analyze content with different questions; or highlight any snippet and use the popover's Ask AI for a quick chat about just that part
• Multi-select presets — when analyzing YouTube or URLs, select multiple presets (Summarize + Key Points) to get several analyses at once
• Add Notes for external content — use the + button to paste in material from sources outside Coffeescribe (emails, documents, other tools)
• Combine related items — merge excerpts from different sources into a single consolidated reference before pasting into your Workspace
• Edit tray text freely — click any tray item to refine wording, trim irrelevant parts, or add your own annotations inline
• Ask your Cafe — once you have research, use the Ask Your Cafe chat (the reading pane's home view) to ask questions and get referenced answers grounded in your collected material
• Filter Q&A sources — click the funnel icon in the Q&A header to query only specific sources instead of your entire Cafe
• Save Q&A answers — save useful answers back to your Tray, as new sources, or to Notebooks for use in your Scribes. Citations are preserved in all three cases and remain clickable in-Cafe
• Rename sources — double-click any source title to give it a more descriptive name
• Share your research — use the Share button to send a read-only link to collaborators (Cafe sharing). They can browse and ask Q&A questions using their own tokens. To share a specific report only, use the Share button on the report card (see Auto-Write Research Reports)
• Paste a reading list in one go — got a tab-soup or a notes-app dump of links? Paste the whole blob into the search bar and the batch import modal opens automatically (up to 50 items per batch, every signed-in user). Way faster than feeding them in one at a time.
• Paste a DOI or PMID to get a fully enriched source card instantly — the identifier input auto-detects the type and fetches structured metadata so you don't have to copy-paste authors and journals manually (every signed-in user).
• Set your citation style once per Cafe — open Settings (gear icon), pick APA 7, MLA 9, Chicago N-B, or Harvard CTR, and every enriched source card renders formatted citations automatically.
• Check the credibility badge before citing — a High or Medium credibility source with "Academic Journal/Paper" tier and a green freshness badge is your safest bet for academic writing. Remember: the badge is a structural check, not fact-verification — always read the source.
• Enable Academic Sources Only in Settings — flipping this filter in a research Cafe for a dissertation or report hides web articles and social posts so only peer-reviewed and government sources appear.
• Try LinkedIn or Reddit Actors for professional or community insight — enable them via the Provider Picker; the one-time consent modal only appears on the first enable per Cafe (every signed-in user).