Replace string-based file extension checks with pathlib

[davidbonet]

Refactor file handling across multiple modules by adopting pathlib to replace string-based file extension manipulations.

• Path.suffix and Path.suffixes for extension checks and with_suffix/with_name for consistent and cross-platform extension modifications.
• Simplifying the logic for verifying and appending file extensions, ensuring the codebase handles VCF, BCF, MSP, BED, and other file formats in a more Pythonic way.

This refactor improves code readability and reduces potential errors with manual string slicing. All tests related to file handling have been adapted to work with pathlib.

[salcc]

Looks good to me, but a unused import was introduced in read_vcf

[salcc]

And it would be nice to update the plink link to the latest release: https://s3.amazonaws.com/plink2-assets/alpha6/plink2_linux_x86_64_20241114.zip

[salcc]

All good now!