refactor/config: split ApplyRequest and applyDefaults into helpers #95
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Delete branch "refactor/complexity-config"
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Part of #71, the config slice. Merge this one first: applyDefaults crossed Sonar cognitive complexity 25 when #89 added the discover_depth default, and it is the single new-code issue failing the main quality gate right now. applyDefaults now delegates to applyMCPDefaults, applyToolDefaults and applyMCPServerDefaults with the copy, mutate, write-back loop semantics unchanged. ApplyRequest, at 39, delegates to checkDenyConflict, ensureAllowSeq, findRuleBySubcommand and mergeRuleFlags, deny check still first with the same text, validate then atomic write untouched. Reviewer pass dumped the defaulted Config for the scaffold and four hand-written configs and ran 24 ApplyRequest scenarios on main and on this branch, all byte-identical. No test changed. 🤖 Generated with Claude Code