docs: improve README CLI documentation and structure

[shinpr]

Summary

• Add low-poly mole banner with vector space dot cluster
• Split Usage into "Using with MCP" / "Using as CLI" as equal entry points
• Add CLI quick start path alongside MCP setup
• Document CLI configuration with three patterns: flags, env vars, shared config
• Add resolution order (CLI flags > env vars > defaults) with correct examples
• Consolidate env var / CLI flag mapping table in Configuration section (no longer duplicated)
• Warn explicitly that CLI does not read MCP client config files
• Add "Agent reality" paragraph to Why This Exists, connecting CLI + Skills to real-world agent usage
• Promote Configuration from collapsed <details> to a regular section for discoverability
• Update tagline and Features to reflect MCP + CLI parity

Test plan

• Verify banner image renders correctly on GitHub
• Verify all internal anchor links work on GitHub (#agent-skills, #configuration)
• Confirm Configuration section renders correctly (no longer inside <details>)
• Check that collapsed sections (Performance, Troubleshooting, FAQ, Development) still render properly
• Review CLI flag example matches documented global/subcommand option rules

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