feat: add visual graph export, path tracing CLI, architecture metrics, code health audit, and MCP extensions

[Jaymr1031-Z]

Summary of Changes

This PR introduces 5 major enhancements to CodeGraph to extend its visual exporting, pathfinding, architectural metric analysis, dead code auditing, and MCP agent tool capabilities:

1. Visual Graph Exporter (codegraph export):

   • Added support for exporting code knowledge subgraphs and symbol call/impact graphs into Mermaid.js, Graphviz DOT, and JSON Graph formats.
   • Ideal for generating architecture diagrams in markdown documentation and CI/CD artifacts.

2. Multi-Hop Call & Dependency Path Tracing (codegraph trace <from> <to>):

   • Added CLI and API methods (findPathBetweenSymbols) to compute and visually render multi-hop traversal paths between any two symbols.

3. Architectural & Coupling Metrics (codegraph metrics):

   • Implemented MetricsAnalyzer to calculate file-level Afferent Coupling ($C_a$), Efferent Coupling ($C_e$), and Instability Index ($I = C_e / (C_a + C_e)$).
   • Detects structural hotspots with high fan-in, high fan-out, and large blast radii.

4. Code Health & Dead Code Audit (codegraph audit):

   • Scans the codebase for unreferenced non-exported dead symbols and cyclic file dependencies.

5. MCP Tool Suite Extension:

   • Registered and exposed codegraph_trace, codegraph_export, and codegraph_metrics tools to MCP clients (Claude Code, Cursor, Codex, etc.).

---

Verification & Tests

• Added comprehensive unit tests in __tests__/secondary-features.test.ts (13/13 tests passing).
• Verified full TypeScript compilation (npm run build) and asset bundling.
• Verified CLI subcommands output via codegraph --help.