Migrate to Nextflow Plugin Registry and ship 1.0

[drernie]

Background

Nextflow is replacing the legacy nextflow-io/plugins index with the new Nextflow Plugin Registry. Per the migration guide:

• The legacy index repo is closed to new pull requests.
• Starting Nextflow 25.10, the registry becomes the only download source.
• Publishing now uses ./gradlew releasePlugin from the new Nextflow Gradle plugin (≥1.0.0-beta.6) — the existing GithubUploader + publishIndex tasks are obsolete.

This blocks releasing 0.9.2 (the OffsetDateTime fix from #321/#322) and all future versions through the standard channel.

Decision: rather than publish 0.9.2 to the legacy index and 1.0 to the registry, we'll skip publishing 0.9.2 entirely and ship the migration + OffsetDateTime fix together as 1.0.0, our first release on registry.nextflow.io. Users who need the fix sooner can build locally via make install from main.

Required Changes

Per the migration guide:

1. Delete buildSrc/, launch.sh, plugins/build.gradle
2. Move plugins/nf-quilt/src/ → repo-root src/
3. Replace settings.gradle with rootProject.name = 'nf-quilt'
4. Rewrite root build.gradle to use the Nextflow Gradle plugin
5. Rewrite Makefile with the new build targets
6. Update README.md / README-DEV.md
7. Verify make assemble and ./gradlew releasePlugin work

Suggested PR Breakdown

• PR 1 — Restructure (no functional change): delete buildSrc/, launch.sh, plugins/build.gradle; move plugins/nf-quilt/src/ to root; update settings.gradle. Keep CI green by adjusting paths only.
• PR 2 — Build system: new root build.gradle using the Nextflow Gradle plugin; new Makefile targets; ensure unit tests + make pkg-test still pass.
• PR 3 — Docs: update README.md, README-DEV.md, and CHANGELOG.md to reflect new build/publish flow; remove nextflow-io/plugins references.
• PR 4 — Release 1.0.0: bump Plugin-Version from 0.9.2 to 1.0.0 in MANIFEST.MF; finalize CHANGELOG entry; run ./gradlew releasePlugin; register nf-quilt on registry.nextflow.io; close Nextflow version mismatches? #321.

Risks / Open Questions

• Verify the new Gradle plugin handles our quiltcore + Jackson dependencies cleanly (the test suite exercises real S3 against udp-spec).
• Confirm registry account/ownership for nf-quilt (who registers it).
• Does releasePlugin still produce a GitHub release with the meta.json + zip assets, or only push to registry.nextflow.io? Affects whether our Makefile's default NXF_PLUGINS_TEST_REPOSITORY (a GH release URL) keeps working for 1.0+; no impact on historical 0.9.1 and earlier.

References

• Migration guide: https://docs.seqera.io/nextflow/guides/migrate-plugin
• Registry: https://registry.nextflow.io/
• Folded-in fix: PR Fix Jackson OffsetDateTime serialization for Nextflow 24.10+ (#321) #322, issue Nextflow version mismatches? #321