@research-copilot/plugin 1.1.15

package/dist/skills/sanity-check/SKILL.md

@@ -0,0 +1,449 @@
+---
+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"