Update plugins documentation

[christopher-hakkaart]

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[bentsherman]

I have updated the migration guide and various private beta callouts in such a way that I feel comfortable merging this PR now, even ahead of the plugin registry deployment.

To do this, I added a "Timeline" section to the migration guide which lays out our planned changes for the next few releases. This plan is taken from an internal planning doc where we reached some agreement.

The rest of the plugin docs direct you to this timeline via the callouts so that it's clear to anyone looking into the new Gradle plugin that there are some strings attached.

The tl;dr is that we will close the legacy plugin index to new PRs, but keep it in sync with the plugin registry for a time. Eventually after that, we can freeze the legacy index and remove it from new versions of Nextflow when we're ready.

This two-way sync during the transition period will make adopting the Gradle plugin as seamless as possible -- developers can use the new Gradle plugin with confidence that their plugin releases will continue to be accessible to users who aren't on the new registry yet.

[christopher-hakkaart]

I've added a few suggestions. Mostly removing words.

I would unlist the timeline H3 headings so they don't clutter the side navigation. But everything is optional if you think meaning is lost.

[bentsherman]

I rebased the PR and squashed my commits to make it easier to maintain with master.

Also documented the NXF_PLUGINS_INDEX_URL which is how users opt-in to the plugin registry.

@christopher-hakkaart now that we have tutorials and guides, I'm not sure which one you intended for the gradle plugin / plugin registry pages. Also might be worth giving the PR another once-over since it was sitting for a while

[christopher-hakkaart]

Thanks @bentsherman . I'll go through the PR and think about where the pages live and look for anything that might be stale or don't make sense anymore.

[christopher-hakkaart]

This page is orphaned. It was originally created as an example before we had the create command. Can delete unless you think there is value in keeping it.

[christopher-hakkaart]

@bentsherman I've pushed some changes for small fixes/alignment. There is one orphaned page (which I think can be removed), and one comment about the example. Otherwise I'm happy.

[christopher-hakkaart]

This is missing .github/workflows, is this a part of the create command? I can see it in the template but it wasn't generated when I tested. I may be using an older version.

[pditommaso]

@christopher-hakkaart i've updated the docs to reflect latests changes. see
0180c86