docs: add REST API reference for all server endpoints

[akshatmalik-bruh]

Summary

• Created Comprehensive REST API Reference: Added docs/reference/API_REFERENCE.md documenting all 33+ FastAPI router modules exposed by repowise serve (repositories, background jobs, hybrid search, symbols, git intelligence, code health, dead code, architectural decisions, refactoring, workspace, codebase chat, C4 diagrams, webhooks, and cost tracking).
• Documented Authentication & Streaming Protocols: Added formal specifications for Bearer token auth (REPOWISE_API_KEY), error response envelopes, background job SSE progress streams (/api/jobs/{id}/stream), and codebase chat SSE agentic loops (/api/repos/{id}/chat/messages).
• Cross-Linked Architecture Docs: Updated docs/architecture/ARCHITECTURE.md to reference API_REFERENCE.md from the REST API section.

Related Issues

Fixes #2093

Test Plan

• Markdown syntax and relative link resolution verified (API_REFERENCE.md, ARCHITECTURE.md).
• Verified path parameters, query flags, and response schemas against router definitions in packages/server/src/repowise/server/routers/.

Checklist

• My code follows the project's code style
• I have added tests for new functionality (N/A — documentation only)
• All existing tests still pass
• I have updated documentation if needed