From 8cdee988f99c9caf2b15f39b22e044171cce2486 Mon Sep 17 00:00:00 2001
From: xl-openai <xl@openai.com>
Date: Wed, 25 Feb 2026 19:55:28 -0800
Subject: [PATCH] Skip system skills for extra roots (#12744)

When extra roots is set do not load system skills.
---
 codex-rs/core/src/skills/manager.rs | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/codex-rs/core/src/skills/manager.rs b/codex-rs/core/src/skills/manager.rs
index fa00fac41f..7d2c6b89fd 100644
--- a/codex-rs/core/src/skills/manager.rs
+++ b/codex-rs/core/src/skills/manager.rs
@@ -130,6 +130,12 @@ impl SkillsManager {
                 }),
         );
         let mut outcome = load_skills_from_roots(roots);
+        if !extra_user_roots.is_empty() {
+            // When extra user roots are provided, skip system skills before caching the result.
+            outcome
+                .skills
+                .retain(|skill| skill.scope != SkillScope::System);
+        }
         outcome.disabled_paths = disabled_paths_from_stack(&config_layer_stack);
         let (by_scripts_dir, by_doc_path) =
             build_implicit_skill_path_indexes(outcome.allowed_skills_for_implicit_invocation());