From 4617cae7e0e4e47a471deeaebd810328ad857f38 Mon Sep 17 00:00:00 2001
From: Lifei Zhou <lifei@squareup.com>
Date: Mon, 12 Jan 2026 18:31:34 +1100
Subject: [PATCH] check skills with optional rules excluding the symlinks

---
 Cargo.lock                      |  2 +-
 src/agents/claude.rs            |  6 +-----
 src/operations/claude_skills.rs | 30 +++++++++++++++++++++++++++++-
 3 files changed, 31 insertions(+), 7 deletions(-)

diff --git a/Cargo.lock b/Cargo.lock
index 2525cd0..8d32ab8 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -13,7 +13,7 @@ dependencies = [
 
 [[package]]
 name = "ai-rules"
-version = "1.2.0"
+version = "1.3.0"
 dependencies = [
  "anyhow",
  "clap",
diff --git a/src/agents/claude.rs b/src/agents/claude.rs
index 89b8890..ee1962f 100644
--- a/src/agents/claude.rs
+++ b/src/agents/claude.rs
@@ -41,11 +41,7 @@ impl AgentRuleGenerator for ClaudeGenerator {
         if output_file.exists() || output_file.is_symlink() {
             fs::remove_file(&output_file)?;
         }
-
-        // Only clean skills if in skills mode
-        if self.skills_mode {
-            claude_skills::remove_generated_skills(current_dir)?;
-        }
+        claude_skills::remove_generated_skills(current_dir)?;
 
         Ok(())
     }
diff --git a/src/operations/claude_skills.rs b/src/operations/claude_skills.rs
index 28a87d5..ac86ddd 100644
--- a/src/operations/claude_skills.rs
+++ b/src/operations/claude_skills.rs
@@ -113,7 +113,10 @@ pub fn check_skills_in_sync(
         std::fs::read_dir(&skills_dir)?
             .filter_map(Result::ok)
             .filter(|entry| {
-                entry.path().is_dir()
+                let path = entry.path();
+                // Only count directories, not symlinks (symlinks are handled by ExternalSkillsGenerator)
+                path.is_dir()
+                    && !path.is_symlink()
                     && entry
                         .file_name()
                         .to_str()
@@ -391,4 +394,29 @@ mod tests {
         let result = check_skills_in_sync(&source_files, temp_dir.path()).unwrap();
         assert!(!result);
     }
+
+    #[test]
+    fn test_check_skills_in_sync_ignores_symlinks() {
+        let temp_dir = TempDir::new().unwrap();
+        let source_files = vec![create_test_source_file(
+            "optional", "Optional", false, "Content",
+        )];
+
+        create_skill_file(
+            temp_dir.path(),
+            "ai-rules-generated-optional",
+            &generate_skill_content("optional", "Optional", "optional"),
+        );
+
+        let skills_dir = temp_dir.path().join(CLAUDE_SKILLS_DIR);
+        let symlink_target = temp_dir.path().join("fake-skill");
+        std::fs::create_dir_all(&symlink_target).unwrap();
+        std::os::unix::fs::symlink(
+            &symlink_target,
+            skills_dir.join("ai-rules-generated-symlink"),
+        )
+        .unwrap();
+
+        assert!(check_skills_in_sync(&source_files, temp_dir.path()).unwrap());
+    }
 }