Update plugins documentation

[christopher-hakkaart]

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[bentsherman]

When are we going to publish this? If the Gradle plugin only works with the plugin registry then it probably doesn't make sense to publish it until the plugin registry goes live.

[christopher-hakkaart]

My understanding is that make release works with the GitHub repo, so everything that is currently described is accurate. @tom-seqera , can you confirm?

[pditommaso]

We are not going to maintain support for uploading to Github. Documentation should only mention publishing to registry as private beta

[bentsherman]

FYI, I am taking a pass through this PR to clean up some things. Should be done by today.

[bentsherman]

Looking good so far.

The migration guide could use some more information about migrating to the plugin registry -- right now it only covers migrating to the gradle plugin but doesn't mention the fact that the Gradle plugin does not support publishing to GitHub, which is the most important point

[christopher-hakkaart]

FYI, I am taking a pass through this PR to clean up some things. Should be done by today.

Thanks @bentsherman

The migration guide could use some more information about migrating to the plugin registry

Would you like to draft and I clean it up, or is it easier if I draft in the PR and you clean it up?

[bentsherman]

Actually I don't think we have finalized the migration strategy for plugin developers. So this PR is blocked until we do that

[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.