docs: update MCP tool inventory and deprecate manage_code_ux

[numnx]

• Marked manage_code_ux as deprecated in tools-and-contracts, mcp-tools, and management-actions docs.
• Replaced legacy setting routes manage_code_ux with manage_settings in settings-reference.md.
• Added search_knowledge to the domains list in management-actions.md.
• Added documentation for missing alias payload fields (model for agentPresetId, and flattened target fields for schedule/execute calls) to tools-and-contracts.md.

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PR created automatically by Jules for task 11285896668018151551 started by @numnx

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