Updated several Cursor rules documentation files (`mcp.mdc`, `utilities.mdc`, `architecture.mdc`, `new_features.mdc`, `commands.mdc`) to accurately reflect recent refactoring and clarify best practices.
Key documentation updates include:
- Explicitly stating the preference for using MCP tools over CLI commands in integrated environments (`commands.mdc`, `dev_workflow.mdc`).
- Describing the new standard pattern for getting the project root using `getProjectRootFromSession` within MCP tool `execute` methods (`mcp.mdc`, `utilities.mdc`, `architecture.mdc`, `new_features.mdc`).
- Clarifying the simplified role of `findTasksJsonPath` in direct functions (`mcp.mdc`, `utilities.mdc`, `architecture.mdc`, `new_features.mdc`).
- Ensuring proper interlinking between related documentation files.
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