Add cloud development environment setup

[FloWuenne]

Summary

Sets up the development environment for nf-proteindesign on Cursor Cloud VMs and documents how future agents should work in this repo.

Changes

• AGENTS.md — Cloud-specific instructions covering:

  • Nextflow 25.10.2 pin (26.04.x and 24.10.x are incompatible with current pipeline DSL)
  • Docker daemon startup (no systemd in cloud VMs)
  • Stub-run validation command
  • MkDocs build/serve commands
  • Common gotchas (CPU/memory limits, Foldseek, GPU requirements)

• conf/cloud_dev.config — Reduced CPU/memory limits so -stub-run works on 4-CPU / 16 GB cloud VMs (default base.config requests up to 40 GB for GPU processes).

VM update script (approved separately)

NXF_VER=25.10.2 curl -fsSL https://get.nextflow.io | bash
sudo install -m 755 nextflow /usr/local/bin/nextflow
rm -f nextflow
pip3 install -r requirements.txt --user

Verified in cloud VM

Check	Result
Nextflow stub E2E (test_design_rfdiffusion_v3 -stub-run -c conf/cloud_dev.config)	✅ 12 processes completed
MkDocs build	✅ site/ generated
MkDocs serve	✅ HTTP 200 on port 8000
Docker hello-world	✅

Full GPU pipeline runs (-profile test_design_protein,docker) require an NVIDIA GPU host; not available on the default cloud VM.