Improve Python tools for working with parameters

This is a parent issue covering two things:
- A script to query CLM parameters
- A script to set CLM parameters

These scripts should be designed to work with each other where possible. E.g., you should be able to query some parameters, save that output to a file, change the file, then set parameters based on the updated file.

Aims:
1. Reduce duplicated work by users to come up with their own systems.
2. Minimize possibility of user error resulting in broken or silently-incorrect parameter files and settings.
3. Increase abstraction of users from our parameter infrastructure so we can change it with minimal disruption.
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Update 2025-08-25: ctsm5.3.071 brought in the new `query_paramfile` and `set_paramfile` tools. However, this issue and its children are broader than just working with _parameter files_; we want tools to work with namelist parameters too.