@research-copilot/plugin 1.1.15 → 1.1.16

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

@@ -1,244 +0,0 @@
----
-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/sanity-check/SKILL.md

@@ -1,449 +0,0 @@
----
-name: sanity-check
-description: Final 6-dimension sanity check (logic/citation/reproducibility/novelty/venue/de-AI). Use before submission for comprehensive audit.
-triggers:
-  - "sanity check"
-  - "final check"
-  - "audit paper"
-  - "pre-submission audit"
-  - "verify paper ready"
----
-
-# Sanity Check
-
-Final 6-dimension audit without making changes. Verifies paper is submission-ready across all critical dimensions.
-
-## When to Use
-
-Use this skill when:
-- User asks to "sanity check the paper"
-- Paper is ready for final audit before submission
-- After submission sprint completes
-- User wants to "verify paper is ready"
-
-Do NOT use when:
-- Paper needs changes (use submission-sprint or review skills)
-- User wants specific issue fixed (handle directly)
-- Paper is still being drafted (too early)
-
-## Task-First Protocol
-
-Before starting, check if sanity-check task exists:
-
-```powershell
-# Check for existing sanity-check task
-$taskFile = "C:\PythonProject\research_copilot\.rc\tasks\sanity-check.json"
-if (Test-Path $taskFile) {
-    $task = Get-Content $taskFile | ConvertFrom-Json
-    Write-Host "Found existing sanity-check task for: $($task.paper_file)"
-} else {
-    Write-Host "No existing task. Will create one."
-}
-```
-
-Create task if needed:
-
-```powershell
-# Create sanity-check task
-$paperFile = "paper_polished.tex"  # Or user-specified file
-rc task create --type sanity-check --paper $paperFile --output .rc/tasks/sanity-check.json
-```
-
-## Auto-Context Loading
-
-Read all context files before audit:
-
-```powershell
-# Load task context
-$taskFile = "C:\PythonProject\research_copilot\.rc\tasks\sanity-check.json"
-if (Test-Path $taskFile) {
-    $task = Get-Content $taskFile | ConvertFrom-Json
-    Write-Host "Paper file: $($task.paper_file)"
-    
-    # Load PRD for research requirements
-    $prdFile = "C:\PythonProject\research_copilot\.rc\prd.md"
-    if (Test-Path $prdFile) {
-        $prd = Get-Content $prdFile -Raw
-        Write-Host "PRD loaded"
-    }
-    
-    # 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)"
-    }
-    
-    # Load novelty spec
-    $noveltyFile = "C:\PythonProject\research_copilot\.rc\spec\novelty.md"
-    if (Test-Path $noveltyFile) {
-        Write-Host "Novelty spec loaded"
-    }
-    
-    # Load writing conventions
-    $conventionsFile = "C:\PythonProject\research_copilot\.rc\writing\conventions.md"
-    if (Test-Path $conventionsFile) {
-        Write-Host "Writing conventions loaded"
-    }
-}
-```
-
-## Orchestration Logic
-
-Execute 6-dimension audit via @rc-reviewer agent:
-
-```powershell
-# Start task
-rc task start sanity-check
-
-Write-Host "Starting 6-dimension sanity check..."
-
-# Dispatch to reviewer agent with comprehensive 6-dimension prompt
-Write-Host "Dispatching to @rc-reviewer agent..."
-
-# Agent audits 6 dimensions (no changes made):
-# 1. Logic: Claims → Evidence chain complete
-# 2. Citations: All baselines cited, no orphan references
-# 3. Reproducibility: Config/seed/data documented
-# 4. Novelty: Claims match spec/novelty/
-# 5. Venue compliance: Format/length/template correct
-# 6. De-AI: No AI patterns remain
-
-# Wait for completion
-$status = rc task status sanity-check
-Write-Host "Task status: $status"
-```
-
-## 6 Dimensions
-
-### Dimension 1: Logic Integrity
-
-Check claims → evidence chain:
-
-```powershell
-# Verify logic dimension
-$logicFile = "C:\PythonProject\research_copilot\.rc\sanity\logic.json"
-if (Test-Path $logicFile) {
-    $logic = Get-Content $logicFile | ConvertFrom-Json
-    
-    Write-Host "`nDimension 1: Logic"
-    Write-Host "Claims checked: $($logic.claims_checked)"
-    Write-Host "Evidence gaps: $($logic.evidence_gaps.Count)"
-    
-    if ($logic.evidence_gaps.Count -eq 0) {
-        Write-Host "✓ All claims have supporting evidence"
-    } else {
-        Write-Host "✗ Evidence gaps found:"
-        foreach ($gap in $logic.evidence_gaps) {
-            Write-Host "  - $($gap.claim) ($($gap.location))"
-        }
-    }
-}
-```
-
-### Dimension 2: Citation Completeness
-
-Check all baselines cited and no orphan references:
-
-```powershell
-# Verify citations dimension
-$citationsFile = "C:\PythonProject\research_copilot\.rc\sanity\citations.json"
-if (Test-Path $citationsFile) {
-    $citations = Get-Content $citationsFile | ConvertFrom-Json
-    
-    Write-Host "`nDimension 2: Citations"
-    Write-Host "Total citations: $($citations.total_citations)"
-    Write-Host "Orphan references: $($citations.orphan_refs.Count)"
-    Write-Host "Missing baseline citations: $($citations.missing_baselines.Count)"
-    
-    if ($citations.orphan_refs.Count -eq 0 -and $citations.missing_baselines.Count -eq 0) {
-        Write-Host "✓ All citations complete and referenced"
-    } else {
-        if ($citations.orphan_refs.Count -gt 0) {
-            Write-Host "✗ Orphan references (in .bib but not cited):"
-            foreach ($ref in $citations.orphan_refs) {
-                Write-Host "  - $ref"
-            }
-        }
-        if ($citations.missing_baselines.Count -gt 0) {
-            Write-Host "✗ Missing baseline citations:"
-            foreach ($baseline in $citations.missing_baselines) {
-                Write-Host "  - $baseline"
-            }
-        }
-    }
-}
-```
-
-### Dimension 3: Reproducibility
-
-Check config/seed/data documented:
-
-```powershell
-# Verify reproducibility dimension
-$reproducibilityFile = "C:\PythonProject\research_copilot\.rc\sanity\reproducibility.json"
-if (Test-Path $reproducibilityFile) {
-    $repro = Get-Content $reproducibilityFile | ConvertFrom-Json
-    
-    Write-Host "`nDimension 3: Reproducibility"
-    Write-Host "Config documented: $($repro.config_documented)"
-    Write-Host "Seeds documented: $($repro.seeds_documented)"
-    Write-Host "Data documented: $($repro.data_documented)"
-    Write-Host "Code available: $($repro.code_available)"
-    
-    if ($repro.config_documented -and $repro.seeds_documented -and $repro.data_documented) {
-        Write-Host "✓ Reproducibility requirements met"
-    } else {
-        Write-Host "✗ Missing reproducibility elements:"
-        if (-not $repro.config_documented) { Write-Host "  - Configuration details" }
-        if (-not $repro.seeds_documented) { Write-Host "  - Random seeds" }
-        if (-not $repro.data_documented) { Write-Host "  - Dataset details" }
-    }
-}
-```
-
-### Dimension 4: Novelty Alignment
-
-Check claims match spec/novelty/:
-
-```powershell
-# Verify novelty dimension
-$noveltyFile = "C:\PythonProject\research_copilot\.rc\sanity\novelty.json"
-if (Test-Path $noveltyFile) {
-    $novelty = Get-Content $noveltyFile | ConvertFrom-Json
-    
-    Write-Host "`nDimension 4: Novelty"
-    Write-Host "Novelty claims: $($novelty.claims.Count)"
-    Write-Host "Aligned with spec: $($novelty.aligned_with_spec)"
-    Write-Host "Misalignments: $($novelty.misalignments.Count)"
-    
-    if ($novelty.aligned_with_spec) {
-        Write-Host "✓ Novelty claims match specification"
-    } else {
-        Write-Host "✗ Novelty misalignments:"
-        foreach ($misalignment in $novelty.misalignments) {
-            Write-Host "  - $($misalignment.claim)"
-            Write-Host "    Expected: $($misalignment.expected)"
-            Write-Host "    Found: $($misalignment.found)"
-        }
-    }
-}
-```
-
-### Dimension 5: Venue Compliance
-
-Check format/length/template correct:
-
-```powershell
-# Verify venue compliance dimension
-$venueFile = "C:\PythonProject\research_copilot\.rc\sanity\venue.json"
-if (Test-Path $venueFile) {
-    $venueCheck = Get-Content $venueFile | ConvertFrom-Json
-    
-    Write-Host "`nDimension 5: Venue Compliance"
-    Write-Host "Template correct: $($venueCheck.template_correct)"
-    Write-Host "Page count: $($venueCheck.page_count)/$($venueCheck.page_limit)"
-    Write-Host "Format issues: $($venueCheck.format_issues.Count)"
-    
-    if ($venueCheck.template_correct -and $venueCheck.page_count -le $venueCheck.page_limit -and $venueCheck.format_issues.Count -eq 0) {
-        Write-Host "✓ Venue requirements met"
-    } else {
-        Write-Host "✗ Venue compliance issues:"
-        if (-not $venueCheck.template_correct) { Write-Host "  - Incorrect template" }
-        if ($venueCheck.page_count -gt $venueCheck.page_limit) { Write-Host "  - Exceeds page limit" }
-        foreach ($issue in $venueCheck.format_issues) {
-            Write-Host "  - $issue"
-        }
-    }
-}
-```
-
-### Dimension 6: De-AI Verification
-
-Check no AI patterns remain:
-
-```powershell
-# Verify de-AI dimension
-$deAiFile = "C:\PythonProject\research_copilot\.rc\sanity\de-ai.json"
-if (Test-Path $deAiFile) {
-    $deAi = Get-Content $deAiFile | ConvertFrom-Json
-    
-    Write-Host "`nDimension 6: De-AI"
-    Write-Host "AI patterns found: $($deAi.patterns_found.Count)"
-    Write-Host "Mechanical transitions: $($deAi.mechanical_transitions)"
-    Write-Host "Excessive adjectives: $($deAi.excessive_adjectives)"
-    
-    if ($deAi.patterns_found.Count -eq 0) {
-        Write-Host "✓ No AI patterns detected"
-    } else {
-        Write-Host "✗ AI patterns found:"
-        foreach ($pattern in $deAi.patterns_found) {
-            Write-Host "  - $($pattern.type): '$($pattern.text)' ($($pattern.location))"
-        }
-    }
-}
-```
-
-## Quality Gates
-
-All 6 dimensions must pass:
-
-```powershell
-# Quality gate checks
-$passed = $true
-$dimensions = @()
-
-# Check each dimension
-$dimensionFiles = @{
-    "Logic" = "C:\PythonProject\research_copilot\.rc\sanity\logic.json"
-    "Citations" = "C:\PythonProject\research_copilot\.rc\sanity\citations.json"
-    "Reproducibility" = "C:\PythonProject\research_copilot\.rc\sanity\reproducibility.json"
-    "Novelty" = "C:\PythonProject\research_copilot\.rc\sanity\novelty.json"
-    "Venue" = "C:\PythonProject\research_copilot\.rc\sanity\venue.json"
-    "De-AI" = "C:\PythonProject\research_copilot\.rc\sanity\de-ai.json"
-}
-
-foreach ($dimension in $dimensionFiles.Keys) {
-    $file = $dimensionFiles[$dimension]
-    
-    if (-not (Test-Path $file)) {
-        Write-Host "FAIL: $dimension check not completed"
-        $passed = $false
-        $dimensions += @{ name = $dimension; status = "INCOMPLETE" }
-        continue
-    }
-    
-    $data = Get-Content $file | ConvertFrom-Json
-    
-    # Dimension-specific pass criteria
-    $dimPassed = $false
-    switch ($dimension) {
-        "Logic" { $dimPassed = $data.evidence_gaps.Count -eq 0 }
-        "Citations" { $dimPassed = $data.orphan_refs.Count -eq 0 -and $data.missing_baselines.Count -eq 0 }
-        "Reproducibility" { $dimPassed = $data.config_documented -and $data.seeds_documented -and $data.data_documented }
-        "Novelty" { $dimPassed = $data.aligned_with_spec }
-        "Venue" { $dimPassed = $data.template_correct -and $data.page_count -le $data.page_limit -and $data.format_issues.Count -eq 0 }
-        "De-AI" { $dimPassed = $data.patterns_found.Count -eq 0 }
-    }
-    
-    if ($dimPassed) {
-        $dimensions += @{ name = $dimension; status = "PASS" }
-    } else {
-        $dimensions += @{ name = $dimension; status = "FAIL" }
-        $passed = $false
-    }
-}
-
-# Overall status
-Write-Host "`n=== SANITY CHECK RESULTS ==="
-foreach ($dim in $dimensions) {
-    $icon = if ($dim.status -eq "PASS") { "✓" } else { "✗" }
-    Write-Host "$icon $($dim.name): $($dim.status)"
-}
-
-if ($passed) {
-    Write-Host "`n✓ PAPER READY FOR SUBMISSION"
-    rc task complete sanity-check
-} else {
-    Write-Host "`n✗ PAPER NOT READY - Issues must be resolved"
-    Write-Host "Run submission-sprint to fix remaining issues"
-}
-```
-
-## Report Format
-
-Generate final report:
-
-```markdown
-# Sanity Check Report
-
-**Paper**: {paper_file}
-**Date**: {date}
-**Status**: {READY / NOT_READY}
-
-## 6-Dimension Audit
-
-### ✓ 1. Logic Integrity
-- Claims checked: {count}
-- Evidence gaps: 0
-- **Status**: PASS
-
-### ✓ 2. Citation Completeness
-- Total citations: {count}
-- Orphan references: 0
-- Missing baselines: 0
-- **Status**: PASS
-
-### ✓ 3. Reproducibility
-- Configuration documented: Yes
-- Seeds documented: Yes
-- Data documented: Yes
-- Code availability: Yes
-- **Status**: PASS
-
-### ✓ 4. Novelty Alignment
-- Novelty claims: {count}
-- Aligned with spec: Yes
-- Misalignments: 0
-- **Status**: PASS
-
-### ✓ 5. Venue Compliance
-- Template: Correct
-- Page count: {count}/{limit}
-- Format issues: 0
-- **Status**: PASS
-
-### ✓ 6. De-AI Verification
-- AI patterns: 0
-- Mechanical transitions: 0
-- Excessive adjectives: 0
-- **Status**: PASS
-
-## Overall Assessment
-
-✓ **READY FOR SUBMISSION**
-
-All 6 dimensions passed. Paper meets submission requirements.
-
-## Files Audited
-
-- `paper_polished.tex`: Main paper file
-- `references.bib`: Bibliography
-- `figures/`: All figures
-- `.rc/prd.md`: Research requirements
-- `.rc/spec/novelty.md`: Novelty specification
-- `.rc/venue/spec.json`: Venue requirements
-
-## Next Steps
-
-- [ ] Generate submission package
-- [ ] Upload to venue submission system
-- [ ] Prepare supplementary materials (if required)
-```
-
-## Error Recovery
-
-If any dimension fails:
-
-```powershell
-# Show failed dimensions
-Write-Host "Failed dimensions:"
-foreach ($dim in $dimensions) {
-    if ($dim.status -eq "FAIL") {
-        Write-Host "- $($dim.name)"
-        
-        # Show details
-        $file = $dimensionFiles[$dim.name]
-        $data = Get-Content $file | ConvertFrom-Json
-        
-        # Print specific issues (dimension-dependent)
-    }
-}
-
-Write-Host "`nRecommendation: Run submission-sprint to fix issues"
-```
-
-## Example Usage
-
-```
-User: "Sanity check the paper before submission"