* 🔧 refactor: Centralize Collection Existence Checks for Permissions Migration
* Replace individual collection existence checks with a unified function `ensureRequiredCollectionsExist` in the database utility module.
* Update migration scripts for agents and prompts to utilize the new function, ensuring all required collections are verified for existence in a single call.
* Remove redundant collection existence logic from migration files, improving code maintainability and clarity.
* chore: import order in migration scripts
* 🔧 test: Update Token Test Cases for Realistic Scenarios
* Changed email in test data to 'user1-alt@example.com' for a more realistic scenario.
* Clarified expectation comment for token retrieval to indicate it finds the only matching token based on criteria.
* refactor: Resource Migration Scripts for DocumentDB compatibility
* fix: Correct type annotation for `db` parameter in ensureCollectionExists function
* chore: fix mock typing in packages/api tests
* chore: improve imports, type handling and method signatures for MCPServersRegistry
* chore: use enum in migration scripts
* chore: ParsedServerConfig type to enhance server configuration handling
* feat: Implement agent permissions migration check and logging
* feat: Integrate migration checks into server initialization process
* feat: Add prompt permissions migration check and logging to server initialization
* chore: move prompt formatting functions to dedicated prompts dir
