chore(ml): fix Julia dep UUIDs, add Manifest.toml

GraphNeuralNetworks had wrong UUID. Re-added all 15 deps via Pkg.add
to get correct registry UUIDs. All 98 dependencies resolve and
precompile successfully (CUDA + Flux + GNN + Transformers).

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: hyperpolymath