Outputs → Writing

Outputs holds what you hand off. Writing is the manuscript half of it — papers, reports, chapter drafts.

Creating

The New menu at the bottom:

• Draft — a plain manuscript
• Slide — a slide deck (see Figures / Tables / Exports)

You can also Import… or drag files straight onto the list.

Multi-chapter manuscripts

A long paper can be split across several chapter files, which Scholardo recognizes as one manuscript group, displayed as a single row ("N chapters").

Right-click a manuscript group:

• Rename manuscript… — renames the whole thing, every chapter file at once
• Export entire manuscript… — merges all chapters in order and exports

Editing

Manuscripts open in the Markdown editor with the same editing / reading modes as Notes, plus:

• Undo / Redo
• Auto-format markdown — normalize formatting in one click
• Clean hidden characters — strip zero-width characters, non-breaking spaces, and similar invisibles that ride along when you paste from a PDF or web page

Inserting citations

Select a passage in reading mode and the floating toolbar offers Find citations — the AI finds supporting literature from your Refs library and inserts the citation into the text.

Citations render in whatever CSL style you've selected in Refs. See Citations.

The writing brief

Each manuscript can carry a writing brief: who it's for, which journal, what tone, what length limits.

That brief wires up both AI paths:

• Agent side — read and written via the MCP tools get_writing_context / set_writing_context
• API side — injected automatically when you polish or proofread a selection

So you state once that "this is the introduction for a Nature Communications submission, keep it restrained, no hype," and every later polish request honors that constraint.

What Markdown can render

The reading-mode renderer supports a set of fenced blocks common in academic writing:

Fence	Renders as
```mermaid	Flowcharts, sequence diagrams, Gantt charts
```markmap	Mind maps, built from a nested list
```chart	Data charts
```smiles	Chemical structures
```abc	Music notation
```pseudocode	Algorithm pseudocode
$...$ / $$...$$	LaTeX math

Academic numbering is supported too — automatic figure and table numbering with cross-references.

All of it renders offline

Every rendering engine ships inside the app. Nothing goes over the network, and your manuscript doesn't leave the machine just because it contains a diagram.

When a file changes underneath you

If a file is modified externally while open in the editor — an agent wrote to it, git switched branches, another device synced — Scholardo asks:

• Keep mine — keep what's in your editor
• Use the new one (discard mine) — take the version on disk

Neither side is overwritten silently.

While an agent is writing

During active agent work the editor holds off on autosave, so your autosave and the agent's writes don't fight and get misreported as an external modification.