Remove deprecated code

[braingram]

Description

This PR removes deprecated API. See docs link below for more details.

Closes #1698
Closes #1859

It needs:

• docs (including the start of the 4.0 what's new): https://asdf--1852.org.readthedocs.build/en/1852/asdf/whats_new.html#whats-new-4-0-0
• address "TODO"s mentioned below (splitting them into separate issues). I will open these when this PR is approved but prior to merging since we will likely have a discussed plan at that point.

The major changes to make sure to note are:

• no more namedtuple support (so we can handle these with Extensions/Converters)
• use of a tag uri for a schema $ref will no longer resolve
• resolve_references is no longer called for AsdfFile.__init__ or asdf.open

Checklist:

• pre-commit checks ran successfully

• tests ran successfully

• for a public change, added a towncrier news fragment

  changes/<PR#>.<changetype>.rst

  • changes/<PR#>.feature.rst: new feature
  • changes/<PR#>.bugfix.rst: bug fix
  • changes/<PR#>.doc.rst: documentation change
  • changes/<PR#>.removal.rst: deprecation or removal of public API
  • changes/<PR#>.general.rst: infrastructure or miscellaneous change

• for a public change, updated documentation

• for any new features, unit tests were added

[nden]

LGTM, assuming the weldex failure is not an issue.

[braingram]

LGTM, assuming the weldex failure is not an issue.

Thanks! There is a PR that fixes the error:
BAMWelDX/weldx#910

I may open a smaller one that's just that error since the above PR also has schema changes (although those are required for #1744).