maestro-flow 0.5.31 → 0.5.33

package/.agents/skills/scholar-writing/phases/05-anti-ai-polish.md

@@ -0,0 +1,202 @@
+# Phase 5: Anti-AI Polish
+
+> **COMPACT SENTINEL [Phase 5: Anti-AI Polish]**
+> This phase contains 6 execution steps (Step 5.1 -- 5.6).
+> If you can read this sentinel but cannot find the full Step protocol below, context has been compressed.
+> Recovery: `read_file("phases/05-anti-ai-polish.md")`
+
+Remove AI-generated writing patterns from all prose to make the paper sound natural and human-written. Based on Wikipedia's "Signs of AI writing" guide.
+
+## Objective
+
+- Identify and eliminate AI writing patterns from all paper sections
+- Humanize prose while preserving technical accuracy
+- Add voice and personality appropriate for academic writing
+- Score each section and ensure minimum quality threshold
+
+## Core Insight
+
+LLMs use statistical algorithms to predict what comes next. The result tends toward the most statistically likely outcome that applies to the widest variety of cases, creating detectable patterns. Academic reviewers are increasingly trained to spot these patterns.
+
+## Execution
+
+### Step 5.1: Score Each Section (Pre-Polish)
+
+Rate each draft section on 5 dimensions (1-10 each, total 50):
+
+| Dimension | Question |
+|-----------|----------|
+| Directness | Direct statements or announcements? |
+| Rhythm | Varied sentence lengths or metronomic? |
+| Trust | Respects reader intelligence? |
+| Authenticity | Sounds human-written? |
+| Density | Anything cuttable? |
+
+Thresholds:
+- 45-50: Excellent, minimal polish needed
+- 35-44: Good, targeted fixes
+- Below 35: Needs significant revision
+
+Record pre-polish scores for each section.
+
+### Step 5.2: Detect Content Patterns
+
+Scan for these content-level AI patterns in each section:
+
+**Undue emphasis on significance**:
+- "stands as a testament", "crucial role", "pivotal moment"
+- "underscores/highlights its importance", "setting the stage for"
+- Fix: State facts directly. Replace with specific claims.
+
+**Promotional language**:
+- "vibrant", "rich heritage", "groundbreaking", "breathtaking"
+- Fix: Use neutral, precise language.
+
+**Superficial -ing analyses**:
+- "highlighting the importance", "ensuring that", "showcasing"
+- Fix: Use active verbs with specific subjects.
+
+**Vague attributions**:
+- "Experts believe", "Observers note", "Industry reports suggest"
+- Fix: Cite specific sources or remove attribution.
+
+**Formulaic "challenges" sections**:
+- "Despite X, faces challenges", "Despite these challenges"
+- Fix: State specific problems with evidence.
+
+### Step 5.3: Detect Language Patterns
+
+Scan for these language-level AI patterns:
+
+**AI vocabulary** -- replace or remove:
+- Additionally -> Also / [delete]
+- Crucial -> Important / [be specific about why]
+- Delve -> Examine / Analyze
+- Enhance -> Improve / [be specific]
+- Landscape (abstract) -> Field / Area / Domain
+- Furthermore -> [delete, just start the sentence]
+- Leverage -> Use
+- Pivotal -> Important / Key
+- Showcasing -> Showing
+- Testament -> Evidence / Proof
+- Underscore -> Show / Demonstrate
+
+**Copula avoidance**:
+- "serves as" -> "is"
+- "stands as" -> "is"
+- "represents" -> "is"
+- "boasts" -> "has"
+- "features" -> "has" / "includes"
+
+**Negative parallelisms**:
+- "It's not just X, it's Y" -> "X does Y"
+- "not merely A, but B" -> "A and B"
+
+**Rule of three**:
+- Forced groups of three items -> prefer two or four
+
+**Em dash overuse**:
+- Excessive use of -- for parenthetical -> use commas or parentheses
+
+**Elegant variation**:
+- Excessive synonym substitution for the same concept -> pick one term, use consistently
+
+### Step 5.4: Rewrite Sections
+
+> **CHECKPOINT**: Before proceeding, verify:
+> 1. This phase is track_tasks `in_progress` (active phase protection)
+> 2. Full protocol (Step 5.1 -- 5.6) is in active memory, not just sentinel
+> If only sentinel remains -> `read_file("phases/05-anti-ai-polish.md")` now.
+
+For each section, apply fixes:
+
+1. **Cut filler phrases**:
+   - "In order to achieve" -> "To achieve"
+   - "Due to the fact that" -> "Because"
+   - "It is important to note that" -> [delete]
+   - "It is worth mentioning that" -> [delete]
+
+2. **Break formulaic structures**:
+   - Vary sentence lengths. Mix short and long.
+   - End paragraphs differently (not always with a punchy one-liner).
+   - Avoid three consecutive sentences of the same length.
+
+3. **Trust readers**:
+   - State facts directly. Skip softening and hand-holding.
+   - "It could potentially be argued that X might have some effect" -> "X affects Y"
+
+4. **Cut quotables**:
+   - If it sounds like a pull-quote or inspirational statement, rewrite it.
+   - "This represents a major step in the right direction" -> [replace with specific fact]
+
+5. **Preserve technical precision**:
+   - Do NOT change technical terms, mathematical notation, or method names
+   - Do NOT alter the meaning of claims or weaken evidence statements
+   - Do NOT remove necessary hedging for genuinely uncertain claims
+
+Write polished sections to: `outputDir/.writing/polished/`
+
+### Step 5.5: Score Each Section (Post-Polish)
+
+Re-score each section on the same 5 dimensions.
+
+Requirements:
+- All sections must score >= 35
+- If any section scores below 35, re-polish that section
+- Maximum 2 re-polish rounds per section
+
+Record comparison:
+
+```markdown
+## Anti-AI Polish Report
+
+| Section | Pre-Score | Post-Score | Change |
+|---------|-----------|------------|--------|
+| Abstract | 28 | 42 | +14 |
+| Introduction | 32 | 45 | +13 |
+| Methods | 38 | 44 | +6 |
+| Experiments | 35 | 43 | +8 |
+| Related Work | 25 | 40 | +15 |
+| Conclusion | 30 | 41 | +11 |
+```
+
+### Step 5.6: Academic Voice Calibration
+
+Academic writing has different anti-AI considerations than general prose:
+
+**Appropriate for academic papers**:
+- Measured hedging for genuinely uncertain claims ("Our results suggest...")
+- Passive voice for methodology ("The model was trained...")
+- Formal register without being stiff
+- First-person plural ("We propose...", "We observe...")
+
+**NOT appropriate for academic papers**:
+- Casual asides or humor (unlike blog posts)
+- Strong first-person opinions ("I genuinely feel...")
+- Colloquialisms
+
+The goal is natural academic prose, not casual blog writing. The anti-AI patterns to remove are the formulaic, promotional, and vague patterns -- not the formal register itself.
+
+## Common Fixes Quick Reference
+
+| Before | After |
+|--------|-------|
+| "serves as a testament to" | "shows" |
+| "Moreover, it provides" | "It adds" / "It also provides" |
+| "It's not just X, it's Y" | "X does Y" |
+| "Industry experts believe" | "According to [specific source]" |
+| "plays a crucial role in" | "is important for" / [be specific] |
+| "In recent years" | [state the specific timeframe] |
+| "A growing body of research" | "[N] recent studies [refs]" |
+| "has garnered significant attention" | "is widely studied [refs]" |
+
+## Output
+
+- **Files**: Polished sections in `outputDir/.writing/polished/` (same structure as drafts/)
+- **File**: `outputDir/.writing/anti-ai-report.md` (scoring report)
+- **Variable**: `polishedDraft` (path to polished/ directory)
+- **track_tasks**: Mark Phase 5 completed, Phase 6 in_progress
+
+## Next Phase
+
+Return to orchestrator, then continue to [Phase 6: Conference Formatting](06-conference-formatting.md).

package/.agents/skills/scholar-writing/phases/06-conference-formatting.md

@@ -0,0 +1,260 @@
+# Phase 6: Conference Formatting
+
+Assemble all polished sections into a complete LaTeX manuscript using the target conference template. Compile and verify.
+
+## Objective
+
+- Copy the correct conference LaTeX template
+- Assemble polished sections into paper.tex
+- Include verified bibliography
+- Compile and fix any LaTeX errors
+- Apply conference-specific requirements (checklist, disclosures)
+- Ensure page limit compliance
+
+## Execution
+
+### Step 6.1: Setup Conference Template
+
+Copy the appropriate template to the output directory. Templates are available at `G:/github_lib/claude-scholar/skills/ml-paper-writing/templates/`.
+
+| Conference | Template Directory | Main File | Style File |
+|------------|-------------------|-----------|------------|
+| NeurIPS 2025 | `neurips2025/` | `main.tex` | `neurips.sty` |
+| ICML 2026 | `icml2026/` | `example_paper.tex` | `icml2026.sty` |
+| ICLR 2026 | `iclr2026/` | `iclr2026_conference.tex` | `iclr2026_conference.sty` |
+| ACL | `acl/` | `acl_latex.tex` | `acl.sty` |
+| AAAI 2026 | `aaai2026/` | `aaai2026-unified-template.tex` | `aaai2026.sty` |
+| COLM 2025 | `colm2025/` | `colm2025_conference.tex` | `colm2025_conference.sty` |
+
+**Template copy with error handling**:
+```bash
+# Set template source and destination
+TEMPLATE_SOURCE="G:/github_lib/claude-scholar/skills/ml-paper-writing/templates/${CONFERENCE_DIR}"
+OUTPUT_DIR="./paper-output"
+
+# Check if template source exists
+if [ ! -d "$TEMPLATE_SOURCE" ]; then
+  echo "ERROR: Template directory not found: $TEMPLATE_SOURCE"
+  echo "Available templates:"
+  ls -1 "G:/github_lib/claude-scholar/skills/ml-paper-writing/templates/" 2>/dev/null || echo "  Template directory not accessible"
+  echo ""
+  echo "Fallback options:"
+  echo "  1. Download template from conference website"
+  echo "  2. Use generic LaTeX article template"
+  echo "  3. Specify custom template path"
+  exit 1
+fi
+
+# Create output directory
+mkdir -p "$OUTPUT_DIR"
+
+# Copy entire template directory (not just main.tex)
+cp -r "$TEMPLATE_SOURCE"/* "$OUTPUT_DIR/" 2>&1
+COPY_STATUS=$?
+
+if [ $COPY_STATUS -ne 0 ]; then
+  echo "ERROR: Failed to copy template files"
+  echo "Possible causes:"
+  echo "  - Permission denied (check file permissions)"
+  echo "  - Disk space full"
+  echo "  - Path contains special characters"
+  echo ""
+  echo "Manual fallback:"
+  echo "  1. Manually copy files from: $TEMPLATE_SOURCE"
+  echo "  2. To destination: $OUTPUT_DIR"
+  exit 1
+fi
+
+# Verify template structure is complete
+echo "Template files copied successfully:"
+ls -la "$OUTPUT_DIR/"
+# Should see: main.tex, *.sty, *.bst, etc.
+
+# Verify critical files exist
+CRITICAL_FILES=("main.tex" "*.sty")
+for pattern in "${CRITICAL_FILES[@]}"; do
+  if ! ls "$OUTPUT_DIR"/$pattern 1> /dev/null 2>&1; then
+    echo "WARNING: Critical file pattern not found: $pattern"
+    echo "Template may be incomplete. Check manually."
+  fi
+done
+```
+
+IMPORTANT: Copy the ENTIRE directory. Templates include:
+- Style files (`.sty`) -- required for compilation
+- Bibliography styles (`.bst`) -- required for references
+- Makefiles -- for easy compilation
+- Math command definitions (if any)
+
+**If template copy fails**, use fallback strategy:
+1. **Download from conference website**: Most conferences provide LaTeX templates on their submission page
+2. **Use generic template**: Create minimal LaTeX document with `\documentclass{article}`
+3. **Request user assistance**: Ask user to manually place template files in output directory
+
+### Step 6.2: Verify Template Compiles
+
+Before making any changes, compile the template as-is:
+
+```bash
+cd $OUTPUT_DIR
+# Using latexmk (recommended)
+latexmk -pdf main.tex
+
+# Or manual compilation
+pdflatex main.tex
+bibtex main
+pdflatex main.tex
+pdflatex main.tex
+```
+
+If the unmodified template does not compile, fix that first:
+- Missing TeX packages: `tlmgr install <package>`
+- Wrong TeX distribution: use TeX Live (recommended)
+
+### Step 6.3: Assemble Paper Content
+
+Replace template example content with polished sections. Work section by section:
+
+1. **Preamble**: Keep the template preamble intact. Only add:
+   - `\usepackage{booktabs}` (if not present, for tables)
+   - Custom macros for method name: `\newcommand{\method}{YourMethodName}`
+   - Anonymization flag (for blind review)
+
+2. **Title and Authors**: Set title, anonymize authors for submission
+   ```latex
+   \title{Your Paper Title}
+   % For blind review:
+   \author{Anonymous Authors}
+   ```
+
+3. **Content sections**: Replace template content with polished sections
+   - Read each file from `outputDir/.writing/polished/`
+   - Insert into the appropriate `\section{}` blocks
+   - Preserve all `\cite{}` commands
+   - Preserve all figure/table environments
+
+4. **Bibliography**: Copy `references.bib` to the output directory
+   ```bash
+   cp $OUTPUT_DIR/.writing/references.bib $OUTPUT_DIR/references.bib
+   ```
+   Update `\bibliography{references}` or `\addbibresource{references.bib}` as needed.
+
+### Step 6.4: Conference-Specific Additions
+
+Apply requirements specific to the target conference:
+
+| Conference | Required Additions |
+|------------|-------------------|
+| NeurIPS | Paper checklist (appendix), lay summary if accepted |
+| ICML | Broader Impact Statement (after conclusion) |
+| ICLR | LLM usage disclosure, reciprocal reviewing agreement |
+| ACL/EMNLP | Limitations section (mandatory), Ethics Statement |
+| AAAI | Strict adherence to style file (no modifications to .sty) |
+| COLM | Reframe for language model focus if needed |
+
+For NeurIPS checklist, include in appendix:
+```latex
+\section*{NeurIPS Paper Checklist}
+\begin{enumerate}
+  \item Claims: [Yes/No/NA] + justification
+  \item Limitations: [Yes/No] + justification
+  % ... (see references/checklists.md for full list)
+\end{enumerate}
+```
+
+### Step 6.5: Compile and Fix Errors
+
+Compile the assembled paper:
+
+```bash
+cd $OUTPUT_DIR
+pdflatex main.tex
+bibtex main
+pdflatex main.tex
+pdflatex main.tex
+```
+
+Common errors and fixes:
+
+| Error | Fix |
+|-------|-----|
+| Undefined citation | Check .bib key matches \cite{} key |
+| Missing package | Add \usepackage{} or install via tlmgr |
+| Overfull hbox | Adjust line breaks, figure sizes |
+| Encoding error | Ensure UTF-8, use LaTeX escapes for special chars |
+| Bibliography not found | Check \bibliography{} path |
+
+Retry compilation after each fix. Maximum 3 fix-compile cycles.
+
+### Step 6.6: Page Limit Verification
+
+Check that the paper fits within the page limit:
+
+```bash
+# Count pages (requires pdfinfo)
+pdfinfo main.pdf | grep Pages
+```
+
+If over the page limit:
+- Move detailed proofs to appendix
+- Condense related work (cite surveys instead of individual papers)
+- Combine similar experiments into unified tables
+- Use smaller figure sizes with subfigures
+- Tighten writing: eliminate redundancy, use active voice
+- Reduce whitespace between sections (but do NOT modify .sty files)
+
+If under the page limit (by more than 0.5 pages):
+- Expand ablation studies
+- Add qualitative examples
+- Expand limitations discussion
+- Include additional baselines
+
+### Step 6.7: Final Verification Checklist
+
+Before declaring complete:
+
+- [ ] Paper compiles without errors
+- [ ] All citations resolve (no `??` in PDF)
+- [ ] Page limit respected
+- [ ] Authors anonymized (for blind review)
+- [ ] No `[CITATION NEEDED]` or `[TODO]` markers remain (or all are explicitly flagged)
+- [ ] Figures render correctly
+- [ ] Tables use booktabs style
+- [ ] Conference-specific sections included
+- [ ] No modifications to .sty files
+- [ ] References formatted correctly
+
+### Step 6.8: Delivery
+
+Report to user:
+
+> "Paper assembled and compiled successfully.
+> - Conference: [name]
+> - Pages: [N] / [limit]
+> - Citations: [verified] / [total] ([placeholders] need your verification)
+> - Output: [path to paper.tex and paper.pdf]
+>
+> Remaining items for you:
+> - [list of placeholder citations to verify]
+> - [list of figures to create/replace]
+> - [any other action items]"
+
+## Output
+
+- **File**: `outputDir/main.tex` (or conference-specific name) -- complete manuscript
+- **File**: `outputDir/main.pdf` -- compiled PDF
+- **File**: `outputDir/references.bib` -- verified bibliography
+- **track_tasks**: Mark Phase 6 completed
+
+## Completion
+
+The paper writing workflow is complete. The user now has:
+1. A complete LaTeX manuscript formatted for their target conference
+2. A verified bibliography
+3. A list of any remaining action items
+
+Next steps for the researcher:
+- Review and revise the draft
+- Create/finalize figures
+- Verify any placeholder citations
+- Run the `scholar-review` skill for self-review before submission