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Add comments on base_path potential deprecation (#1097)
New `NOTE: ...` comments call out `base_path` settings as something considered problematic, as they've hampered us in the past. Removing them is a significant breaking change, and as class attributes, they would require a more elaborate deprecation strategy if we wanted to have them actually issue deprecation warnings. Limiting ourselves to a comment for now helps authors know not to use `base_path` for new classes without having to solve how we can actually deprecate and remove the setting.
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