Fix parseArgs flag handling for --variables option

[Copilot]

The --variables flag was checked via process.argv.includes('--variables') instead of using the parsed value, breaking syntaxes like --variables=true and being inconsistent with parseArgs patterns.

Changes

• Use Boolean(values.variables) instead of process.argv.includes('--variables') to match existing --diagram flag pattern
• Supports all flag syntaxes: --variables, --variables=true, etc.

// Before
const includeVariables = process.argv.includes('--variables');

// After  
const includeVariables = Boolean(values.variables);

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