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/codex.rs

@@ -70,8 +70,8 @@ use codex_protocol::items::PlanItem;
 use codex_protocol::items::TurnItem;
 use codex_protocol::items::UserMessageItem;
 use codex_protocol::mcp::CallToolResult;
-use codex_protocol::models::AdditionalPermissions;
 use codex_protocol::models::BaseInstructions;
+use codex_protocol::models::PermissionProfile;
 use codex_protocol::models::format_allow_prefixes;
 use codex_protocol::openai_models::ModelInfo;
 use codex_protocol::protocol::FileChange;
@@ -2571,7 +2571,7 @@ impl Session {
         reason: Option<String>,
         network_approval_context: Option<NetworkApprovalContext>,
         proposed_execpolicy_amendment: Option<ExecPolicyAmendment>,
-        additional_permissions: Option<AdditionalPermissions>,
+        additional_permissions: Option<PermissionProfile>,
     ) -> ReviewDecision {
         //  command-level approvals use `call_id`.
         // `approval_id` is only present for subcommand callbacks (execve intercept)