Two bugs caused workflow.research to silently reset to false:
1. new-milestone.md unconditionally overwrote workflow.research via
config-set after asking about research — coupling a per-milestone
decision to a persistent user preference. Now the research question
is per-invocation only; persistent config changes via /gsd:settings.
2. verify.cjs health repair (createConfig/resetConfig) used flat keys
(research, plan_checker, verifier) instead of the canonical nested
workflow object from config.cjs, also missing branch templates,
nyquist_validation, and brave_search fields.
Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>
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