feat!: prepare 2.0.0 application packages and release pipeline

[fabricebrito]

This prepares the application packages for 2.0.0 and brings the metadata, packaged tools, notebooks, documentation, and release pipeline into develop.

Changes

• Adopt typed EOAP CWL inputs, shared enums, richer software metadata, and generated workflow references and SVG diagrams.
• Package the four processing tools and stage-in/out commands with Python 3.12+, console entrypoints, tests, and multistage container images.
• Add Taskfile commands and Hatch notebook environments; align labs, Kubernetes examples, and documentation with the packaged commands and typed inputs.
• Redesign documentation navigation and add FAIR citation, RO-Crate, and optional Zenodo Sandbox exercises.
• Gate releases on package tests and image vulnerability scans; pack workflows with immutable image references, extract OCI annotations with transpiler-mate cwl2oci, publish with ORAS, and verify artifacts before publishing the GitHub release.
• Align current package and CWL versions to 2.0.0, update release metadata, and use the changelog for release notes.

Migration

This is a major release: existing string/bounding-box CWL inputs must be converted to GeoJSON Polygon and typed URI records, and direct app.py/container invocations must use the packaged console commands. See CHANGELOG.md for migration instructions. Historical released examples retain their original interfaces.

Validation

• 33 processing, staging, pipeline, and release-metadata tests passed.
• All tracked CWL documents validated; all six 2.0.0 package wheels built.
• Three packed release workflows and their cwl2oci annotations validated using test image digest fixtures.
• Local ORAS round trips verified workflow content and manifest annotations.
• Citation generation, Workflow RO-Crate validation, attachments, and ZIP contents verified locally.
• actionlint and strict MkDocs builds passed.
• Packaged and Hatch Minikube lab validation is recorded in the documentation.

Production image builds, vulnerability scans, GHCR publication, and GitHub release publication remain CI steps. No production release or Zenodo deposit has been performed.