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/protocol/src/approvals.rs

@@ -2,7 +2,7 @@ use std::collections::HashMap;
 use std::path::PathBuf;
 
 use crate::mcp::RequestId;
-use crate::models::AdditionalPermissions;
+use crate::models::PermissionProfile;
 use crate::parse_command::ParsedCommand;
 use crate::protocol::FileChange;
 use schemars::JsonSchema;
@@ -106,7 +106,7 @@ pub struct ExecApprovalRequestEvent {
     /// Optional additional filesystem permissions requested for this command.
     #[serde(default, skip_serializing_if = "Option::is_none")]
     #[ts(optional)]
-    pub additional_permissions: Option<AdditionalPermissions>,
+    pub additional_permissions: Option<PermissionProfile>,
     pub parsed_cmd: Vec<ParsedCommand>,
 }