#9883 refactor: Use `ProjectDirsService` in all remaining places Pull request opened by edgarrmondragon Description SSIA. Checklist • I have read the contribution guide Was generative AI tooling used to co-author this PR? • Yes (please specify the tool below) Related Issues • #9580 Summary by Sourcery Refactor remaining project path usages to consistently rely on ProjectDirsService across core code and tests. Enhancements: • Replace deprecated project path helper methods with ProjectDirsService directory accessors in core services and utilities. • Relax deprecation warning categories for legacy project path helpers to use standard DeprecationWarning instead of internal-only warnings. • Adjust plugin lock and location handling to resolve paths via the centralized project directory service. Documentation: • Clarify deprecation guidance for when to emit MeltanoInternalDeprecationWarning in AGENTS.md. Tests: • Update CLI, plugin, locking, tracking, and invoker tests to use ProjectDirsService-based paths and improve type annotations for project-related fixtures. meltano/meltano