standardize diff logic for diff_deps only

[sanchitram1]

Need to test it against local pipelines, but tests are passing so far

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PR-Codex overview

This PR primarily focuses on enhancing the package management system by normalizing and diffing dependencies across various package managers, improving logging, and updating test cases to ensure accuracy and reliability.

Detailed summary

• Updated set command in alembic/run_migrations.sh for better debugging.
• Adjusted docker-compose.yml for PostgreSQL volume path.
• Removed unused import in package_managers/pkgx/loader.py.
• Improved logging formatting in ranker/main.py.
• Updated dependency versions in pyproject.toml and pkgx.yaml.
• Enhanced error messages in scripts/chai-legacy-loader/batch_insert_package_urls.py.
• Refined assertions in test files for better clarity.
• Added new normalizer functions for crates, pkgx, and debian packages.
• Implemented shared dependency diffing logic across package managers.
• Updated tests to cover new normalizer functionality and ensure accurate dependency handling.

The following files were skipped due to too many changes: tests/package_managers/pkgx/test_pkgx_normalizer.py, core/diff.py, tests/core/test_diff.py, uv.lock

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[sanchitram1]

note that this fixes teaxyz#126 from teaxyz/chai