Add config toggles for orchestrator skills and MCP (#28942)

## Why

Orchestrator-provided skills and Codex Apps MCP tools add model-visible
instructions, resources, and tools beyond the local workspace. Hosts
need config-level switches to disable those orchestrator-owned surfaces
independently, without disabling regular skills or regular MCP servers.

## What changed

- Adds `[orchestrator.skills].enabled` and `[orchestrator.mcp].enabled`
config entries, both defaulting to `true`.
- Includes the new settings in `config.schema.json` and in the config
lock so resolved thread configuration preserves the same orchestrator
exposure decisions.
- Threads `orchestrator.skills.enabled` through the app-server skills
extension so disabled orchestrator skills do not expose the `skills`
namespace or inject orchestrator skill context.
- Gates Codex Apps MCP exposure, app instructions, and app auth
eligibility on `orchestrator.mcp.enabled` while leaving non-Codex-Apps
MCP tools available.
- Updates the thread-manager sample config to disable both
orchestrator-owned surfaces.

## Verification

- Added config parsing, loading, defaulting, and schema coverage for the
new settings.
- Added MCP exposure coverage that `orchestrator.mcp.enabled = false`
removes Codex Apps tools while preserving regular MCP tools.
- Added app-server coverage that `orchestrator.skills.enabled = false`
prevents orchestrator skill tools, prompts, and resource reads from
reaching the model turn.

codex-rs/app-server/src/extensions.rs

@@ -88,6 +88,7 @@ where
         |config: &Config| codex_skills_extension::SkillsExtensionConfig {
             include_instructions: config.include_skill_instructions,
             bundled_skills_enabled: config.bundled_skills_enabled(),
+            orchestrator_skills_enabled: config.orchestrator_skills_enabled,
         },
     );
     Arc::new(builder.build())