Add deprecations page to docs

[bentsherman]

Adds a Deprecations page under "Updates" in the docs. It lists discouraged, deprecated, and recently removed features, along with the stable version in which each was deprecated or removed. The goal is to give users one place to check what is going away, and to give us one place to track deprecations.

Docs fixes

• Use DeprecatedInVersion consistently, replacing a lowercase tag in config.mdx and ChangedInVersion in two places
• Mark -entry as deprecated in the launch reference and in the 24.10 migration notes
• Mark aws.client.uploadStorageClass as deprecated in favor of aws.client.storageClass
• Remove -with-weblog from the kuberun options list
• Describe legacy operators as discouraged rather than deprecated in the 26.04 migration notes
• Recommend workflow outputs over publishDir, and warn that kuberun is no longer maintained
• Link the new page from "Updating Nextflow"

Removals

These features have been deprecated, and undocumented, for years:

• k8s.volumeClaims config option (use k8s.storageClaimName and k8s.storageMountPath)
• REDUCED_REDUNDANCY S3 storage class
• -pod-image option of kuberun (use -head-image)
• Leftover handling of process.$name selectors in Session.fetchContainers(). The selector syntax itself was removed in 20.07, but this code still warned about it and reported the container in workflow.container metadata.

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[bentsherman]

Note: the deprecations page is not meant to be exhaustive. I trimmed several entries from the original list discovered by the agent (e.g. config option renames). The goal is more to track the deprecation / removal of major user-facing features

[bentsherman]

exit() was not added to the deprecated table because it is being un-deprecated by #7570

[jorgee]

A few suggestions:

1. List this PR's own removals on the new page

The "Removed" table and the 26.10 migration notes don't mention the features this PR removes:

• k8s.volumeClaims config option, replaced by k8s.storageClaimName and k8s.storageMountPath
• -pod-image option of kuberun, replaced by -head-image
• REDUCED_REDUNDANCY value of aws.client.storageClass. It is still accepted by the publishDir and workflow.output storageClass options, which do no validation, so it might be worth saying it is only removed from the config option.

k8s.volumeClaims matters most here. With this change, kuberun stops with "Missing K8s storage volume claim", and that message doesn't point to the replacement options. A row on this page and a bullet in the 26.10 breaking changes would help users find the replacement.

2. Discouraged vs deprecated mismatches

• Workflow | and & are listed as discouraged here, but docs/workflow.mdx tags them with <DeprecatedInVersion version="26.04">.
• The process when section is listed as discouraged here and in strict-syntax.mdx, but docs/reference/syntax.mdx calls it deprecated.

It would be good to pick one status and use it everywhere.

3. Minor

• Path.listFiles() is deprecated in 26.04 (it is in the 26.04 migration notes, and this PR updates its tag), but it is not on the page. Suggested row: listFiles() | 26.04 | listDirectory().
• The -entry row only mentions run, but this PR also marks the option as deprecated in launch.

[bentsherman]

Thanks Jorge.

1. List this PR's own removals on the new page

I don't mention these in the docs because they were deprecated many years ago and have not been documented for a long time either. So I think it is safe to simply remove all trace of them

2. Discouraged vs deprecated mismatches

I resolved all of these

3. Minor

I reworded the -entry note.

Some deprecations like listFiles() are just renames, so I don't want to document them here because they distract from the main thrust, which is features that are going away.