Update jbrowse2 4.2.1

[rlibouba]

Hello, I'm opening this PR to update JBrowse2. There have been many changes and improvements since version 4.+.
I have started adding them.

Thank you, and have a great day,
Romane

---

FOR CONTRIBUTOR:

• I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• Use of AI
  • The contribution is mostly AI generated
  • The contribution has been assisted by AI
• 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)

There are two labels that allow to ignore specific (false positive) tool linter errors:

• skip-version-check: Use it if only a subset of the tools has been updated in a suite.
• skip-url-check: Use it if github CI sees 403 errors, but the URLs work.

To request a review once your PR is ready, comment "please review" on the PR. This will
automatically apply the ready-for-review label if the PR is not a draft, all review
threads are resolved, and all CI checks have passed.