@research-copilot/plugin 1.1.17 → 1.1.19

package/dist/skills/composer/references/section_guides.md

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+# Section Writing Guides
+
+This document provides detailed guidance on writing each type of section in academic papers.
+
+## Abstract Writing Guide
+
+### Structure Template
+
+```markdown
+**Sentence 1-2: The Problem/Puzzle**
+State the core problem or puzzle your paper addresses.
+Example: "Personal identity across sleep-wake cycles poses a puzzle for theories of self-continuity."
+
+**Sentence 3-4: Limitations of Existing Approaches**
+Briefly note what existing work misses or gets wrong.
+Example: "Existing accounts either ignore discontinuity or fail to explain how continuity is maintained."
+
+**Sentence 5-7: This Paper's Contribution**
+State what this paper does differently.
+Example: "This paper proposes a narrative compression framework that explains..."
+
+**Sentence 8-10: Main Argument/Findings**
+Summarize the key argument or finding.
+Example: "I argue that the self is periodically deconstructed and reconstructed through..."
+
+**Sentence 11-12: Significance**
+Why this matters.
+Example: "This framework bridges phenomenological and neuroscientific accounts of self-continuity."
+```
+
+### Quality Checklist
+
+- [ ] **Standalone**: Can be understood without reading the paper
+- [ ] **Accurate**: Faithfully represents paper content
+- [ ] **Specific**: Avoids vague claims like "I explore..."
+- [ ] **Compelling**: Makes reader want to read the full paper
+- [ ] **Word count**: 250-300 words
+- [ ] **No citations**: Unless platform specifically requires them
+- [ ] **Jargon-free**: Or defines essential technical terms
+
+### Common Mistakes
+
+**❌ Too vague**: "This paper explores issues of self and sleep."
+**✓ Specific**: "This paper proposes a narrative compression model of self-continuity across sleep-wake cycles."
+
+**❌ Too detailed**: Including chapter-by-chapter descriptions
+**✓ Appropriate**: High-level summary of main argument and contribution
+
+**❌ Over-promising**: "This solves the problem of personal identity."
+**✓ Realistic**: "This provides a novel framework for understanding self-continuity."
+
+---
+
+## Introduction Writing Guide
+
+### Structure Template (for ~2000-word introduction)
+
+#### 1. Opening Hook (150-250 words)
+**Purpose**: Grab attention and establish the puzzle
+
+**Strategies**:
+- **Vivid example**: "Every night, we lose consciousness for hours. Yet we wake convinced we're the same person who fell asleep."
+- **Paradox**: "We both are and are not continuous across sleep."
+- **Surprising fact**: "The average person spends 26 years asleep, yet theories of self rarely address this."
+- **Thought experiment**: "Imagine a being that exists only during waking hours..."
+
+**Quality markers**:
+- Reader immediately understands the puzzle
+- Establishes stakes (why this matters)
+- Accessible to educated non-specialist
+
+#### 2. Background Context (300-400 words)
+**Purpose**: Provide necessary background to understand the problem
+
+**Include**:
+- Key concepts (what is "self-continuity"? what is "sleep"?)
+- Disciplinary context (is this philosophy of mind? phenomenology? neuroscience?)
+- Historical context (how has this problem been approached?)
+
+**Quality markers**:
+- Just enough context, not comprehensive literature review
+- Defines technical terms that will be used throughout
+- Situates the problem clearly
+
+#### 3. Literature Review (600-800 words)
+**Purpose**: Show what's been tried and what's missing
+
+**Structure**:
+```markdown
+**Approach 1: [Name of approach]**
+- Who: [Key proponents with citations]
+- Core idea: [Brief explanation]
+- Limitation: [What it misses or gets wrong]
+
+**Approach 2: [Name of approach]**
+- Who: [Key proponents]
+- Core idea: [Brief explanation]
+- Limitation: [What it misses]
+
+**Approach 3: [Name of approach]**
+- Who: [Key proponents]
+- Core idea: [Brief explanation]
+- Limitation: [What it misses]
+
+**The Gap**: [Synthesize what's missing across approaches]
+```
+
+**Quality markers**:
+- Groups literature thematically, not chronologically
+- Charitable interpretation of each approach
+- Explicitly identifies the gap this paper addresses
+- 15-25 citations typical for philosophy papers
+
+#### 4. This Paper's Approach (300-400 words)
+**Purpose**: Clearly state what you're doing differently
+
+**Include**:
+- **Thesis statement**: Clear, one-sentence statement of main claim
+- **Method**: What approach you're taking (phenomenological analysis, conceptual analysis, etc.)
+- **Key concepts**: Introduce any novel terminology
+- **Strategy**: How you'll proceed
+
+**Example structure**:
+```markdown
+I argue that [THESIS].
+
+My approach draws on [METHOD/FRAMEWORK], specifically [KEY CONCEPTS].
+
+The strategy is threefold: First, [CHAPTER 2 GOAL]. Second, [CHAPTER 3 GOAL]. Third, [CHAPTER 4 GOAL].
+```
+
+**Quality markers**:
+- Thesis is one clear sentence
+- Originality explicitly stated
+- Method justified (why this approach?)
+- Connection to literature gap clear
+
+#### 5. Contribution Summary (150-250 words)
+**Purpose**: Explicitly state what's new
+
+**Template**:
+```markdown
+This paper makes three contributions:
+
+**Theoretical contribution**: [New framework/model/concept you're proposing]
+
+**Methodological contribution**: [New approach or application of existing method]
+
+**Substantive contribution**: [What you explain/resolve/clarify that wasn't before]
+```
+
+**Quality markers**:
+- Concrete and specific
+- Clearly differentiated from existing work
+- Realistic scope (not over-claiming)
+
+#### 6. Roadmap (200-300 words)
+**Purpose**: Preview chapter structure
+
+**Template**:
+```markdown
+The paper proceeds as follows.
+
+Section 2 [DOES X]. This establishes [PURPOSE].
+
+Section 3 [DOES Y]. This provides [PURPOSE].
+
+Section 4 [DOES Z]. This demonstrates [PURPOSE].
+
+Section 5 concludes by [SUMMARY + IMPLICATIONS].
+```
+
+**Quality markers**:
+- Matches actual chapter structure exactly
+- Explains purpose of each chapter, not just topic
+- Shows logical progression
+- Brief (2-3 sentences per chapter)
+
+### Introduction Quality Checklist
+
+- [ ] **Hook**: Compelling opening that establishes puzzle
+- [ ] **Context**: Sufficient background to understand problem
+- [ ] **Literature**: Key approaches covered, gap identified
+- [ ] **Thesis**: Clear one-sentence statement of main claim
+- [ ] **Method**: Approach explicit and justified
+- [ ] **Contribution**: Originality clearly articulated
+- [ ] **Roadmap**: Matches actual chapter structure
+- [ ] **Citations**: 15-25 sources cited
+- [ ] **Length**: 15-20% of total paper
+- [ ] **Flow**: Smooth transitions between sub-sections
+
+---
+
+## Main Body Chapter Writing Guides
+
+### Conceptual/Theoretical Chapter
+
+**Purpose**: Define key concepts or develop theoretical framework
+
+**Typical structure** (for ~1500-word chapter):
+
+#### 1. Opening (150-200 words)
+- Why this concept matters for your argument
+- Preview of what this section establishes
+
+#### 2. Concept Definition (400-500 words)
+- Precise definition
+- Distinguish from related concepts
+- Examples to illustrate
+- Cite sources for existing uses
+
+#### 3. Theoretical Development (600-700 words)
+- Elaborate the concept
+- Show how it functions in your framework
+- Address potential confusions
+- Provide additional examples
+
+#### 4. Implications (200-300 words)
+- What follows from this concept
+- How it connects to next chapter
+- Bridge to next section
+
+**Quality markers**:
+- Concepts defined with precision
+- Examples aid understanding
+- Distinctions clearly drawn
+- Terminology consistent
+
+### Argument Chapter
+
+**Purpose**: Present and justify a specific claim
+
+**Typical structure** (for ~1500-word chapter):
+
+#### 1. Opening (150-200 words)
+- State the specific claim this chapter defends
+- Why this claim matters for overall thesis
+- Preview of argument structure
+
+#### 2. Premises (600-800 words)
+**For each premise**:
+- **State premise explicitly**: "Premise 1: [Clear statement]"
+- **Justify premise**: Why should we accept this?
+  - Empirical support (cite studies)
+  - Philosophical argument
+  - Common intuition
+  - Prior argument in paper
+- **Address worries**: Potential objections to this premise
+
+**Example**:
+```markdown
+**Premise 1**: Self-continuity requires memory integration.
+
+[200 words justifying this premise with citations and argument]
+
+**Potential objection**: One might worry that this assumes...
+
+[100 words addressing objection]
+```
+
+#### 3. Inference (300-400 words)
+- Show how conclusion follows from premises
+- Make logical steps explicit
+- Address potential gaps
+
+#### 4. Objections and Replies (300-400 words)
+- Strongest objection to conclusion
+- Your response
+- Why response succeeds
+
+**Quality markers**:
+- Argument structure explicit (numbered premises)
+- Each premise independently justified
+- Inference steps clear
+- Strongest objections addressed
+
+### Critical Review Chapter
+
+**Purpose**: Evaluate and critique an existing approach
+
+**Typical structure** (for ~1500-word chapter):
+
+#### 1. Opening (150-200 words)
+- Whose view you're examining
+- Why it's important to address
+- Preview of your critique
+
+#### 2. Charitable Reconstruction (400-500 words)
+- Present the view in its best light
+- Use quotes from original sources
+- Explain motivation/appeal
+- Acknowledge strengths
+
+**Key principle**: Pass the "ideological Turing test" - could a proponent recognize their view?
+
+#### 3. Critical Analysis (600-700 words)
+**For each criticism**:
+- **State the problem**: What specific issue you've identified
+- **Explain why it's a problem**: Why this undermines the view
+- **Provide evidence**: Citations, examples, or argument
+- **Consider replies**: Address likely responses
+
+**Quality markers**:
+- Criticism is internal (uses view's own standards) or external (challenges assumptions)
+- Not merely assertion, but argued
+- Addresses strongest version, not straw man
+
+#### 4. Implications (200-300 words)
+- What this critique shows
+- How it motivates your alternative
+- Transition to next section
+
+**Quality markers**:
+- Fair and charitable representation
+- Substantive criticism
+- Addresses likely replies
+- Not ad hominem or dismissive
+
+### Case Study / Analysis Chapter
+
+**Purpose**: Apply your framework to analyze specific case or phenomenon
+
+**Typical structure** (for ~1500-word chapter):
+
+#### 1. Opening (150-200 words)
+- Introduce the case
+- Why this case is interesting/important
+- What you'll show through analysis
+
+#### 2. Case Description (400-500 words)
+- Detailed description of case/phenomenon
+- Include relevant details
+- Establish facts clearly
+- Cite sources for empirical claims
+
+#### 3. Analysis (600-700 words)
+- Apply your framework systematically
+- Work through each element
+- Show how framework illuminates case
+- Compare to how alternative approaches would handle it
+
+**Template**:
+```markdown
+On the compression framework:
+- [Element 1 of framework]: In this case, we see...
+- [Element 2 of framework]: This manifests as...
+- [Element 3 of framework]: Which explains why...
+
+By contrast, [alternative approach] would predict/explain...
+But this fails to account for [feature of case].
+```
+
+#### 4. Implications (200-300 words)
+- What this case reveals
+- How it supports your thesis
+- What it suggests for other cases
+
+**Quality markers**:
+- Case richly described with sufficient detail
+- Framework applied systematically
+- Comparison to alternatives
+- Analysis reveals something non-obvious
+
+---
+
+## Conclusion Writing Guide
+
+**Purpose**: Synthesize findings, reiterate significance, acknowledge limitations, suggest future work
+
+**Typical structure** (for ~1200-word conclusion):
+
+### 1. Thesis Restatement (150-200 words)
+- Restate main thesis (in different words than introduction)
+- Frame in light of arguments presented
+- Emphasize what's been shown
+
+**Example**:
+```markdown
+This paper has argued that self-continuity across sleep depends on narrative compression—the periodic deconstruction and reconstruction of autobiographical memory. This framework explains both the phenomenology of waking (the sense of uninterrupted identity) and the neuroscience of sleep (memory consolidation processes).
+```
+
+### 2. Summary of Main Findings (400-500 words)
+- Recap each major chapter/argument
+- Emphasize how they fit together
+- Show cumulative case
+
+**Template (adjust to your paper)**:
+```markdown
+I began by establishing [CHAPTER 2 FINDING]. This was necessary because...
+
+I then showed [CHAPTER 3 FINDING]. This addresses the gap in literature by...
+
+Building on this, I demonstrated [CHAPTER 4 FINDING]. This resolves the puzzle of...
+
+Finally, I applied the framework to [CHAPTER 5 CASE], revealing...
+```
+
+**Quality markers**:
+- Summarizes findings, not just topics
+- Shows connections between chapters
+- Emphasizes cumulative argument
+- Addresses introduction promises
+
+### 3. Significance (250-300 words)
+- Why these findings matter
+- Implications for the field
+- What changes given your argument
+
+**Structure**:
+```markdown
+**Theoretical significance**: This framework provides...
+
+**Methodological significance**: The approach demonstrates...
+
+**Practical significance**: Understanding this has implications for...
+```
+
+**Quality markers**:
+- Significance clearly articulated
+- Realistic (not over-claiming)
+- Specific implications identified
+- Connected to literature
+
+### 4. Limitations (200-250 words)
+- Honest assessment of what paper doesn't do
+- Scope limitations
+- Methodological limitations
+- Empirical limitations (if applicable)
+
+**Template**:
+```markdown
+This paper has several limitations. First, I have focused on [SCOPE], leaving [EXCLUDED TOPIC] for future work. Second, the framework is [METHODOLOGICAL LIMITATION]. Third, I have not addressed [OUTSTANDING QUESTION].
+```
+
+**Important**: Frame limitations honestly but don't undermine contribution
+- ❌ "This paper has solved nothing"
+- ✓ "While this paper has focused on X, Y remains an open question"
+
+**Quality markers**:
+- Honest acknowledgment
+- Specific, not vague
+- Doesn't undermine contribution
+- Suggests future work directions
+
+### 5. Future Work (200-250 words)
+- 2-3 concrete directions for future research
+- Make specific and feasible
+
+**Template for each direction**:
+```markdown
+**Direction 1: [Title]**
+One promising extension would be [SPECIFIC SUGGESTION]. This would address [LIMITATION OR OPEN QUESTION]. The approach might involve [POTENTIAL METHOD]. Such work would shed light on [EXPECTED CONTRIBUTION].
+```
+
+**Quality markers**:
+- Specific, not vague
+- Feasible, not pie-in-the-sky
+- Genuinely interesting questions
+- Builds on this paper's findings
+
+### 6. Closing Statement (50-100 words)
+- Strong final paragraph
+- Return to opening puzzle
+- Memorable final thought
+
+**Strategies**:
+- **Circle back to opening**: Reference the vivid example or paradox from introduction
+- **Broader implications**: Zoom out to bigger picture
+- **Open question**: Leave reader with thought-provoking question
+- **Call to action**: What should happen next (research or practical)
+
+**Quality markers**:
+- Memorable and impactful
+- Not just summary
+- Provides closure
+- Leaves positive impression
+
+### Conclusion Quality Checklist
+
+- [ ] **Thesis restatement**: Clear restatement in light of arguments
+- [ ] **Findings summary**: All major chapters recapped
+- [ ] **Significance**: Why findings matter clearly stated
+- [ ] **Limitations**: Honest but not undermining
+- [ ] **Future work**: 2-3 specific, feasible directions
+- [ ] **Closing**: Strong final statement
+- [ ] **No new arguments**: Only synthesis of existing content
+- [ ] **Length**: 10-15% of total paper
+- [ ] **Addresses introduction**: Returns to promises made
+
+---
+
+## Transition Writing
+
+Transitions are critical for flow. Here are strategies:
+
+### Between Paragraphs
+
+**Forward-pointing** (end of paragraph):
+```markdown
+Having established [CURRENT POINT], we can now turn to [NEXT POINT].
+
+This raises the question: [NEXT QUESTION]
+
+With this framework in place, we can apply it to [NEXT CASE].
+```
+
+**Backward-pointing** (start of paragraph):
+```markdown
+Given [PREVIOUS POINT], it follows that...
+
+This account, however, faces a challenge...
+
+Building on this analysis...
+```
+
+**Combined**:
+```markdown
+While [PREVIOUS POINT] provides necessary groundwork, it leaves [GAP]. The next section addresses this by [NEXT POINT].
+```
+
+### Between Sections
+
+**End of section**:
+```markdown
+This section has established [SECTION GOAL]. With this in place, we can now [NEXT SECTION GOAL].
+```
+
+**Beginning of section**:
+```markdown
+The previous section established [PREVIOUS RESULT]. This section builds on this by [CURRENT GOAL].
+```
+
+### Between Chapters
+
+Use opening paragraphs (150-200 words) to:
+1. Recap what previous chapter accomplished
+2. State what this chapter will do
+3. Explain connection between them
+
+**Template**:
+```markdown
+Chapter [N-1] established [KEY RESULT]. This provides the groundwork for [CURRENT CHAPTER GOAL]. Specifically, [EXPLAIN CONNECTION]. This chapter proceeds by [PREVIEW STRUCTURE].
+```
+
+---
+
+## Common Writing Mistakes and Fixes
+
+### Mistake 1: Unclear Thesis
+
+**Symptoms**:
+- Can't state thesis in one sentence
+- Thesis changes partway through
+- Reader unclear what you're arguing
+
+**Fix**:
+- Write one-sentence thesis statement
+- Put it in introduction and conclusion
+- Check every chapter contributes to it
+- Remove material that doesn't support thesis
+
+### Mistake 2: Unsupported Claims
+
+**Symptoms**:
+- Assertions without justification
+- Missing citations
+- Leaps in logic
+
+**Fix**:
+- Mark every claim (highlight in color)
+- For each: Is this supported by argument or citation?
+- Add justification where missing
+- If can't justify, remove claim
+
+### Mistake 3: Unclear Structure
+
+**Symptoms**:
+- Paragraphs could be reordered without loss
+- Unclear why chapters come in this order
+- Reader gets lost
+
+**Fix**:
+- Create reverse outline (summary of each paragraph)
+- Check: Does paragraph N+1 build on paragraph N?
+- Add transition sentences
+- Frontload: Tell reader what you're doing before doing it
+
+### Mistake 4: Jargon Overload
+
+**Symptoms**:
+- Technical terms undefined
+- Accessible only to narrow specialists
+- Unnecessarily complex prose
+
+**Fix**:
+- Define technical terms at first use
+- Use examples to illustrate abstract concepts
+- Check: Could a smart graduate student in adjacent field follow this?
+- Simplify sentences where possible
+
+### Mistake 5: Weak Objections
+
+**Symptoms**:
+- Objections easily dismissed
+- No real engagement with criticism
+- Appears to avoid hard questions
+
+**Fix**:
+- State objections as strongly as possible
+- Consider: What would a critic actually say?
+- Address strongest version, not weakest
+- If can't answer objection, acknowledge as limitation
+
+---
+
+## Platform-Specific Style Guidance
+
+### PhilArchive / PhilPapers
+
+**Voice**: First-person acceptable ("I argue that...")
+**Structure**: Flexible, but clearly organized
+**Citations**: Author-year format typical (APA or Chicago)
+**Length**: 5,000-12,000 words typical
+**Terminology**: Philosophical precision expected
+
+**Example opening**:
+```markdown
+I argue that personal identity across sleep-wake cycles depends on narrative compression. Existing accounts either ignore the discontinuity of sleep (Thompson 2015; Zahavi 2018) or fail to explain how continuity is maintained (Metzinger 2003). I propose a framework that...
+```
+
+### arXiv (philosophy-related categories)
+
+**Voice**: More formal, third-person or passive common
+**Structure**: Often more rigid (Introduction, Related Work, Main Results, Conclusion)
+**Citations**: Numbered or author-year, varies by sub-field
+**Length**: Varies widely (3,000-20,000 words)
+**Terminology**: Interdisciplinary, define field-specific terms
+
+**Example opening**:
+```markdown
+The problem of self-continuity across discontinuous conscious states has been extensively studied in philosophy of mind [1,2,3] and more recently in computational neuroscience [4,5]. However, existing approaches fail to account for... This paper proposes...
+```
+
+### PhilSci-Archive
+
+**Voice**: Formal but first-person acceptable in philosophy sections
+**Structure**: Often combines philosophical analysis with formal/empirical sections
+**Citations**: Author-year typical
+**Length**: 6,000-15,000 words typical
+**Terminology**: Bridge philosophical and scientific terminology
+
+**Example opening**:
+```markdown
+Scientific models of memory consolidation during sleep (Born & Wilhelm 2012) raise philosophical questions about personal identity. If memories are restructured during sleep, what ensures the continuity of self? I argue that a narrative compression framework, informed by both phenomenology (Thompson 2015) and neuroscience (Rasch & Born 2013), provides a solution...
+```
+
+---
+
+## Summary Checklist
+
+Before writing each section, verify you:
+- [ ] Understand the purpose of this section type
+- [ ] Have reviewed the structure template
+- [ ] Know what quality markers to aim for
+- [ ] Have reviewed relevant sample papers
+- [ ] Have outline specifications for this section
+
+After writing each section, verify:
+- [ ] All elements from structure template present
+- [ ] Quality checklist items satisfied
+- [ ] Transitions smooth to/from adjacent sections
+- [ ] Citations adequate and properly formatted
+- [ ] Conforms to platform style guidance
+
+This ensures systematic quality across all sections.