R2: decompose agent.rs god object into module directory

[bug-ops]

Epic: #268 | Phase: 1 — Structural | Priority: P0 | Complexity: L

Problem

agent.rs is 4695 lines with 30+ struct fields. Multiple 80-116 line functions.

Tasks

• R2.6 [S] Convert agent.rs → agent/mod.rs directory
• R2.1 [M] Extract AgentBuilder with builder pattern
• R2.2 [M] Extract MCP subsystem → agent/mcp.rs
• R2.3 [M] Extract self-learning → agent/learning.rs
• R2.5 [M] Extract code index → agent/index.rs
• R2.4 [L] Extract context management → agent/context_manager.rs

Order: R2.6 → R2.1 → (R2.2, R2.3, R2.5) → R2.4