Previously some of them were saved only for current .blend file, moving them to preferences will make it more consistent with usual Blender UX. If needed we'll be able to add some way to fine-grain them later.
There's also a temporary patch that's going to migrate old .blend-props to new preferences-props to make process less disruptive.
Previously cache_dir was located under site-packages, which is managed
by blender and could be read-only. Now location defaults to eg.
~/.cache/bonsai or equivalent location on other platforms. See #5564
Note this adds a dependency on the platformdirs python module
Previously it would fail with:
PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'bonsai\\bim\\data\\cache\\988c190483ae6bab7cf6b00cee78694d.h5'