diff --git a/server/src/agents/merge.rs b/server/src/agents/merge.rs
index 64b43e4b..2aa06a4b 100644
--- a/server/src/agents/merge.rs
+++ b/server/src/agents/merge.rs
@@ -247,7 +247,7 @@ pub(crate) fn run_squash_merge(
             .output()
             .map_err(|e| format!("Failed to check merge diff: {e}"))?;
         let changed_files = String::from_utf8_lossy(&diff_check.stdout);
-        let has_code_changes = changed_files.lines().any(|f| !f.starts_with(".storkit/"));
+        let has_code_changes = changed_files.lines().any(|f| !f.starts_with(".storkit/work/"));
         if !has_code_changes {
             all_output.push_str(
                 "=== Merge commit contains only .storkit/ file moves, no code changes ===\n",