Update nextclade to version 3.16.0

[pvanheus]

FOR CONTRIBUTOR:

• I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• License permits unrestricted use (educational + commercial)
• This PR adds a new tool or tool collection
• This PR updates an existing tool or tool collection
• This PR does something else (explain below)

[pvanheus]

This PR removes the nextalign tool, which is not part of nextclade version 3: https://docs.nextstrain.org/projects/nextclade/en/stable/user/migration-v3.html

[pvanheus]

When the Auspice JSON dataset PR (galaxyproject/galaxy#20466) gets merged, the JSON input for the custom tree should be changed to auspicejson.

[bgruening]

@pvanheus is this one ready?

[bgruening]

@wm75 is that something you want to take a look at?

[pvanheus]

@pvanheus is this one ready?

It is, as soon as the tests complete.