System Diagnostician

What this skill does

# System Diagnostician

**Analyze project health and recommend capabilities using Codex-powered system understanding**

## Purpose

Performs comprehensive project health analysis to diagnose issues, identify missing capabilities, and recommend improvements. Uses Codex to understand project structure, detect anti-patterns, analyze dependencies, and suggest optimal capability additions based on project goals.

## When to Use

- New project onboarding: "What does this project need?"
- Health checks: "Is this project following best practices?"
- Gap analysis: "What's missing to achieve X?"
- Performance audits: "Why is this slow?"
- Security audits: "What security risks exist?"
- Dependency audits: "Are dependencies up to date and safe?"

## Key Capabilities

- **Project Structure Analysis**: Understands project type, framework, architecture
- **Capability Gap Detection**: Identifies missing or incomplete capabilities
- **Health Scoring**: Quantifies project health across multiple dimensions
- **Recommendation Engine**: Suggests capabilities with impact/effort estimates
- **Dependency Analysis**: Checks for outdated, vulnerable, or unnecessary dependencies
- **Anti-Pattern Detection**: Identifies code smells and architectural issues
- **Prioritized Action Plan**: Orders recommendations by impact and effort

## Inputs

```yaml
inputs:
  project_path: string # Path to project directory
  capability_graph: string # Path to capability-graph.json
  focus_areas: array # Optional: ["security", "performance", "testing"]
  include_metrics: boolean # Include detailed metrics (default: false)
```

## Process

### Step 1: Project Discovery

```bash
#!/bin/bash
# Analyze project structure

PROJECT_PATH="${1:-.}"
cd "$PROJECT_PATH"

echo "Discovering project structure..."

# Detect project type
PROJECT_TYPE="unknown"
FRAMEWORK="unknown"

if [ -f "package.json" ]; then
  PROJECT_TYPE="nodejs"

  # Detect framework
  if grep -q "\"next\"" package.json; then
    FRAMEWORK="nextjs"
  elif grep -q "\"react\"" package.json; then
    FRAMEWORK="react"
  elif grep -q "\"express\"" package.json; then
    FRAMEWORK="express"
  fi
elif [ -f "requirements.txt" ] || [ -f "pyproject.toml" ]; then
  PROJECT_TYPE="python"
fi

# Gather file statistics
FILE_COUNT=$(find . -type f -not -path "./node_modules/*" -not -path "./.git/*" | wc -l)
CODE_FILES=$(find . -name "*.js" -o -name "*.ts" -o -name "*.jsx" -o -name "*.tsx" -o -name "*.py" | wc -l)
TEST_FILES=$(find . -name "*.test.*" -o -name "*.spec.*" | wc -l)

# Check for common directories
HAS_TESTS=$([ -d "tests" ] || [ -d "test" ] || [ -d "__tests__" ] && echo "true" || echo "false")
HAS_DOCS=$([ -f "README.md" ] && echo "true" || echo "false")
HAS_CI=$([ -d ".github/workflows" ] || [ -f ".gitlab-ci.yml" ] && echo "true" || echo "false")

# Package.json analysis
if [ -f "package.json" ]; then
  DEPENDENCIES=$(jq -r '.dependencies // {} | keys | length' package.json)
  DEV_DEPENDENCIES=$(jq -r '.devDependencies // {} | keys | length' package.json)
  SCRIPTS=$(jq -r '.scripts // {} | keys | length' package.json)
fi

# Generate project state
cat > /tmp/project-state.json <<EOF
{
  "project_type": "$PROJECT_TYPE",
  "framework": "$FRAMEWORK",
  "statistics": {
    "total_files": $FILE_COUNT,
    "code_files": $CODE_FILES,
    "test_files": $TEST_FILES
  },
  "has_tests": $HAS_TESTS,
  "has_docs": $HAS_DOCS,
  "has_ci": $HAS_CI,
  "dependencies": ${DEPENDENCIES:-0},
  "dev_dependencies": ${DEV_DEPENDENCIES:-0},
  "scripts": ${SCRIPTS:-0}
}
EOF
```

### Step 2: Health Assessment with Codex

```bash
# Use Codex to assess project health
PROJECT_STATE=$(cat /tmp/project-state.json)

# Get file listing for context
FILE_STRUCTURE=$(find . -type f -not -path "./node_modules/*" -not -path "./.git/*" | head -100)

codex exec "
Analyze this project's health and identify issues:

PROJECT STATE:
$PROJECT_STATE

FILE STRUCTURE (first 100 files):
$FILE_STRUCTURE

PACKAGE.JSON:
$(cat package.json 2>/dev/null || echo "{}")

Perform health assessment across these dimensions:

1. **Testing**: Test coverage, test quality, missing tests
2. **Documentation**: README quality, API docs, comments
3. **Security**: Vulnerabilities, exposed secrets, auth patterns
4. **Performance**: Bottlenecks, optimization opportunities
5. **Code Quality**: Linting, formatting, type safety
6. **Architecture**: Structure, patterns, scalability
7. **Dependencies**: Outdated packages, security issues, bloat
8. **CI/CD**: Automation, deployment strategy

For each dimension, provide:
- score: 0.0-1.0
- status: \"excellent\" | \"good\" | \"needs_improvement\" | \"critical\"
- issues: array of problems found
- recommendations: array of specific actions

Output JSON:
{
  \"overall_health\": 0.75,
  \"dimensions\": {
    \"testing\": {
      \"score\": 0.60,
      \"status\": \"needs_improvement\",
      \"issues\": [\"Only 15% test coverage\", \"No E2E tests\"],
      \"recommendations\": [\"Add unit tests for core functions\", \"Set up Playwright for E2E\"]
    },
    \"security\": {
      \"score\": 0.50,
      \"status\": \"critical\",
      \"issues\": [\"No input validation\", \"SQL injection possible\"],
      \"recommendations\": [\"Add input sanitization\", \"Use parameterized queries\"]
    }
  }
}

Output ONLY valid JSON.
" > /tmp/health-assessment.json
```

### Step 3: Capability Gap Analysis

```bash
# Identify missing capabilities using capability graph
HEALTH_ASSESSMENT=$(cat /tmp/health-assessment.json)
CAPABILITY_GRAPH=$(cat META/capability-graph.json)

codex exec "
Based on this health assessment, identify missing or incomplete capabilities:

HEALTH ASSESSMENT:
$HEALTH_ASSESSMENT

AVAILABLE CAPABILITIES:
$CAPABILITY_GRAPH

For each identified issue, suggest capabilities that would address it.

Output JSON:
{
  \"gaps\": [
    {
      \"issue\": \"No input validation\",
      \"severity\": \"high\",
      \"dimension\": \"security\",
      \"suggested_capabilities\": [\"security-engineer\", \"input-validator-mcp\"],
      \"impact\": \"high\",
      \"effort\": \"medium\"
    }
  ]
}

Output ONLY valid JSON.
" > /tmp/capability-gaps.json
```

### Step 4: Generate Recommendations

```bash
# Prioritize recommendations by impact and effort
python3 <<'PYTHON_SCRIPT'
import json

# Load data
with open('/tmp/health-assessment.json') as f:
    health = json.load(f)

with open('/tmp/capability-gaps.json') as f:
    gaps = json.load(f)

# Score recommendations
for gap in gaps['gaps']:
    # Impact score
    impact_scores = {'critical': 1.0, 'high': 0.8, 'medium': 0.5, 'low': 0.3}
    impact = impact_scores.get(gap.get('impact', 'medium'), 0.5)

    # Effort score (inverted - lower effort = higher score)
    effort_scores = {'low': 1.0, 'medium': 0.6, 'high': 0.3}
    effort = effort_scores.get(gap.get('effort', 'medium'), 0.6)

    # Priority = impact * effort
    gap['priority_score'] = round(impact * effort, 3)

# Sort by priority
gaps['gaps'].sort(key=lambda x: x['priority_score'], reverse=True)

# Write prioritized gaps
with open('/tmp/recommendations.json', 'w') as f:
    json.dump(gaps, f, indent=2)

print(f"Generated {len(gaps['gaps'])} recommendations")
PYTHON_SCRIPT
```

### Step 5: Generate Action Plan

```bash
# Create structured action plan
python3 <<'PYTHON_SCRIPT'
import json
from datetime import datetime

# Load all data
with open('/tmp/health-assessment.json') as f:
    health = json.load(f)

with open('/tmp/recommendations.json') as f:
    recommendations = json.load(f)

# Generate action plan
action_plan = {
    'project': 'PROJECT_NAME',
    'analyzed_at': datetime.utcnow().isoformat() + 'Z',
    'overall_health': health.get('overall_health', 0),
    'health_assessment': health,
    'recommendations': recommendations['gaps'][:10],  # Top 10
    'quick_wins': [
        r for r in recommendations['gaps']
        if r.get('effort') == 'low' and r.get('impact') in ['high', 'critical']
    ][:3],
    'critical_issues': [
        r for r in recommendations['gaps'