skills: remove unused skill permission metadata (#15900)

## Why

Skill metadata accepted a `permissions` block and stored the result on
`SkillMetadata`, but that data was never consumed by runtime behavior.
Leaving the dead parsing path in place makes it look like skills can
widen or otherwise influence execution permissions when, in practice,
declared skill permissions are ignored.

This change removes that misleading surface area so the skill metadata
model matches what the system actually uses.

## What changed

- removed `permission_profile` and `managed_network_override` from
`core-skills::SkillMetadata`
- stopped parsing `permissions` from skill metadata in
`core-skills/src/loader.rs`
- deleted the loader tests that only exercised the removed permissions
parsing path
- cleaned up dependent `SkillMetadata` constructors in tests and TUI
code that were only carrying `None` for those fields

## Testing

- `cargo test -p codex-core-skills`
- `cargo test -p codex-tui
submission_prefers_selected_duplicate_skill_path`
- `just argument-comment-lint`

codex-rs/core-skills/src/loader.rs

@@ -2,7 +2,6 @@ use crate::model::SkillDependencies;
 use crate::model::SkillError;
 use crate::model::SkillInterface;
 use crate::model::SkillLoadOutcome;
-use crate::model::SkillManagedNetworkOverride;
 use crate::model::SkillMetadata;
 use crate::model::SkillPolicy;
 use crate::model::SkillToolDependency;
@@ -13,10 +12,6 @@ use codex_config::ConfigLayerStackOrdering;
 use codex_config::default_project_root_markers;
 use codex_config::merge_toml_values;
 use codex_config::project_root_markers_from_config;
-use codex_protocol::models::FileSystemPermissions;
-use codex_protocol::models::MacOsSeatbeltProfileExtensions;
-use codex_protocol::models::NetworkPermissions;
-use codex_protocol::models::PermissionProfile;
 use codex_protocol::protocol::Product;
 use codex_protocol::protocol::SkillScope;
 use codex_utils_absolute_path::AbsolutePathBufGuard;
@@ -59,8 +54,6 @@ struct SkillMetadataFile {
     dependencies: Option<Dependencies>,
     #[serde(default)]
     policy: Option<Policy>,
-    #[serde(default)]
-    permissions: Option<SkillPermissionProfile>,
 }
 
 #[derive(Default)]
@@ -68,28 +61,6 @@ struct LoadedSkillMetadata {
     interface: Option<SkillInterface>,
     dependencies: Option<SkillDependencies>,
     policy: Option<SkillPolicy>,
-    permission_profile: Option<PermissionProfile>,
-    managed_network_override: Option<SkillManagedNetworkOverride>,
-}
-
-#[derive(Debug, Default, Deserialize, PartialEq, Eq)]
-struct SkillPermissionProfile {
-    #[serde(default)]
-    network: Option<SkillNetworkPermissions>,
-    #[serde(default)]
-    file_system: Option<FileSystemPermissions>,
-    #[serde(default)]
-    macos: Option<MacOsSeatbeltProfileExtensions>,
-}
-
-#[derive(Debug, Default, Deserialize, PartialEq, Eq)]
-struct SkillNetworkPermissions {
-    #[serde(default)]
-    enabled: Option<bool>,
-    #[serde(default)]
-    allowed_domains: Option<Vec<String>>,
-    #[serde(default)]
-    denied_domains: Option<Vec<String>>,
 }
 
 #[derive(Debug, Default, Deserialize)]
@@ -551,8 +522,6 @@ fn parse_skill_file(path: &Path, scope: SkillScope) -> Result<SkillMetadata, Ski
         interface,
         dependencies,
         policy,
-        permission_profile,
-        managed_network_override,
     } = load_skill_metadata(path);
 
     validate_len(&name, MAX_NAME_LEN, "name")?;
@@ -574,8 +543,6 @@ fn parse_skill_file(path: &Path, scope: SkillScope) -> Result<SkillMetadata, Ski
         interface,
         dependencies,
         policy,
-        permission_profile,
-        managed_network_override,
         path_to_skills_md: resolved_path,
         scope,
     })
@@ -639,54 +606,14 @@ fn load_skill_metadata(skill_path: &Path) -> LoadedSkillMetadata {
         interface,
         dependencies,
         policy,
-        permissions,
     } = parsed;
-    let (permission_profile, managed_network_override) = normalize_permissions(permissions);
     LoadedSkillMetadata {
         interface: resolve_interface(interface, skill_dir),
         dependencies: resolve_dependencies(dependencies),
         policy: resolve_policy(policy),
-        permission_profile,
-        managed_network_override,
     }
 }
 
-fn normalize_permissions(
-    permissions: Option<SkillPermissionProfile>,
-) -> (
-    Option<PermissionProfile>,
-    Option<SkillManagedNetworkOverride>,
-) {
-    let Some(permissions) = permissions else {
-        return (None, None);
-    };
-    let managed_network_override = permissions
-        .network
-        .as_ref()
-        .map(|network| SkillManagedNetworkOverride {
-            allowed_domains: network.allowed_domains.clone(),
-            denied_domains: network.denied_domains.clone(),
-        })
-        .filter(SkillManagedNetworkOverride::has_domain_overrides);
-    let permission_profile = PermissionProfile {
-        network: permissions.network.and_then(|network| {
-            let network = NetworkPermissions {
-                enabled: network.enabled,
-            };
-            (!network.is_empty()).then_some(network)
-        }),
-        file_system: permissions
-            .file_system
-            .filter(|file_system| !file_system.is_empty()),
-        macos: permissions.macos,
-    };
-
-    (
-        (!permission_profile.is_empty()).then_some(permission_profile),
-        managed_network_override,
-    )
-}
-
 fn resolve_interface(interface: Option<Interface>, skill_dir: &Path) -> Option<SkillInterface> {
     let interface = interface?;
     let interface = SkillInterface {