Rename Boltz utility commands

[SergeiNikolenko]

Summary

• rename the existing-pose scoring CLI to boltz-affinity
• rename the crystal-pocket docking CLI to boltz-dock
• update README/docs, doc filenames, default output names, and entrypoint tests

Speed notes

• boltz-affinity skips Boltz diffusion and is the fast path for already-built poses.
• boltz-dock still runs Boltz diffusion; it constrains the receptor/pocket but should not be presented as a scoring-fast path.
• On gauss, a valid 1HTB micro-run with 1 sample / 1 recycle / 20 sampling steps took 64s for unconstrained Boltz and 69s for boltz-dock.
• A cold boltz-affinity score of an existing Boltz CIF took 63s; batch scoring is expected to benefit from avoiding diffusion and from --reuse_trunk for same-topology poses.

Tests

• UV_CACHE_DIR=/private/tmp/uv-cache-abcfold uv run --extra test python -m pytest tests/test_boltz_entrypoints.py tests/test_boltz_dock_crystal.py -q
• UV_CACHE_DIR=/private/tmp/uv-cache-abcfold uv run --reinstall-package abcfold boltz-affinity --help
• UV_CACHE_DIR=/private/tmp/uv-cache-abcfold uv run boltz-dock --help