[Feature]: Clean up input/output nomenclature and formatting

[JesseJenkins]

Feature description

Next major version update: we need to comprehensively audit/clean up the input and output file naming conventions, formatting (snake case, title case etc).

Motivation

They are all over the place (inconsistencies) and we use too many abbreviations that make interpretation harder for non-expert users.

Implementation strategy

Develop a clear style guide for filenames, column headers, etc. and publish. Align all input and output files with this style guide.

Additional context

No response