Update Bonsai to version 2.9 #1625
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This PR updates the bonsai to the latest version (2.9). It also tries to update packages to a more recent version. I tried to be careful and only update packages I was fairly certain wouldn't lead to issues.
This PR should be tested in a few long sessions to make sure everything is working as intended.
Once it is tested, there are a few QOL worth considering before merging this PR: