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-server/Cargo.toml

@@ -22,7 +22,7 @@ mcp-types = { path = "../mcp-types" }
 schemars = "0.8.22"
 serde = { version = "1", features = ["derive"] }
 serde_json = "1"
-toml = "0.8"
+toml = "0.9"
 tracing = { version = "0.1.41", features = ["log"] }
 tracing-subscriber = { version = "0.3", features = ["fmt", "env-filter"] }
 tokio = { version = "1", features = [