Summary

The current Dockerfile relies on an outdated custom base image (quay.io/matsengrp/linearham:2022-11-29-base-image) built on Debian Stretch, which is no longer maintained. This PR updates the Dockerfile to use a modern Debian base image and eliminates the need for maintaining a separate base image.

Changes needed

1. Update base image: Change from custom base image to debian:latest
2. Update Python: Migrate from Python 2 to Python 3 (python3-dev, python3-pip, python3-setuptools)
3. Integrate RevBayes: Add RevBayes installation directly in the main Dockerfile
4. Use pip-installed partis: Install partis-bcr from PyPI instead of building from source
5. Update SConstruct: Change --build-partis-linearham to --build (builds only linearham)
6. Update requirements.txt: Remove version pins and add partis-bcr and scons packages
7. Platform specification: Explicitly set platform to linux/amd64 due to partis-bcr's x86-specific code

Benefits

• Eliminates maintenance burden of custom base image
• Uses modern, supported Debian version
• Simplifies build process
• Better compatibility with modern Python ecosystem
• Faster builds (RevBayes binary download is quick)

Testing

• Successfully builds on Apple Silicon (using platform emulation)
• All changes align with colleague's local testing and git diff