docs: add code-intelligence.md, update README + AGENT.md for Phase 1-3

[ajianaz]

Summary

Adds missing documentation for Code Intelligence and Brain Mode features (Phase 1-3), and updates stale AGENT.md for AI agents.

Changes

New

• docs/code-intelligence.md — comprehensive guide for:
  • cora index (multi-project, 15 languages, schema v4)
  • cora brain (hybrid search: FTS5 + usearch KNN + graph BFS → RRF k=60)
  • cora trace, cora arch, cora callers, cora impact, cora affected
  • Data directory structure (~/.codecora/cora-code/)
  • Schema versioning (v1→v4)
  • Embedding engine explanation (static tokens, 256d)
  • MCP integration tools

Updated

• README.md:
  • Tagline updated: “code review and code intelligence”
  • 5 new bullets in “Why Cora”: Code Intelligence, Brain Mode, Multi-project DB, tree-sitter, MCP 15 tools
  • Commands table reorganized into 3 sections: Code Review / Code Intelligence / Config
• AGENT.md:
  • Project overview expanded (review + intelligence)
  • Test count: 567 → 708
  • src/ tree updated: added embed/, data_dir.rs, brain_cmd.rs, trace_cmd.rs, arch_cmd.rs, vector.rs, brain.rs
  • MCP tool count: 5 → 15
  • Key files table: added brain.rs, vector.rs, schema.rs, tokens.rs
  • Pre-release checklist: added code-intelligence.md check
  • External submissions: updated metrics (708 tests, 26.4K LOC, 15 tools)

Motivation

Code Intelligence and Brain Mode represent ~2K lines of new code across 3 phases (PR #338-362) but had zero user-facing documentation. A new user or AI agent reading the docs would have no idea these features exist.

Testing

• cargo clippy -- -D warnings — clean
• cargo test — 708 pass
• cargo fmt --check — clean