Bump proto-tools to latest main (55339880)

[bviggiano]

Moves the proto-tools pin from 63dc3a2b to 55339880, the current tip of evo-design/proto-tools main. 15 commits.

Notable in the delta:

• Genomic Intelligence sequence-scoring toolkit (#83), plus three follow-up fixes that missed that merge (#98).
• get_tool_info (#82), and a single shared envelope for both discovery tools with the discovery field renamed (#81).
• rfdiffusion3-design now rejects select_hotspots without a contig before dispatch, following rfd3's own composition rules.
• Network resilience: UniProt (#84) and further database/search fetches (#93) retry through a reset connection.
• Packaging: pruned PyTorch wheels sourced from PyPI for evo2, progen3 and germinal, with an index-pruning canary test (#80); dssp pins a compatible libmcfp ABI.

Pointer-only change; no proto-language source is touched. Leaving the unit tests to run rather than labelling skip-tests, since the delta changes tool-facing APIs.