Deep refactoring: architectural cleanup and deduplication

[bug-ops]

Overview

Deep architectural refactoring of the Zeph codebase (36K LOC, 10 crates). Addresses structural debt, error handling violations, code duplication, and oversized modules.

Plan: .local/plan/refactoring-plan.md

Issues

Phase 1 — Structural (P0)

• R2: decompose agent.rs god object into module directory #269 — Decompose agent.rs god object (4695 LOC) into module directory

Phase 2 — Error Handling (P0)

• R1: migrate library crates from anyhow to thiserror #270 — Migrate 7 library crates from anyhow to thiserror

Phase 3 — Deduplication (P1)

• R3: eliminate code duplication across crates #271 — Eliminate code duplication (Qdrant, file watcher, blake3, test mocks)
• R4: decompose oversized files #272 — Decompose oversized files (config.rs, sqlite.rs, orchestrator.rs)

Phase 4 — Architecture (P1)

• R6+R7: type system improvements and API surface cleanup #273 — Fix architectural layering (CliChannel, Embedder trait)
• R5: fix architectural layering violations #274 — Type system improvements and API surface cleanup

Phase 5 — Polish (P2)

• R9+R10: dependency audit, dead code removal, test expansion #275 — Dependency audit, dead code removal, test expansion

Dependency Graph

#269 (agent decomposition)
  ↓
#270 (error handling) → #271 (deduplication, needs error enums)
  ↓                      ↓
#273 (architecture)    #272 (file decomposition, independent)
  ↓
#274 (types & API)
  ↓
#275 (polish)

Metrics

Priority	Count	Est. Effort
P0	11	~30h
P1	13	~25h
P2	10	~12h
Total	34	~67h