w1b: Reload all effective config sources without restart

[penso]

Automated handoff for w1b.

Issue:
Base branch: main
Head branch: beads-polyphony-w1b
Commit: 3019910

[penso]

Summary

This branch fixes a real gap in workflow reload detection by fingerprinting the user config file and by adding watch targets for missing config/prompt paths. The targeted orchestrator tests I ran for the new fingerprint and reload cases passed.

I found one correctness risk in the new watcher fallback logic.

Risks

• crates/orchestrator/src/handoff.rs:516 can fall back to a recursive watch on the entire workflow root when .polyphony/agents does not exist. That is much broader than the actual config surface. Every unrelated file change under the repo can now emit RuntimeCommand::Refresh, and the runtime currently handles that by clearing throttles before forcing a reload (crates/orchestrator/src/runtime.rs:91 and crates/orchestrator/src/runtime.rs:112). In practice, ordinary source edits can reset rate-limit/backoff state and cause noisy manual-refresh behavior even when no workflow input changed.

Recommended human checks

• Start the orchestrator with no repo .polyphony/agents directory, edit an unrelated tracked file, and confirm that it does not trigger a workflow refresh or clear throttles.
• Exercise a provider-throttled state, then touch unrelated repo files, and confirm the throttle window is preserved.
• Create the missing repo/user config and agent prompt paths from a cold start and confirm reload still happens when those inputs actually appear.