feat: refactor Charon.toml to use Cargo.toml and add support for start_from, hide_marker_traits

[oliver-butterley]

The Charon.toml config file previously supported only four fields (extract_opaque_bodies, include, opaque, exclude) and rustc flags.

This PR refactors the functionality to avoid the Charon.toml file and instead uses a [metadata] section in Cargo.toml. Moreover we extend functionality to cover other commonly-needed options:

• start_from / start_from_if_exists / start_from_attribute / start_from_pub — control translation entry points
• hide_marker_traits — suppress marker traits from output

The --help text for the cargo subcommand now mentions that the [package.metadata.charon] section in Cargo.toml is read when present.

Note: The charon option preset is not exposed in the config. The rationale being that this depends on which tool will consume Charon's output rather than on the crate itself, so it doesn't belong in the crate's Cargo.toml.

[oliver-butterley]

I noticed there is an existing integration test for the config file (tests/cargo/toml/). It could be extended to cover the new fields, in particular [cargo] flags and start_from.

Concrete possibilities:

• A project with a feature-gated function and [cargo] flags = ["--features", "my_feature"] in Charon.toml: confirms the function appears in the output (analogous to the existing [rustc] flags test).
• A project with two modules and start_from = ["crate::included"]: confirms the excluded module is absent from the output.
• A bad preset name in Charon.toml should produce a clear error message: I could also do a test for this although there is likely a slight maintenance burden here since the panic output includes an internal file:line location that would make change with later updates.

Currently such tests are drafted in another branch (config-file-tests), let me know if they should be added to this PR.

[Nadrieril]

I kinda want to rip out Charon.toml and replace it with a [metadata] section in Cargo.toml as is more standard

[Nadrieril]

would you wanna do taht instead?

[oliver-butterley]

I kinda want to rip out Charon.toml and replace it with a [metadata] section in Cargo.toml as is more standard

We are very flexible with our needs. Just needs to have something in order to have a convenient way to write the flags. E.g., our repos currently need to pass many flags like seen in this.

[oliver-butterley]

would you wanna do taht instead?

OK! Will do.

[Nadrieril]

Please merge these new tests into one, many cargo tests are not fun to have around.

[oliver-butterley]

Thanks for your patience!

Summary of the latest updates following all the comments:

• Dropped [package.metadata.charon.cargo] flags entirely
• Dropped preset entirely. (it's tool-dependent rather than crate-dependent)
• The additional tests added in the previous version of the PR have been removed. What remains is the single test from before, updated to the latest functionality.
• docs/usage.md is now very concise info

Note: Updated read_toml reads ./Cargo.toml directly like was done before for Charon.toml. It's possible that for Cargo.toml there is a specific procedure which should be used but searching I didn't find a solution which was clearly better than the current version.