Pydantic-based configuration and setting objects

[csmith49]

End-user friendly description of the problem this fixes or functionality that this introduces

• Include this change in the Release Notes. If checked, you must provide an end-user friendly description for your change below

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Give a summary of what the PR does, explaining any non-trivial design decisions

This PR standardizes configuration objects to use pydantic.BaseModel objects over data classes. These changes were originally from #6176, but needed to be reverted in #6214 due to typing issues with Settings (which are now fixed).

Other changes:

• Certain api_key-type fields, especially in AppConfig and LLMConfig, are now SecretStr instead of str. The values can only be accessed by calling a field.get_secret_value() function, which complicates some accesses but ensures the key won't be leaked by, e.g., serializing config objects during logging.
• Minor clean-up of config parsing from environment variables and TOML files.
• Fixes to tests.
• Minor updates to serialization in evaluation.

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Link of any specific issues this addresses

#6015

[enyst]

Thank you for this!

Meanwhile I also want to simplify the llm config (it doesn't need a nested version of itself): #6281 ), then it should be easier to work with.

[enyst]

@csmith49 Please feel free to merge this PR whenever you see fit.

If there are conflicts with the other (although there might not be), no problem, I'll fix that tomorrow.