Refactor setup engine into smaller phases

[cedric013]

Problem

run_setup_with_options has grown into a large setup engine that mixes orchestration with shell hook setup, daemon setup, editor configuration, rules injection, skill installation, proxy setup, doctor checks, indexing, and report persistence. That makes the setup flow harder to review and maintain because each phase is embedded in one long function.

Proposed change

Refactor the setup engine conservatively by keeping run_setup_with_options as the orchestrator and moving each phase into private helper functions. Preserve the existing execution order, report wording, and side effects.

Validation

• rustfmt --check src/setup/mod.rs
• git diff --check -- rust/src/setup/mod.rs
• VS Code diagnostics for rust/src/setup/mod.rs: no errors