Feat/126/update the department controller

[Kimoo193]

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Related Issue

Closes #126

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[Kimoo193]

This pull request includes several updates and improvements across different parts of the codebase, focusing on user management, department handling, and documentation enhancements.

User Management Changes:

• Updated src/controllers/user.controller.js to remove encryption for phone numbers during user account updates.
• Modified src/controllers/user.controller.js to use findFirst instead of findUnique for soft-deleting users, and improved error handling for already deleted users.

Department Handling Enhancements:

• Updated department routes in src/routes/department.routes.js to include organization and manager IDs in the path and added routes for getting created departments. Removed middleware imports for role verification.
• Removed verifyManagerPermission and verifyOwnerOrAdmin middlewares. [1] [2]
• Updated src/validations/department.validation.js to remove organizationId and managerId from the validation schema.

Documentation and API Specification:

• Enhanced swagger.json with detailed descriptions, examples, and improved error responses for department-related endpoints. [1] [2] [3] [4]
• Updated src/docs/TODO.md to reflect new tasks and removed old task assignments.

Miscellaneous Changes:

• Added email notifications for new owners in src/controllers/organization.controller.js.
• Corrected routes in src/routes/user.routes.js to use consistent API paths and changed HTTP methods for updating passwords. [1] [2]

These changes aim to improve the overall functionality, maintainability, and clarity of the codebase.