Bealign refactor and upgrade

[stephenshank]

The following would be nice to have:

• extract bealign as a standalone C application
• come up with a working WASM build, ideally with parallelism (need to gather requirements and see if WASM supports things like OpenMP or pthreads)
• algorithmic improvements (@spond feel free to chime in here)

[stephenshank]

Slack correspondence 10/31/23:

The main headache is reading/storing correctly formatted scoring matrices, which are currently being consumed as HyPhy dictionaries. I think the way to go is to use JSON for storage, and stdlib for processing.