15 KiB
15 KiB
Example: Research Paper with Presentation and Documentation
This example shows what the meta-automation-architect generates for a research project that combines LaTeX (paper), HTML (presentation), and Markdown (documentation).
Project Context
- Type: Academic Writing (primary) + Research (secondary)
- Content:
- LaTeX research paper (25 pages, 8 chapters, 45 references)
- HTML presentation slides (30 slides)
- Markdown documentation and notes (50+ files)
- Pain Points: Broken cross-references, unused citations, broken links, inconsistent formatting
- Priority: Citation validation and link checking
Project Structure
research-paper/
├── paper/
│ ├── main.tex # Main LaTeX document
│ ├── chapters/
│ │ ├── 01_introduction.tex
│ │ ├── 02_related_work.tex
│ │ ├── 03_methodology.tex
│ │ ├── 04_results.tex
│ │ ├── 05_discussion.tex
│ │ └── 06_conclusion.tex
│ ├── figures/
│ │ ├── figure1.pdf
│ │ ├── figure2.pdf
│ │ └── ... (15 figures)
│ ├── tables/
│ │ ├── table1.tex
│ │ └── ... (5 tables)
│ ├── references.bib # Bibliography (45 entries)
│ └── custom.sty # Custom LaTeX style
├── presentation/
│ ├── index.html # Main presentation
│ ├── slides/
│ │ ├── 01_intro.html
│ │ ├── 02_methods.html
│ │ ├── 03_results.html
│ │ └── ... (30 slides)
│ ├── assets/
│ │ ├── figures/
│ │ ├── css/
│ │ └── js/
│ └── notes/
│ └── speaker_notes.md
├── notes/
│ ├── literature_review.md
│ ├── methodology_notes.md
│ ├── experiment_logs.md
│ ├── analysis/
│ │ ├── [[statistical_tests]].md
│ │ └── [[data_processing]].md
│ └── ideas/
│ └── future_work.md
└── README.md
User Conversation
User: "Help me automate my research paper project"
Meta-Skill: Analyzing project...
- Detected: Academic Writing (68% confidence)
- Found 25 .tex files
- Found 1 .bib file with 45 entries
- Found 30 HTML slides
- Found 50+ interconnected markdown files
- Secondary: Research (32% confidence)
- Research methodology documentation
- Experiment logs and analysis
Meta-Skill: What are your main pain points?
Options:
- Broken LaTeX references (RECOMMENDED: Manual checking takes 30 min)
- Unused bibliography entries (RECOMMENDED: 12 unused entries detected)
- Broken HTML/Markdown links (RECOMMENDED: 8 broken links found)
- Inconsistent formatting
User: [Selects: Broken references, Unused citations, Broken links]
Meta-Skill: Automation opportunities identified:
- Validate LaTeX cross-references: Saves 30 min/compile
- Clean bibliography: Saves 20 min/review
- Check all links: Saves 30 min/validation
- Total potential savings: 80+ hours over project lifecycle
Meta-Skill: Generating automation system...
Session ID: research-paper-abc123
Generated Automation System
1. Custom Subagents (8)
Universal Agents
- structure-analyzer - Reviews document organization across all formats
- workflow-analyzer - Analyzes compilation and publishing workflow
Academic Writing Domain Agents
- latex-structure-analyzer - LaTeX document structure and cross-references
- citation-analyzer - Bibliography validation and citation usage
- html-structure-analyzer - Presentation hierarchy and semantics
- link-validator - All links across HTML and Markdown
- cross-reference-analyzer - Cross-references across all document types
- formatting-analyzer - Formatting consistency
2. Custom Skills (4)
latex-validator - Comprehensive LaTeX validation
Example:
Running LaTeX validation...
✅ Document Structure
- 6 chapters found
- Proper hierarchy: chapter → section → subsection
- TOC depth: 2 levels
⚠️ Cross-References
- 23/25 \\ref commands valid
- 2 broken references:
* Line 145: \\ref{fig:missing} - target not found
* Line 289: \\ref{sec:old-name} - outdated reference
✅ Figures/Tables
- 15/15 figures referenced
- 5/5 tables referenced
- All captions present
⚠️ Bibliography
- 45 entries in references.bib
- 33 cited in text
- 12 unused entries:
* [Smith2020] - Never cited
* [Jones2019] - Never cited
* ...
📊 Compilation Status
- pdflatex: ✅ Success
- bibtex: ✅ Success
- Output: main.pdf (2.3 MB)
💡 Recommendations:
1. Fix 2 broken \\ref references
2. Remove 12 unused bibliography entries (saves 20% .bib size)
3. Consider adding \\label for Section 4.2 (referenced but not labeled)
link-checker - Validates all links in HTML and Markdown
Example:
Checking links across project...
📁 HTML Presentation (30 slides)
✅ Internal links: 45/45 valid
✅ External links: 12/12 valid
✅ Asset references: 28/28 valid
📁 Markdown Notes (52 files)
✅ Wiki-style [[links]]: 67/75 valid
⚠️ Broken wiki links (8):
* notes/analysis/stats.md → [[missing_page]]
* notes/ideas/future.md → [[old-experiment]]
* ...
✅ External links: 34/35 valid
⚠️ 1 broken external link:
* http://oldwebsite.com/data → 404 Not Found
📊 Summary
- Total links checked: 185
- Valid: 177 (95.7%)
- Broken: 8 (4.3%)
- Orphaned pages: 2 (no incoming links)
💡 Recommendations:
1. Fix 8 broken wiki links
2. Update 1 broken external link
3. Consider linking to orphaned pages
4. Estimated fix time: 15 minutes
cross-reference-checker - Validates references across all formats
Example:
Analyzing cross-references...
📄 LaTeX Paper
- \\ref commands: 25 (23 valid, 2 broken)
- \\cite commands: 33 (all valid)
- Figure refs: 15 (all valid)
- Table refs: 5 (all valid)
🖥️ HTML Presentation
- Internal anchor links: 45 (all valid)
- Figure references: 12 (all valid)
- Paper references: 8 links to LaTeX sections
📝 Markdown Notes
- Internal [[links]]: 75 (67 valid, 8 broken)
- Cross-format refs: 5 links to paper sections
🔗 Cross-Format Consistency
✅ Methodology: Consistent between paper and presentation
✅ Results: Figures match in paper and slides
⚠️ Discussion section in paper not reflected in presentation
💡 Consider adding discussion slide
📊 Overall Reference Health: 96.2%
bibliography-manager - Manages .bib entries and citations
Example:
Analyzing bibliography...
📚 references.bib
- Total entries: 45
- Used in paper: 33 (73%)
- Unused: 12 (27%)
🔍 Citation Analysis
- Most cited: [Smith2020] (8 times)
- Least cited: [Wang2021] (1 time)
- Average citations: 2.4 per entry
⚠️ Issues Found
1. Unused entries (12):
* [Smith2020] - Never cited (can be removed)
* [Jones2019] - Never cited (can be removed)
* ...
2. Missing fields (3):
* [Brown2021] - Missing 'pages' field
* [Davis2022] - Missing 'doi' field
* [Wilson2020] - Inconsistent author format
3. Duplicate entries (2):
* [Lee2019] and [Lee2019b] - Same paper
* [Miller2020] and [Miller2020a] - Same paper
💡 Recommendations:
1. Remove 12 unused entries → 27% smaller .bib file
2. Merge 2 duplicate entries
3. Complete missing fields for better citations
4. Run: /clean-bibliography to apply fixes
3. Custom Commands (4)
/validate-latex
/validate-latex # Full validation
/validate-latex --refs-only # Only check references
/validate-latex --fix # Auto-fix common issues
/check-links
/check-links # Check all links
/check-links presentation/ # Only HTML slides
/check-links notes/ # Only Markdown notes
/check-links --external # Include external links
/clean-bibliography
/clean-bibliography # Interactive cleanup
/clean-bibliography --remove-unused # Auto-remove unused entries
/clean-bibliography --fix-format # Fix formatting issues
/build-paper
/build-paper # Compile LaTeX to PDF
/build-paper --watch # Auto-compile on changes
/build-paper --validate # Validate before building
4. Hooks (3)
validate_on_save.py (PreToolUse)
- Triggers when .tex or .bib files are saved
- Runs quick validation checks
- Alerts if new issues introduced
update_references.py (PostToolUse)
- Triggers after editing .tex files
- Updates cross-reference index
- Checks for new broken references
link_check_on_md_save.py (PostToolUse)
- Triggers when .md files are saved
- Validates wiki-style links
- Alerts if broken links created
5. Impact
Time Savings:
- Manual LaTeX validation: 30 min/compile → 2 minutes automated (93% reduction)
- Bibliography cleanup: 45 min/cleanup → 5 minutes automated (89% reduction)
- Link checking: 30 min/check → 1 minute automated (97% reduction)
- Cross-reference validation: 20 min/review → 2 minutes automated (90% reduction)
- Total: 125 min → 10 min (92% time reduction per validation cycle)
Over typical paper lifecycle (50 validation cycles):
- Manual: 104 hours
- Automated: 8 hours
- Savings: 96 hours (92%)
Quality Improvements:
- Cross-reference accuracy: Manual checking → 100% validated automatically
- Bibliography: 12 unused entries → 0 unused (27% smaller .bib)
- Link health: 92% valid → 100% valid (8 broken links fixed)
- Compilation success rate: 80% → 100% (catches issues before compile)
Concrete Fixes Applied:
- Fixed 2 broken LaTeX \ref references
- Removed 12 unused bibliography entries
- Fixed 8 broken Markdown wiki links
- Updated 1 broken external link
- Merged 2 duplicate .bib entries
- Completed 3 missing bibliography fields
Example Results
Before Automation
LaTeX Compilation:
! LaTeX Error: Reference `fig:missing' on page 12 undefined.
! LaTeX Error: Reference `sec:old-name' on page 23 undefined.
Warning: Citation 'Smith2020' unused
Warning: Citation 'Jones2019' unused
... (10 more unused citations)
Output: main.pdf generated with warnings
Manual Link Checking:
Manually clicking through 185 links...
Found broken link after 15 minutes
Found another after 20 minutes
Gave up after 30 minutes, unsure if all checked
Bibliography Management:
45 entries in .bib file
Manually grep for each to see if cited
Takes 45 minutes to identify 12 unused entries
Not sure about duplicates or format issues
After Automation
/validate-latex Output:
✅ Running comprehensive LaTeX validation...
📊 Results (completed in 2 minutes):
✅ Document structure: Valid
⚠️ Cross-references: 2 issues found
✅ Bibliography: All citations valid
⚠️ Unused entries: 12 found
✅ Compilation: Success
🔧 Auto-fix available:
Run: /validate-latex --fix
/check-links Output:
✅ Link validation complete (1 minute):
- 185 total links
- 177 valid (95.7%)
- 8 broken (4.3%)
📋 Detailed report: reports/link-validator.json
💡 Run: /check-links --fix to auto-fix wiki links
/clean-bibliography Output:
✅ Bibliography analysis complete (5 minutes):
- Removed 12 unused entries
- Merged 2 duplicates
- Fixed 3 incomplete entries
- New size: 33 entries (73% of original)
💾 Backup: references.bib.backup
✅ Updated: references.bib
Agent Communication
reports/latex-structure-analyzer.json (excerpt):
{
"agent_name": "latex-structure-analyzer",
"summary": "Paper structure is sound. Found 2 broken cross-references and compilation warnings.",
"findings": [
{
"type": "broken_reference",
"severity": "high",
"location": "chapters/03_methodology.tex:145",
"description": "\\ref{fig:missing} references non-existent label",
"recommendation": "Add \\label{fig:missing} to appropriate figure or fix reference"
},
{
"type": "unused_bibliography",
"severity": "medium",
"description": "12 bibliography entries never cited in text",
"entries": ["Smith2020", "Jones2019", ...],
"recommendation": "Remove unused entries or add citations where appropriate"
}
],
"metrics": {
"total_chapters": 6,
"total_sections": 24,
"total_references": 25,
"valid_references": 23,
"broken_references": 2,
"bibliography_entries": 45,
"cited_entries": 33,
"unused_entries": 12
},
"automation_impact": {
"time_saved": "30 min/validation (manual checking)",
"quality_improvement": "100% reference validation vs. manual spot-checking"
}
}
reports/link-validator.json (excerpt):
{
"agent_name": "link-validator",
"summary": "Found 8 broken links across HTML and Markdown. 95.7% link health.",
"findings": [
{
"type": "broken_wiki_link",
"severity": "medium",
"location": "notes/analysis/stats.md:23",
"description": "[[missing_page]] does not exist",
"recommendation": "Create missing_page.md or update link to correct page"
},
{
"type": "broken_external_link",
"severity": "high",
"location": "notes/literature_review.md:156",
"description": "http://oldwebsite.com/data returns 404",
"recommendation": "Update to current URL or mark as archived"
}
],
"metrics": {
"total_links": 185,
"valid_links": 177,
"broken_links": 8,
"link_health_percentage": 95.7,
"html_links": 57,
"markdown_wiki_links": 75,
"markdown_external_links": 35,
"orphaned_pages": 2
},
"automation_impact": {
"time_saved": "30 min/check (manual link clicking)",
"quality_improvement": "100% coverage vs. ~60% manual coverage"
}
}
Result
Researcher now has:
- ✅ 100% validated cross-references - No more broken \ref in paper
- ✅ Clean bibliography - 27% smaller, no unused entries
- ✅ All links validated - 8 broken links fixed, 100% health
- ✅ Consistent formatting - Across LaTeX, HTML, and Markdown
- ✅ Fast compilation - Issues caught before build
- ✅ 96 hours saved over project lifecycle (92% reduction)
Before vs After:
| Metric | Before | After | Improvement |
|---|---|---|---|
| Cross-reference validation | Manual, 30 min | 2 min automated | 93% faster |
| Bibliography unused entries | 12 (27%) | 0 (0%) | 100% clean |
| Link health | 92% (manual partial check) | 100% (full automated) | +8% |
| Validation coverage | ~60% (time limited) | 100% (comprehensive) | +40% |
| Time per validation cycle | 125 min | 10 min | 92% reduction |
| Time over project (50 cycles) | 104 hours | 8 hours | 96 hours saved |
Ongoing Benefits:
- Every save triggers validation
- New issues caught immediately
- No broken references in final paper
- Bibliography stays clean
- All links remain valid
- Compilation always succeeds
Publication Quality:
- Zero broken cross-references in submitted paper
- Professional bibliography (no unused entries)
- All presentation links work during defense
- Documentation fully interconnected
- Reviewers praise technical quality