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+# 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`**
+```bash
+/validate-latex                  # Full validation
+/validate-latex --refs-only      # Only check references
+/validate-latex --fix            # Auto-fix common issues
+```
+
+**`/check-links`**
+```bash
+/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`**
+```bash
+/clean-bibliography              # Interactive cleanup
+/clean-bibliography --remove-unused  # Auto-remove unused entries
+/clean-bibliography --fix-format     # Fix formatting issues
+```
+
+**`/build-paper`**
+```bash
+/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):
+```json
+{
+  "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):
+```json
+{
+  "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