fix(harness): make startup derived-state discovery reproducible

Parent: #384 (P1-3).

## Scope
Remove the clean-checkout contradiction around ignored active-features.json by using authoritative feature lists at startup or mechanically regenerating the derived view.

## Acceptance
- A clean checkout following the standard startup path can discover the unique in-progress feature.
- If a derived file is generated, it is deterministic and equivalent to feature_list.json.
- AGENTS/bootstrap/init instructions agree with behavior.

Delivery discipline: one issue, one worker branch, one PR.

Read the startup path and the AGENTS/bootstrap/init instructions, then compare active-features.json with feature_list.json in a clean checkout. Verify how startup discovers the unique in-progress feature and choose the stated authoritative-list or deterministic-generation path. Done means clean-checkout discovery works, any generated view matches feature_list.json deterministically, and the instructions agree with the behavior.

Written by the indexing model from the issue text.