@research-copilot/plugin 1.1.15

package/dist/skills/literature-search/SKILL.md

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+---
+name: literature-search
+description: Focused literature search skill. Searches papers, locks baselines, builds related-work map. Use for standalone literature tasks.
+triggers:
+  - "search papers"
+  - "find baselines"
+  - "literature review"
+  - "related work"
+  - "find research on"
+---
+
+# Literature Search
+
+Orchestrate focused literature search: create task → dispatch @rc-literature → verify results.
+
+## When to Use
+
+Use this skill when:
+- User asks to "search papers for X"
+- User wants to "find baselines for Y"
+- User needs a "literature review on Z"
+- Standalone literature search (NOT part of full pipeline)
+
+Do NOT use when:
+- Part of full-research-workflow (that handles literature internally)
+- User only wants a quick web search (use web-search skill)
+
+## Task-First Protocol
+
+Before starting, check if task exists:
+
+```powershell
+# Check for existing literature task
+$taskFile = "C:\PythonProject\research_copilot\.rc\tasks\literature-search.json"
+if (Test-Path $taskFile) {
+    $task = Get-Content $taskFile | ConvertFrom-Json
+    Write-Host "Found existing task: $($task.query)"
+} else {
+    Write-Host "No existing task. Will create one."
+}
+```
+
+Create task if needed:
+
+```powershell
+# Create literature search task
+rc task create --type literature --query "user query here" --output .rc/tasks/literature-search.json
+```
+
+## Auto-Context Loading
+
+Read task context before orchestration:
+
+```powershell
+# Load task context
+$taskFile = "C:\PythonProject\research_copilot\.rc\tasks\literature-search.json"
+if (Test-Path $taskFile) {
+    $task = Get-Content $taskFile | ConvertFrom-Json
+    
+    Write-Host "Task Query: $($task.query)"
+    Write-Host "Target Baselines: $($task.target_baselines)"
+    Write-Host "Categories Required: $($task.categories_required)"
+    
+    # Load PRD if referenced
+    if ($task.prd_file -and (Test-Path $task.prd_file)) {
+        $prd = Get-Content $task.prd_file -Raw
+        Write-Host "PRD loaded: $($task.prd_file)"
+    }
+}
+```
+
+## Orchestration Logic
+
+Execute literature search via agent dispatch:
+
+```powershell
+# Start task
+rc task start literature-search
+
+# Dispatch to literature agent
+Write-Host "Dispatching to @rc-literature agent..."
+
+# Agent will:
+# 1. Parse query and extract search terms
+# 2. Search multiple sources (arXiv, Semantic Scholar, Google Scholar)
+# 3. Extract baselines and build comparison table
+# 4. Categorize papers (method, survey, application)
+# 5. Generate related-work map
+# 6. Save results to .rc/literature/
+
+# Wait for completion (agent runs autonomously)
+# Check status
+$status = rc task status literature-search
+Write-Host "Task status: $status"
+```
+
+Verify results:
+
+```powershell
+# Verify literature search outputs
+$litDir = "C:\PythonProject\research_copilot\.rc\literature"
+
+# Check baselines file
+$baselinesFile = Join-Path $litDir "baselines.json"
+if (Test-Path $baselinesFile) {
+    $baselines = Get-Content $baselinesFile | ConvertFrom-Json
+    Write-Host "Found $($baselines.Count) baselines"
+} else {
+    Write-Host "WARNING: No baselines file found"
+}
+
+# Check papers file
+$papersFile = Join-Path $litDir "papers.json"
+if (Test-Path $papersFile) {
+    $papers = Get-Content $papersFile | ConvertFrom-Json
+    Write-Host "Found $($papers.Count) papers"
+} else {
+    Write-Host "WARNING: No papers file found"
+}
+
+# Check related-work map
+$relatedWorkFile = Join-Path $litDir "related-work.md"
+if (Test-Path $relatedWorkFile) {
+    Write-Host "Related-work map generated"
+} else {
+    Write-Host "WARNING: No related-work map found"
+}
+```
+
+Complete task:
+
+```powershell
+# Mark task complete if quality gates passed
+rc task complete literature-search
+```
+
+## Quality Gates
+
+Verify before marking complete:
+
+```powershell
+# Quality gate checks
+$passed = $true
+
+# Gate 1: Minimum baselines
+$baselinesFile = "C:\PythonProject\research_copilot\.rc\literature\baselines.json"
+if (Test-Path $baselinesFile) {
+    $baselines = Get-Content $baselinesFile | ConvertFrom-Json
+    if ($baselines.Count -lt 3) {
+        Write-Host "FAIL: Need ≥3 baselines, found $($baselines.Count)"
+        $passed = $false
+    }
+} else {
+    Write-Host "FAIL: No baselines file"
+    $passed = $false
+}
+
+# Gate 2: Category coverage
+$papersFile = "C:\PythonProject\research_copilot\.rc\literature\papers.json"
+if (Test-Path $papersFile) {
+    $papers = Get-Content $papersFile | ConvertFrom-Json
+    $categories = $papers | Select-Object -ExpandProperty category -Unique
+    if ($categories.Count -lt 2) {
+        Write-Host "FAIL: Need ≥2 categories, found $($categories.Count)"
+        $passed = $false
+    }
+} else {
+    Write-Host "FAIL: No papers file"
+    $passed = $false
+}
+
+# Gate 3: PRD claim support
+$prdFile = "C:\PythonProject\research_copilot\.rc\prd.md"
+if (Test-Path $prdFile) {
+    $prd = Get-Content $prdFile -Raw
+    $claims = [regex]::Matches($prd, '\[CLAIM:([^\]]+)\]')
+    $supportedClaims = 0
+    
+    foreach ($claim in $claims) {
+        $claimId = $claim.Groups[1].Value
+        $citationPattern = "\[$claimId\]"
+        if ($prd -match $citationPattern) {
+            $supportedClaims++
+        }
+    }
+    
+    if ($supportedClaims -lt $claims.Count) {
+        Write-Host "FAIL: Only $supportedClaims/$($claims.Count) claims supported"
+        $passed = $false
+    }
+}
+
+if ($passed) {
+    Write-Host "All quality gates passed"
+} else {
+    Write-Host "Quality gates failed - review needed"
+}
+```
+
+## Report Format
+
+Generate final report:
+
+```markdown
+# Literature Search Report
+
+**Query**: {user_query}
+**Date**: {date}
+**Baselines Found**: {baseline_count}
+**Papers Reviewed**: {paper_count}
+
+## Baselines
+
+| Method | Year | Metric | Score | Paper |
+|--------|------|--------|-------|-------|
+| {name} | {year} | {metric} | {score} | [{title}]({url}) |
+
+## Paper Categories
+
+- **Methods**: {count} papers
+- **Surveys**: {count} papers
+- **Applications**: {count} papers
+
+## Related Work Map
+
+{content from related-work.md}
+
+## Key Findings
+
+- Finding 1
+- Finding 2
+- Finding 3
+
+## Next Steps
+
+- [ ] Review baselines for integration
+- [ ] Extract method details from top papers
+- [ ] Update PRD with new citations
+```
+
+## Example Usage
+
+```
+User: "Search papers on graph neural networks for recommendation"

package/dist/skills/paper-polish/SKILL.md

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+---
+name: paper-polish
+description: Polishes paper text and removes AI patterns. Use after writing stage to refine language and ensure venue compliance.
+triggers:
+  - "polish paper"
+  - "de-AI"
+  - "remove AI flavor"
+  - "refine writing"
+  - "clean up text"
+---
+
+# Paper Polish
+
+Orchestrate paper polishing: create task → dispatch @rc-polisher → verify changes → complete.
+
+Removes AI-generated patterns, ensures venue style compliance, validates that only wording changed (no data/formulas modified).
+
+## When to Use
+
+Use this skill when:
+- User asks to "polish the paper"
+- User wants to "remove AI patterns" or "de-AI the text"
+- After drafting is complete and paper needs language refinement
+- Before final submission to ensure professional writing style
+
+Do NOT use when:
+- Paper is still being drafted (use writing skills)
+- User wants content changes (use revision skills)
+- Only formatting/LaTeX fixes needed (handle directly)
+
+## Task-First Protocol
+
+Before starting, check if polish task exists:
+
+```powershell
+# Check for existing polish task
+$taskFile = "C:\PythonProject\research_copilot\.rc\tasks\paper-polish.json"
+if (Test-Path $taskFile) {
+    $task = Get-Content $taskFile | ConvertFrom-Json
+    Write-Host "Found existing polish task: $($task.paper_file)"
+} else {
+    Write-Host "No existing task. Will create one."
+}
+```
+
+Create task if needed:
+
+```powershell
+# Create paper polish task
+$paperFile = "paper_draft.tex"  # Or user-specified file
+rc task create --type polish --paper $paperFile --output .rc/tasks/paper-polish.json
+```
+
+## Auto-Context Loading
+
+Read all context files before orchestration:
+
+```powershell
+# Load task context
+$taskFile = "C:\PythonProject\research_copilot\.rc\tasks\paper-polish.json"
+if (Test-Path $taskFile) {
+    $task = Get-Content $taskFile | ConvertFrom-Json
+    Write-Host "Paper file: $($task.paper_file)"
+    
+    # Load PRD for research context
+    $prdFile = "C:\PythonProject\research_copilot\.rc\prd.md"
+    if (Test-Path $prdFile) {
+        $prd = Get-Content $prdFile -Raw
+        Write-Host "PRD loaded for context"
+    }
+    
+    # Load venue specification
+    $venueFile = "C:\PythonProject\research_copilot\.rc\venue\spec.json"
+    if (Test-Path $venueFile) {
+        $venue = Get-Content $venueFile | ConvertFrom-Json
+        Write-Host "Venue: $($venue.name)"
+        Write-Host "Style guide: $($venue.style_guide)"
+    } else {
+        Write-Host "WARNING: No venue spec found"
+    }
+    
+    # Load writing conventions
+    $conventionsFile = "C:\PythonProject\research_copilot\.rc\writing\conventions.md"
+    if (Test-Path $conventionsFile) {
+        Write-Host "Writing conventions loaded"
+    }
+}
+```
+
+## Orchestration Logic
+
+Execute polishing via agent dispatch:
+
+```powershell
+# Start task
+rc task start paper-polish
+
+# Create backup before polishing
+$paperFile = "paper_draft.tex"
+$backupFile = "paper_draft.backup.tex"
+Copy-Item $paperFile $backupFile -Force
+Write-Host "Backup created: $backupFile"
+
+# Dispatch to polisher agent
+Write-Host "Dispatching to @rc-polisher agent..."
+
+# Agent will:
+# 1. Scan for AI patterns (excessive adjectives, mechanical transitions)
+# 2. Check venue style compliance (citation format, section structure)
+# 3. Refine wording while preserving meaning
+# 4. Ensure no numbers/formulas are modified
+# 5. Generate diff showing only text changes
+# 6. Save polished version to paper_polished.tex
+
+# Wait for completion
+$status = rc task status paper-polish
+Write-Host "Task status: $status"
+```
+
+Verify polishing results:
+
+```powershell
+# Verify polish outputs
+$polishedFile = "paper_polished.tex"
+
+if (-not (Test-Path $polishedFile)) {
+    Write-Host "ERROR: Polished file not generated"
+    exit 1
+}
+
+# Check that file was actually modified
+$originalSize = (Get-Item $paperFile).Length
+$polishedSize = (Get-Item $polishedFile).Length
+if ($originalSize -eq $polishedSize) {
+    Write-Host "WARNING: File sizes identical - may be no changes"
+}
+
+# Verify polish report exists
+$reportFile = "C:\PythonProject\research_copilot\.rc\polish\report.md"
+if (Test-Path $reportFile) {
+    Write-Host "Polish report generated"
+} else {
+    Write-Host "WARNING: No polish report found"
+}
+```
+
+Complete task:
+
+```powershell
+# Mark task complete if quality gates passed
+rc task complete paper-polish
+```
+
+## Quality Gates
+
+Verify before marking complete:
+
+```powershell
+# Quality gate checks
+$passed = $true
+
+# Gate 1: No AI patterns remain
+$polishedFile = "paper_polished.tex"
+if (Test-Path $polishedFile) {
+    $content = Get-Content $polishedFile -Raw
+    
+    # Check for AI patterns
+    $aiPatterns = @(
+        'very\s+important',
+        'highly\s+significant',
+        'it\s+is\s+worth\s+noting',
+        'arguably',
+        'In\s+conclusion,\s+we\s+have',
+        'Furthermore,\s+we',
+        'Moreover,\s+it',
+        'bullet\s+list'
+    )
+    
+    $patternsFound = @()
+    foreach ($pattern in $aiPatterns) {
+        if ($content -match $pattern) {
+            $patternsFound += $pattern
+        }
+    }
+    
+    if ($patternsFound.Count -gt 0) {
+        Write-Host "FAIL: AI patterns found: $($patternsFound -join ', ')"
+        $passed = $false
+    }
+} else {
+    Write-Host "FAIL: No polished file"
+    $passed = $false
+}
+
+# Gate 2: Venue style compliance
+$venueFile = "C:\PythonProject\research_copilot\.rc\venue\spec.json"
+if (Test-Path $venueFile) {
+    $venue = Get-Content $venueFile | ConvertFrom-Json
+    
+    # Check citation format
+    if ($venue.citation_style -eq "numeric") {
+        if ($content -notmatch '\\\cite\{[^\}]+\}') {
+            Write-Host "FAIL: No numeric citations found"
+            $passed = $false
+        }
+    }
+    
+    # Check section structure
+    $requiredSections = @('Introduction', 'Related Work', 'Method', 'Experiments', 'Conclusion')
+    foreach ($section in $requiredSections) {
+        if ($content -notmatch "\\section\{$section\}") {
+            Write-Host "FAIL: Missing required section: $section"
+            $passed = $false
+        }
+    }
+}
+
+# Gate 3: Diff verification (only wording changed)
+$diffFile = "C:\PythonProject\research_copilot\.rc\polish\diff.txt"
+if (Test-Path $diffFile) {
+    $diff = Get-Content $diffFile -Raw
+    
+    # Check that no numbers were modified
+    $numberChanges = [regex]::Matches($diff, '-.*\d+.*\n\+.*\d+')
+    if ($numberChanges.Count -gt 0) {
+        Write-Host "WARNING: Numbers may have been modified - manual review needed"
+    }
+    
+    # Check that no formulas were modified
+    $formulaChanges = [regex]::Matches($diff, '-.*\$.*\$.*\n\+.*\$.*\$')
+    if ($formulaChanges.Count -gt 0) {
+        Write-Host "WARNING: Formulas may have been modified - manual review needed"
+    }
+} else {
+    Write-Host "WARNING: No diff file found"
+}
+
+if ($passed) {
+    Write-Host "All quality gates passed"
+} else {
+    Write-Host "Quality gates failed - review needed"
+}
+```
+
+## Report Format
+
+Generate final report:
+
+```markdown
+# Paper Polish Report
+
+**Paper**: {paper_file}
+**Date**: {date}
+**AI Patterns Removed**: {pattern_count}
+**Changes Made**: {change_count}
+
+## AI Patterns Removed
+
+- Excessive adjectives: {count} instances
+- Mechanical transitions: {count} instances  
+- Bullet lists in prose: {count} instances
+- Hedging phrases: {count} instances
+
+## Venue Style Compliance
+
+✓ Citation format: {venue.citation_style}
+✓ Section structure: {venue.required_sections}
+✓ Page limit: {current_pages}/{venue.page_limit}
+
+## Diff Verification
+
+✓ Only wording changed
+✓ No numbers modified
+✓ No formulas modified
+✓ No citations removed
+
+## Key Changes
+
+1. Changed "very important" → "critical"
+2. Removed "It is worth noting that"
+3. Simplified "Furthermore, we observe" → "We observe"
+
+## Files Generated
+
+- `paper_polished.tex`: Polished version
+- `paper_draft.backup.tex`: Original backup
+- `.rc/polish/diff.txt`: Detailed changes
+- `.rc/polish/report.md`: This report
+
+## Next Steps
+
+- [ ] Review polished version
+- [ ] Compile LaTeX to verify formatting
+- [ ] Run sanity-check before submission
+```
+
+## Error Recovery
+
+If polishing fails:
+
+```powershell
+# Restore from backup
+$backupFile = "paper_draft.backup.tex"
+if (Test-Path $backupFile) {
+    Copy-Item $backupFile $paperFile -Force
+    Write-Host "Restored from backup"
+}
+
+# Check agent error log
+$errorLog = "C:\PythonProject\research_copilot\.rc\polish\error.log"
+if (Test-Path $errorLog) {
+    $error = Get-Content $errorLog -Raw
+    Write-Host "Agent error: $error"
+}
+```
+
+## Example Usage
+
+```
+User: "Polish the paper and remove AI patterns"