barrel files - remove or refactor

[claytercek]

We could enable this rule: https://biomejs.dev/linter/rules/no-barrel-file/

Or at least come up with more consistency/intention with how we're using barrel files.

We DEFINITELY want to change how we're using barrel files in the CLI. Re-exporting everything from the subpackages from index is not great.

This could go into our next major update, as changing the import paths would be a breaking change