diff --git a/server/src/agents/merge.rs b/server/src/agents/merge.rs
index 88a7790e..64b43e4b 100644
--- a/server/src/agents/merge.rs
+++ b/server/src/agents/merge.rs
@@ -419,9 +419,10 @@ pub(crate) fn run_squash_merge(
     }
 
     // Verify HEAD commit has actual code changes (not an empty cherry-pick).
-    // Exclude .storkit/ so that story-file-only commits don't pass this check.
+    // Exclude .storkit/work/ (pipeline file moves) but keep .storkit/project.toml
+    // and other config files which are legitimate deliverables.
     let diff_stat = Command::new("git")
-        .args(["diff", "--stat", "HEAD~1..HEAD", "--", ".", ":(exclude).storkit"])
+        .args(["diff", "--stat", "HEAD~1..HEAD", "--", ".", ":(exclude).storkit/work"])
         .current_dir(project_root)
         .output()
         .map(|o| String::from_utf8_lossy(&o.stdout).trim().to_string())