chore: prepare v3.1.0 release

[claude]

Requested by Phil Ewels · Slack thread

Description of changes

Release prep for v3.1.0. This release ships the changes merged in #251:

• New install-java input — lets workflows skip the bundled Java installation and use the Java already available on the runner (e.g. a pre-configured JDK), with an early, actionable failure if install-java: false is set but no Java is found via JAVA_HOME or the PATH (Add input to skip installing java #234).
• Fix for the version-list / CI failure — malformed entries in the nf-co.re version metadata (historical Nextflow releases without a second download asset) are now skipped instead of failing partial version matching such as version: '22.04', falling back to the GitHub releases API if no valid entries remain. This is the failure that was breaking the example-usage (22.04, *) CI jobs on master.

New feature, no breaking changes, so per semver this is a minor bump: 3.0.1 → 3.1.0.

What changed in this PR

Mirrors the v3.0.1 prep (#244) exactly — same three files:

• CHANGELOG.md: converted the ## [Unreleased] section into ## [3.1.0] - 2026-08-13 and added the compare links ([unreleased] now points at v3.1.0...HEAD).
• package.json / package-lock.json: version bumped to 3.1.0 (npm version 3.1.0 --no-git-tag-version).
• dist/ was rebuilt locally (npm run package) and is byte-identical — the bundle does not embed the version, so no dist changes, same as chore: prepare v3.0.1 release #244.

PR checklist

• This comment contains a description of changes (with reason)
• Make sure your code lints (npm run lint)
• Make sure your code passes formatting checks (npm run format:check)
• Ensure the unit test suite passes (npm run test) — 28/29 pass locally; the Install Nextflow test downloads a real Nextflow binary and timed out in the sandbox used to prep this PR (known sandbox network limitation), CI should exercise it
• CHANGELOG.md is updated

Post-merge: publishing the release

Merging this PR does not publish anything. A maintainer still needs to create the release the same way v3.0.1 was published (an orphan snapshot commit with signed tags):

1. Check out the merged master and build the bundle: npm ci && npm run package.
2. Create an orphan snapshot commit containing only the runtime files, matching the v3.0.1 release commit (893c28b): CHANGELOG.md, LICENSE, README.md, action.yml, dist/, docs/, subaction/ — no sources, tests, or dev config. Commit message convention: bump to 3.1.0.
3. Create signed annotated tags on that commit: git tag -s v3.1.0 -m v3.1.0 and git tag -s v3.1 -m v3.1, and move the major tag: git tag -fs v3 -m v3.
4. Push them: git push origin v3.1.0 v3.1 and git push -f origin v3.
5. Publish a GitHub release for tag v3.1.0, using the ## [3.1.0] CHANGELOG section as the release notes (same format as the v3.0.1 release).

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