Support enable/disable skill via config/api. (#9328)

In config.toml:
```
[[skills.config]]
path = "/Users/xl/.codex/skills/my_skill/SKILL.md"
enabled = false
```

API:
skills/list, skills/config/write

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

@@ -85,6 +85,8 @@ use codex_app_server_protocol::ServerNotification;
 use codex_app_server_protocol::SessionConfiguredNotification;
 use codex_app_server_protocol::SetDefaultModelParams;
 use codex_app_server_protocol::SetDefaultModelResponse;
+use codex_app_server_protocol::SkillsConfigWriteParams;
+use codex_app_server_protocol::SkillsConfigWriteResponse;
 use codex_app_server_protocol::SkillsListParams;
 use codex_app_server_protocol::SkillsListResponse;
 use codex_app_server_protocol::Thread;
@@ -131,6 +133,7 @@ use codex_core::auth::login_with_api_key;
 use codex_core::config::Config;
 use codex_core::config::ConfigOverrides;
 use codex_core::config::ConfigService;
+use codex_core::config::edit::ConfigEdit;
 use codex_core::config::edit::ConfigEditsBuilder;
 use codex_core::config::types::McpServerTransportConfig;
 use codex_core::default_client::get_codex_user_agent;
@@ -400,6 +403,9 @@ impl CodexMessageProcessor {
             ClientRequest::SkillsList { request_id, params } => {
                 self.skills_list(request_id, params).await;
             }
+            ClientRequest::SkillsConfigWrite { request_id, params } => {
+                self.skills_config_write(request_id, params).await;
+            }
             ClientRequest::TurnStart { request_id, params } => {
                 self.turn_start(request_id, params).await;
             }
@@ -3246,7 +3252,7 @@ impl CodexMessageProcessor {
         for cwd in cwds {
             let outcome = skills_manager.skills_for_cwd(&cwd, force_reload).await;
             let errors = errors_to_info(&outcome.errors);
-            let skills = skills_to_info(&outcome.skills);
+            let skills = skills_to_info(&outcome.skills, &outcome.disabled_paths);
             data.push(codex_app_server_protocol::SkillsListEntry {
                 cwd,
                 skills,
@@ -3258,6 +3264,37 @@ impl CodexMessageProcessor {
             .await;
     }
 
+    async fn skills_config_write(&self, request_id: RequestId, params: SkillsConfigWriteParams) {
+        let SkillsConfigWriteParams { path, enabled } = params;
+        let edits = vec![ConfigEdit::SetSkillConfig { path, enabled }];
+        let result = ConfigEditsBuilder::new(&self.config.codex_home)
+            .with_edits(edits)
+            .apply()
+            .await;
+
+        match result {
+            Ok(()) => {
+                self.thread_manager.skills_manager().clear_cache();
+                self.outgoing
+                    .send_response(
+                        request_id,
+                        SkillsConfigWriteResponse {
+                            effective_enabled: enabled,
+                        },
+                    )
+                    .await;
+            }
+            Err(err) => {
+                let error = JSONRPCErrorError {
+                    code: INTERNAL_ERROR_CODE,
+                    message: format!("failed to update skill settings: {err}"),
+                    data: None,
+                };
+                self.outgoing.send_error(request_id, error).await;
+            }
+        }
+    }
+
     async fn interrupt_conversation(
         &mut self,
         request_id: RequestId,
@@ -3918,25 +3955,30 @@ impl CodexMessageProcessor {
 
 fn skills_to_info(
     skills: &[codex_core::skills::SkillMetadata],
+    disabled_paths: &std::collections::HashSet<PathBuf>,
 ) -> Vec<codex_app_server_protocol::SkillMetadata> {
     skills
         .iter()
-        .map(|skill| codex_app_server_protocol::SkillMetadata {
-            name: skill.name.clone(),
-            description: skill.description.clone(),
-            short_description: skill.short_description.clone(),
-            interface: skill.interface.clone().map(|interface| {
-                codex_app_server_protocol::SkillInterface {
-                    display_name: interface.display_name,
-                    short_description: interface.short_description,
-                    icon_small: interface.icon_small,
-                    icon_large: interface.icon_large,
-                    brand_color: interface.brand_color,
-                    default_prompt: interface.default_prompt,
-                }
-            }),
-            path: skill.path.clone(),
-            scope: skill.scope.into(),
+        .map(|skill| {
+            let enabled = !disabled_paths.contains(&skill.path);
+            codex_app_server_protocol::SkillMetadata {
+                name: skill.name.clone(),
+                description: skill.description.clone(),
+                short_description: skill.short_description.clone(),
+                interface: skill.interface.clone().map(|interface| {
+                    codex_app_server_protocol::SkillInterface {
+                        display_name: interface.display_name,
+                        short_description: interface.short_description,
+                        icon_small: interface.icon_small,
+                        icon_large: interface.icon_large,
+                        brand_color: interface.brand_color,
+                        default_prompt: interface.default_prompt,
+                    }
+                }),
+                path: skill.path.clone(),
+                scope: skill.scope.into(),
+                enabled,
+            }
         })
         .collect()
 }