Chapter Outline

If relevant knowledge files exist, use them to skip or accelerate subsequent research steps (e.g., if definitions are already extracted, skip that portion of literature research).

Step 1: Context Analysis

Understand where this chapter fits in the larger picture.

1. Read Root Outline: view_file outline.md. Identify the chapter's Scope, Key Contribution, Section Structure, and how it connects to the previous and next chapters.
2. Check Existing Artifacts: Look for any existing files in the chapter directory (references.md, chapter_outline.md, etc.) from prior work.

Step 2: Source Registry

Run the source_registry skill to obtain categorized source IDs.

→ Call source_registry skill
→ Obtain: author_paper_ids, review_ids, general_ids

This step is required before any NotebookLM queries.

Step 3: Literature Research

Run the literature_research skill to produce the chapter's references.md and data table.

→ Call literature_research skill for the target chapter
→ Input: chapter sections from outline.md, source IDs from Step 2
→ Output: chapter_XX/references.md (with data table + bib-key lookups)

Follow the granular per-subsection approach defined in the literature_research skill.

Step 4: Review Analysis

For the key review articles identified in Step 3, run review_analysis to extract detailed, citation-ready content.

→ Call review_analysis skill
→ Input: specific 002) source IDs for the most relevant reviews
→ Output: structured extraction notes, saved to .agent/knowledge/

Focus on reviews that will be heavily cited in this chapter.

Step 5: Paper Analysis (if applicable)

If an author paper is inserted in or near this chapter, run paper_analysis to extract key contributions and transition points.

→ Call paper_analysis skill
→ Input: specific 001) source ID(s) for papers relevant to this chapter
→ Output: methodology summary, key results, contribution statement, transition notes

Refer to the paper-to-chapter mapping in the paper_analysis skill.

Step 6: Structural Research

Use NotebookLM directly to study how experts structure arguments on this chapter's topic.

mcp_notebooklm_notebook_query(
    notebook_id="1b7df790-7858-4fc8-879c-39f41238c4ae",
    query="What is the detailed structure of [Reference X] regarding [Topic]? 
           List the section headers and summarize the argumentation flow. 
           How do they transition from [Concept A] to [Concept B]?",
    source_ids=<review_ids>
)

Focus on:

• How experts order their arguments
• How they introduce complex concepts
• How they transition between topics

Step 7: Draft chapter_outline.md

Create (or update) chapter_XX/chapter_outline.md.

Synthesis: Combine:

• Chapter requirements from outline.md
• References from references.md (Step 3)
• Review extractions (Step 4)
• Paper contributions and transitions (Step 5)
• Structural best practices (Step 6)

Format: Use a nested structure:

# Chapter [XX]: [Title]

## Connections
- **Previous Chapter**: [How this chapter follows from the previous one]
- **Next Chapter**: [How this chapter leads into the next one]
- **Inserted Paper**: [If applicable, which paper is inserted and its key contribution]

## [X.0] Chapter Introduction
**Goal**: Provide a brief, untitled opening (2–4 paragraphs) that orients the reader before the first numbered section. This text appears at the start of the chapter with no section heading.
**Narrative**: Follow a funnel structure:
- Opening context: broad motivation for the chapter's topic
- The central question this chapter addresses
- Chapter roadmap: one-sentence preview of each main section (X.1, X.2, …) and how they connect
- Bridge to the thesis: how the chapter's content feeds into the rest of the thesis

## [X.1] [Section Title]
**Goal**: [What this section achieves in the argument]
**Narrative**: [How the story progresses through this section]

### [X.1.1] [Subsection Title]
- Key point 1 → cite [Reference] (Sec X.X)
- Key point 2 → cite [Reference]
- **Figure**: [description] → from [arXiv:XXXX.XXXXX], Fig. N
- Transition: [How this leads to the next subsection]

### [X.1.2] [Subsection Title]
- ...

## [X.2] [Section Title]
...

## Chapter Summary
- [Key takeaway 1]
- [Key takeaway 2]
- [Bridge to next chapter / inserted paper]

Rules:

• Chapter Introduction (X.0): Mandatory for every chapter. Untitled in the final output — provides opening paragraphs before the first numbered section
• H2 sections: Main structural divisions
• H3 subsections: Specific logical steps
• Bullets: Key points with specific reference citations
• Figure annotations: Mark key literature figures with **Figure**: [description] → from [arXiv:ID], Fig. N. These signal to section_drafting Step 4b which figures to fetch and download
• Transitions: Explicitly note how each section leads to the next
• Connections: First section documents how this chapter connects to the rest of the thesis

Step 8: Review and Refine

Iterate on the draft:

1. Logical Flow: Does Section A naturally lead to Section B? Are prerequisites defined before use?
2. Coverage: Are all topics from outline.md addressed?
3. Weakness Check: Are there "jumps" in logic? Missing definitions?
4. Self-Contained vs. Connected: The chapter should stand on its own while explicitly linking to previous/future chapters.
5. Insert Transitions: If a paper is inserted after this chapter, does the outline build up to it properly?

Output

• chapter_XX/chapter_outline.md — the detailed structural outline
• chapter_XX/references.md — references with data table (produced in Step 3)
• .agent/knowledge/ — key insights saved via the knowledge skill (produced in Steps 3–5)