Manuscript Editor

Manuscript Mode is a specialized writing environment for long-form academic documents. It extends the standard Write workspace with section-based navigation, focused editing, and AI-powered critique runs. Access it at /write/manuscript or via the "Manuscript Mode" button on the Write page.

Section Map Navigation

Long documents benefit from structured navigation. The manuscript editor provides a section map -- a sidebar outline of all sections and subsections in your document. Sections are detected automatically from Markdown headings (e.g., ## Introduction, ### Methods).

The section map lets you:

• Jump to any section by clicking its title in the outline.
• See document structure at a glance, including heading levels and hierarchy.
• Track your progress through the document as you work through each section.

As you edit, the section map updates in real time to reflect new headings or structural changes.

Focused Editing

Manuscript Mode lets you focus on one section at a time. When you select a section from the section map, the editor scrolls to that section and highlights it. This is especially useful for documents with many sections, where scrolling through the entire text would be disorienting.

Focused editing helps maintain concentration on the current section's argument and flow without being distracted by the rest of the document.

AI-Powered Critique

The manuscript editor integrates with the Research AI Panel to provide agentic critique runs. These are AI-powered analyses that evaluate your manuscript across several dimensions:

• Research question clarity -- Is your research question stated clearly and positioned effectively?
• Argument structure -- Does each section contribute to a coherent overall argument?
• Section transitions -- Are transitions between sections smooth and logical?
• Evidence support -- Are claims supported with appropriate evidence and citations?
• Structural balance -- Are sections proportionally balanced in length and depth?

To run a critique, open the Research AI Panel while in Manuscript Mode and ask the AI to review your manuscript. The AI uses the full document context, including any linked research context, to provide targeted feedback.

Formatting

The manuscript editor supports standard Markdown formatting:

• Headings: Use #, ##, ### for heading levels
• Bold: Wrap text in **double asterisks**
• Italic: Wrap text in *single asterisks*
• Lists: Use - or 1. for unordered and ordered lists
• Block quotes: Start lines with >
• Code blocks: Use triple backticks for code or formatted data

The editor renders Markdown in real time, so you can see the formatted output as you write.

Saving and Versions

Manuscript Mode shares the same save system as the standard Write workspace. Each save creates a version with a version number and optional label. You can return to previous versions from the Documents management page.

Save your work regularly, especially before running AI critique or making structural changes. This ensures you can always revert to a previous state if needed.

When to Use Manuscript Mode

Manuscript Mode is designed for documents that are long enough to benefit from section navigation -- typically anything beyond a few pages. Good candidates include:

• Full research papers (IMRAD format or otherwise)
• Grant proposals with multiple sections
• Thesis chapters
• Literature reviews with many subsections
• Book chapters or monographs

For shorter documents like cover letters or abstracts, the standard Write workspace is more appropriate.

Tips

• Structure your document with clear Markdown headings before entering Manuscript Mode. The section map depends on heading syntax to build the outline.
• Use AI critique iteratively. Write a draft, run a critique, address the feedback, and run it again. Each pass typically produces diminishing but still valuable suggestions.
• Link your manuscript to relevant projects and publications before requesting critique. The AI provides more useful feedback when it has access to your source materials.