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refactor(logging): replace logging with custom logger across modules
* Updated logging implementation to use `get_logger` from tdoc_crawler. * Refactored migration.py, pg0_manager.py, processor.py, rag.py, shared_storage.py, seeder.py, classify.py, extraction.py, figure_descriptor.py, llm_client.py, summarize.py, workspace_registry.py, and workspaces.py. * Improved consistency in logging practices across the codebase.