Update toml configuration files without losing comments

[svarlamov]

Find something similar to jsonc that will retain comments when we update TOML configuration files. Came up with Codex's config.toml initially but other agents may also use TOML

[dlight]

The toml_edit crate can be used to edit a toml file while preserving comments and whitespace.

The only thing it doesn't preserve is the ordering of keys, there's a PR for that but it's stuck in a limbo of sorts.

[svarlamov]

Would love to accept a PR if you have some time to pull that toml_edit-basedimplementation together @dlight!