Clarify and be consistent in the help messages for command-line flags

### Context
While I've been reviewing PRs I noticed various help strings that conflate paths and files. I'd like the help messages to be clearer and to be consistent in their use of terms. It'd be useful to also check the project's README mentions command-line flags and how to see them from the command line (e.g. via a `--help` and/or a `--usage`).

Inspect the command-line flag help strings and the project's README, focusing first on how the CLI exposes --help or --usage. Standardize the terminology for paths and files in the help messages, and document how to view the available flags in the README.

Written by the indexing model from the issue text.