chore: remove codex-core public protocol/shell re-exports (#12432)

## Why

`codex-rs/core/src/lib.rs` re-exported a broad set of types and modules
from `codex-protocol` and `codex-shell-command`. That made it easy for
workspace crates to import those APIs through `codex-core`, which in
turn hides dependency edges and makes it harder to reduce compile-time
coupling over time.

This change removes those public re-exports so call sites must import
from the source crates directly. Even when a crate still depends on
`codex-core` today, this makes dependency boundaries explicit and
unblocks future work to drop `codex-core` dependencies where possible.

## What Changed

- Removed public re-exports from `codex-rs/core/src/lib.rs` for:
- `codex_protocol::protocol` and related protocol/model types (including
`InitialHistory`)
  - `codex_protocol::config_types` (`protocol_config_types`)
- `codex_shell_command::{bash, is_dangerous_command, is_safe_command,
parse_command, powershell}`
- Migrated workspace Rust call sites to import directly from:
  - `codex_protocol::protocol`
  - `codex_protocol::config_types`
  - `codex_protocol::models`
  - `codex_shell_command`
- Added explicit `Cargo.toml` dependencies (`codex-protocol` /
`codex-shell-command`) in crates that now import those crates directly.
- Kept `codex-core` internal modules compiling by using `pub(crate)`
aliases in `core/src/lib.rs` (internal-only, not part of the public
API).
- Updated the two utility crates that can already drop a `codex-core`
dependency edge entirely:
  - `codex-utils-approval-presets`
  - `codex-utils-cli`

## Verification

- `cargo test -p codex-utils-approval-presets`
- `cargo test -p codex-utils-cli`
- `cargo check --workspace --all-targets`
- `just clippy`

codex-rs/linux-sandbox/tests/suite/landlock.rs

@@ -7,9 +7,9 @@ use codex_core::error::SandboxErr;
 use codex_core::exec::ExecParams;
 use codex_core::exec::process_exec_tool_call;
 use codex_core::exec_env::create_env;
-use codex_core::protocol::SandboxPolicy;
-use codex_core::protocol_config_types::WindowsSandboxLevel;
 use codex_core::sandboxing::SandboxPermissions;
+use codex_protocol::config_types::WindowsSandboxLevel;
+use codex_protocol::protocol::SandboxPolicy;
 use codex_utils_absolute_path::AbsolutePathBuf;
 use pretty_assertions::assert_eq;
 use std::collections::HashMap;