Major refactor of the database generation tool

[ypriverol]

Summary by CodeRabbit

• New Features

  • Project renamed to "pgatk"; new CLI commands for digesting mutant proteins, mapping peptides to genome, ClinVar pipeline and NCBI downloader; centralized config loader.

• Documentation

  • Full MkDocs site, new guides (installation, CLI, formats, changelog) and design/plan documents.

• Bug Fixes & Improvements

  • Improved typing, logging, multiprocessing; removed pathos dependency; various robustness fixes.

• Chores

  • Updated release notes/README, CI workflows, container metadata, and expanded test suite.