DO NOT MERGE: Remove obsolete schema variants, eliminate extra carets in patterns, and update dependency to avoid security bug

[turbomam]

• Remove nmdc_schema/nmdc_schema_accepting_legacy_ids.yaml and all references to it (branch minimal-acceptance)
• Limit regex-anchoring carets (^) to LinkML settings, not structured_patterns (branch 2092-extra-leading-caret-in-structured_patterns)
• Use newer version of urllib3 to avoid moderate security bug (branch 2096-update-urllib3-version)
• Remove nmdc_schema/nmdc_schema_merged.yaml along with all references to it (branch 2095-replace-uses-of-nmdc_schema_mergedyaml-with-nmdc_schema_accepting_legacy_idsyaml)

This PR also removes some commented-out-code on top of those PRs above

[github-actions[bot]]

PR Preview Action v1.4.7 :---: :rocket: Deployed preview to https://microbiomedata.github.io/nmdc-schema/pr-preview/pr-2110/ on branch gh-pages at 2024-07-03 19:09 UTC

[eecavanna]

I recommend updating the PR title to summarize what the PR "does" (i.e. what Git would "do" if the commits on the branch were merged in).

I propose:

Remove obsolete schema variants, eliminate extra carets in patterns, and update dependency to avoid security bug