CLI - Preserve comments when mutating the config file

[bfops]

Background

We currently parse, update, and write out the entire config file whenever the CLI is mutating the file. This has the side effect of removing any comments.

We would like to preserve a user's manual edits, including comments, whenever possible.

Definition of "Done"

• We use toml_edit or some similar crate in order to apply edits to the spacetime config file.
• When the CLI mutates the config, user comments are preserved.