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This is a major version bump mainly as a signal of potential breakage due to the upgrades of some dependencies, notably:
There are not a ton of other changes otherwise. This major version bump is similar to our decision to major version bump in our "v2.0.0" release https://jbrowse.org/jb2/blog/2022/07/07/v2.0.0-release/
This loses our "vanity version number" of v2 to correspond to JBrowse 2. We can continue calling it "JBrowse 2 v3.0.0" or we can just say "JBrowse v3.0.0" (https://paulrrogers.com/2014/09/vanity-versioning/)
if there is a particular branding that is preferable, we could discuss.