chore: migrate additional permissions to PermissionProfile (#12731)

This PR replaces the old `additional_permissions.fs_read/fs_write` shape
with a shared `PermissionProfile`
model and wires it through the command approval, sandboxing, protocol,
and TUI layers. The schema is adopted from the
`SkillManifestPermissions`, which is also refactored to use this unified
struct. This helps us easily expose permission profiles in app
server/core as a follow-up.

codex-rs/core/src/unified_exec/mod.rs

@@ -29,7 +29,7 @@ use std::sync::Weak;
 use std::time::Duration;
 
 use codex_network_proxy::NetworkProxy;
-use codex_protocol::models::AdditionalPermissions;
+use codex_protocol::models::PermissionProfile;
 use rand::Rng;
 use rand::rng;
 use tokio::sync::Mutex;
@@ -90,7 +90,7 @@ pub(crate) struct ExecCommandRequest {
     pub network: Option<NetworkProxy>,
     pub tty: bool,
     pub sandbox_permissions: SandboxPermissions,
-    pub additional_permissions: Option<AdditionalPermissions>,
+    pub additional_permissions: Option<PermissionProfile>,
     pub justification: Option<String>,
     pub prefix_rule: Option<Vec<String>>,
 }