- Added `codemode` option to `ReaOptions` for flexible tool behavior.
- Updated `parseOptions` to validate and handle `codemode` correctly.
- Enhanced readiness reporting to include `codemodeToolCount` and `directToolCount`.
- Implemented `countReaToolsByMode` to categorize tools based on their mode.
- Introduced `applyReaToolCatalogPolicy` to manage tool registration and options.
- Registered new commands for REA, ensuring they operate within the context of the server.
- Updated tests to cover new functionality and ensure correctness of tool counts and options.
- Adjusted documentation to reflect changes in options and tool behavior.
T09: register rea (switch to rea agent + staged investigation), rea-doctor (server_readiness check), and rea-report (evidence report + rea-auditor check) via ctx.command.transform. Wire into plugin setup. T09 integration test proves live in-process registration; T04 setup stub gains the command.transform no-op (same pattern as T05/T07). No shadowing of the six rea:<prompt> MCP prompt commands.