release: prepare CORNETO 1.0.0-rc.1

[pablormier]

Summary

Prepare CORNETO 1.0.0 RC1 by merging the reviewed dev branch into main.

This release candidate converges the documented public API for CORNETO 1.0, removes obsolete and duplicated code & old research method implementations.

Highlights

• Finalize the documented CORNETO 1.0 public API.
• Promote stable implementations out of future packages.
• Retain deprecated corneto.methods.future, corneto.methods.signal, and backend alias imports with warnings.
• Consolidate signaling, graph, backend, sampler, shortest-path, CARNIVAL, FBA, and IMAT interfaces.
• Add initial AnnNet interoperability for converting CORNETO graphs into trainable neural-network models.
• Support shared multi-condition conventions across modern formulations.
• Promote the documented machine-learning API to corneto.ml.
• Add public API contract and behavioral tests.
• Support Python 3.11–3.13.
• Fix warning-free documentation builds and package validation.
• Add RC1 release notes and the CORNETO 1.0 migration guide.

Validation

• Tests pass on Python 3.11, 3.12, and 3.13.
• Documentation builds successfully with warnings treated as errors.
• Ruff, formatting, and package metadata checks pass.
• Wheel and source distributions build and pass installation checks.
• Private and public dev are synchronized at 2b09ecec.

Release

After this PR is merged, RC1 will be validated with:

poetry run release v1.0.0-rc.1 --remote public --dry-run

The release tag will only be pushed after separate explicit approval.