Group Agent loose fields into RuntimeConfig struct

Part of #391

## Problem

Agent struct has ~30 fields. Partially addressed with MemoryState, SkillState, etc., but remaining loose fields (security, timeouts, model_name, cost_tracker, permission_policy) are ungrouped.

**File:** `crates/zeph-core/src/agent/mod.rs` lines 99-131

## Proposed Solution

Group remaining fields into a `RuntimeConfig` struct.

**Priority:** P2 | **Effort:** Medium