chore(rs): update dependencies (#1494)

### Chores
- Update cargo dependencies
- Remove unused cargo dependencies
- Fix clippy warnings
- Update Dockerfile (package.json requires node 22)
- Let Dependabot update bun, cargo, devcontainers, docker,
github-actions, npm (nix still not supported)

### TODO
- Upgrade dependencies with breaking changes

```shell
$ cargo update --verbose
   Unchanged crossterm v0.28.1 (available: v0.29.0)
   Unchanged schemars v0.8.22 (available: v1.0.4)
```

codex-rs/mcp-client/Cargo.toml

@@ -21,6 +21,3 @@ tokio = { version = "1", features = [
     "sync",
     "time",
 ] }
-
-[dev-dependencies]
-pretty_assertions = "1.4.1"