merge upstream af3 updates
Syncs 21 upstream commits from google-deepmind/alphafold3 into the fork (#2), keeping the OpenFold3 / ColabFold MSA additions intact.
Notable from upstream:
- jax 0.10.2 + tokamax 0.0.12;
jax[cuda12]is no longer pulled in on macOS gs://path support viaetils.epaththroughout- Lower memory use in
OuterProductMean - Chain IDs in the summary confidence JSON
- Example input JSONs under
examples/
Fork-specific:
--jax_backendnow defaults toauto, probing for a JAX GPU and falling back to CPU (setting--flash_attention_implementation=xlaitself), so CPU-only and macOS runs still need no extra flags- Generated converter pickles are gitignored; rebuild with
ccd_pickle_gen.py