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The runtime now discovers both legacy and current Claude config files at user and project scope, merges them in precedence order, and carries the resolved model, permission mode, instruction files, and MCP server configuration into session startup. This keeps CLI defaults aligned with project policy and exposes configured MCP tools without requiring manual flags. Constraint: Must support both legacy .claude.json and current .claude/settings.json layouts Constraint: Session startup must preserve CLI flag precedence over config defaults Rejected: Read only project settings files | would ignore user-scoped defaults and MCP servers Rejected: Delay MCP tool discovery until first tool call | model would not see configured MCP tools during planning Confidence: high Scope-risk: moderate Reversibility: clean Directive: Keep config precedence synchronized between prompt loading, session startup, and status reporting Tested: cargo fmt --all --check; cargo clippy --workspace --all-targets --all-features -- -D warnings; cargo test --workspace --all-features Not-tested: Live remote MCP servers and interactive REPL session startup against external services