Refactor data extraction functions: rename extract_pmc_data to extract_sd_data, add extract_phys_data, and update file handling for new data sources

Update pmc.py

Add count of category and PMC IDs to data output in extract_arxiv_data and extract_pmc_data functions

Refactor imports and consolidate utility functions into utils.py; remove tools.py

Update pmc.py

Update pmc.py

Update pmc.py

Update pmc.py

Update pmc.py

Refactor ID extraction logic in arvix and improve DOI fetching in pmc

Add initial project structure with core functionality and dependencies