Standardize shell execution on unified exec (#39757)

## What changed

- Remove the legacy `shell_command` handler and runtime, leaving `exec_command`
  and `write_stdin` as the shell execution tools.
- Treat legacy `shell_command` model metadata as `unified_exec`, and normalize
  legacy user opt-outs so they do not disable command execution. Managed feature
  requirements and `shell_tool` can still disable it.
- Preserve shell approvals, sandboxing, zsh-fork support, and output truncation
  through the unified execution path.

## Testing

- Cover legacy configuration and model-metadata compatibility.
- Exercise unified shell execution, approvals, truncation, and `apply_patch`
  serialization across the app-server and core test suites.

GitOrigin-RevId: 5c2fd6164fc3519cdae4944cb9db276b8467311c

codex-rs/tools/Cargo.toml

@@ -17,7 +17,6 @@ codex-extension-items = { workspace = true }
 codex-protocol = { workspace = true }
 codex-utils-absolute-path = { workspace = true }
 codex-utils-output-truncation = { workspace = true }
-codex-utils-pty = { workspace = true }
 codex-utils-string = { workspace = true }
 jsonptr = { workspace = true }
 rmcp = { workspace = true, default-features = false, features = [