* 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
