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- Changed resource setup commands to setup commands in cli.js, db.js, agent-registry.js, pack-flags.js, and registry.js. - Updated help text in index.js to reflect new setup commands. - Introduced workflow status evaluation in workflow-status.js to enhance workflow readiness checks. - Modified workspace-status.js to derive setup readiness based on workflow evaluation. - Removed legacy resource commands and references to research and design commands. - Improved code formatting and consistency across various files.
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