Fix CI

[jeffcharles]

Description of the change

Removing deprecated crates from the workspace, the fmt checks for deprecated crates from the makefile, and a few updates to appease the new version of Clippy:

• changing &mut store to store.as_mut_context()
• adjust indentation in one set of docs
• mark two imports that are only used if a particular feature is enabled are only imported when that feature is enabled

Why am I making this change?

CI always uses the latest stable version of Clippy and that version of Clippy introduced new checks which our code fails. I adjusted the workspace and the Makefile since I don't want to make changes to the deprecated quickjs-wasm-sys or quickjs-wasm-rs crates but still want to be able to run make fmt to see all failing Clippy checks that would show up in CI.

For the &mut store to store.as_mut_context() changes, Clippy seems to sometimes get confused when passing &mut store to a Wasmtime method that takes store: impl AsContextMut and states we should only pass store. Unfortunately the Rust compiler obviously complains when passing store without the &mut if store is referenced again later because Rust will treat it as a move. At first I wrote I just updated call sites where Clippy complained but then it looks inconsistent within a function or file where sometimes we're passing store.as_context_mut() and sometimes we're passing &mut store and it's not obvious why we're using the first in some places and the second in others. So, I decided to make passing stores consistent since the behaviour is identical anyway.

Checklist

• I've updated the relevant CHANGELOG files if necessary. Changes to javy-cli and javy-core do not require updating CHANGELOG files.
• I've updated the relevant crate versions if necessary. Versioning policy for library crates
• I've updated documentation including crate documentation if necessary.

[saulecabrera]

The change looks good to me. I'm concerned with the clippy/rustc dance, though. I'm wondering, as I've mentioned informally in the past, if we should consider removing clippy altogether or at the very least reduce the lints, similar to https://github.com/bytecodealliance/wasmtime/blob/main/Cargo.toml#L174, to avoid this from happening in the future. Personally I don't find it useful and can't remember an instance in which it was useful to the project.