Make build infra‑agnostic: update README, add Packer examples, improve build playbook and docs

[Mitchob]

Summary

• This PR updates documentation and build tooling to make BioImage infrastructure‑agnostic and easier to build from scratch.
• Primary aim: verify building the bioimage end‑to‑end using the available scripts and document the process for different OpenStack providers (tested on Nectar and Nirin).

What I changed:

• README.md: Rewrote and expanded the README to be infra‑agnostic. Added a clear intro to BioImage, step‑by‑step instructions for creating a head VM, obtaining/sourcing OpenStack RC files, activating the environment, and building images. Included example references for Nectar and Nirin (tested on 2026-02-02).
• .gitignore: added patterns for credentials, logs, and local virtualenvs.
  • build/build-bioimage.yml: reliability fixes and small functional changes:
  • Wait for apt/dpkg locks before operations.
  • Retry apt updates with retries/delay.
  • Install Java 21 and set it as the default java (required for Nextflow).
  • Set Nextflow-related env vars for deterministic checks.
  • Default CVMFS_HTTP_PROXY to 'DIRECT' (increase portability) and removed aggressive probes.
• Packer configs:
  • Added a generic template: build/openstack-bioimage.pkr.hcl (template requiring user to fill flavor, networks, availability_zone, source_image).
  • Moved/added provider examples:
    • build/examples/openstack-bioimage-nectar.pkr.hcl (example config used for Nectar)
    • build/examples/openstack-bioimage-nirin.pkr.hcl (example config used for Nirin)
  • Provisioner ansible blocks improved to set ansible env vars and avoid host key checking in automated builds.
• Docs:
  • docs/cvmfs.md: new doc explaining CVMFS usage in BioImage.
  • docs/nirin.md: provider‑specific guidance for Nirin (instance creation, scripts, common tasks).
• Renames/relocations in build folder to separate examples from template and make it clear which values must be filled per provider.

Testing performed

• Built the image using the example Packer configs against Nectar and Nirin environments (example configs included).
• Verified the build playbook handles apt locks and apt update retry behavior and that Nextflow can be interrogated via nextflow -version in the image build step.
• Confirmed that CVMFS is configured as DIRECT by default (portable across clouds), with instructions for setting cloud-specific proxies if available.

Next steps

• see if we can move the tasks out of the playbook as they are, and into a separate bioimage role
• refactor to ensure that anything specifically needed for NCI/Nectar/AWS/anywhere else is templated out into variables
• Intoduce tests to make sure updates arent breaking things