R4: decompose oversized files

[bug-ops]

Epic: #268 | Phase: 3 — Decomposition | Priority: P1 | Complexity: L

Tasks

R4.1 — config.rs (2937 LOC) [L]

Split into config/mod.rs + config/types.rs + config/env.rs + config/parse.rs.

R4.2 — sqlite.rs (1689 LOC) [M]

Split into sqlite/mod.rs + sqlite/messages.rs + sqlite/skills.rs + sqlite/summaries.rs.

R4.3 — orchestrator.rs (1174 LOC) [M]

Split into orchestrator/mod.rs + orchestrator/classifier.rs + orchestrator/router.rs.

R4.4 — shell.rs execute_bash (77 LOC) [S]

Extract timeout handling and output collection into helpers.

All tasks are independent and can be parallelized.