Add AGENTS.md with Cursor Cloud development environment setup - #103

Description

Add AGENTS.md with Cursor Cloud-specific development environment instructions for future cloud agents. This documents the required tools, linting commands, testing procedures, Docker-in-Docker setup caveats, and the critical cgroup v2 workaround for the cloud VM environment.

Key learnings documented

• Cloud VM's cgroup v2 is in "threaded" mode, which prevents Docker resource limits (--memory, --cpu-shares). Nextflow passes these by default, breaking all containerized processes.
• Workaround: NXF_DOCKER_LEGACY=true + a Nextflow config that nullifies process { memory = null; cpus = null; time = null }.
• Docker socket requires chmod 666 after daemon start for non-root Nextflow execution.

Validation

• Pipeline ran end-to-end with -profile test,docker: 3 SEQERA_RUNS_DUMP + 1 MULTIQC all completed successfully
• nf-test benchmark test: PASSED
• nf-test default test: snapshot mismatch (pre-existing upstream data drift, not related to changes)
• pre-commit run --all-files: PASSED
• nf-core pipelines lint: 142 passed, 0 failed

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>). — Pipeline runs successfully end-to-end
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).