From 08301ccd06e804001464602dd969e9cc1463e169 Mon Sep 17 00:00:00 2001
From: Satvik Shrivas <44926681+theSatvik@users.noreply.github.com>
Date: Thu, 3 Sep 2026 02:07:26 +0530
Subject: [PATCH] fix(watch): preserve pending semantic update flag

---
 graphify/watch.py   | 13 -------------
 tests/test_watch.py | 26 ++++++++++++++++++++++++++
 2 files changed, 26 insertions(+), 13 deletions(-)

diff --git a/graphify/watch.py b/graphify/watch.py
index fbcbbc011..847ab20d7 100644
--- a/graphify/watch.py
+++ b/graphify/watch.py
@@ -1846,11 +1846,6 @@ def _failed(f: str) -> bool:
             except Exception:
                 pass
 
-            # clear stale needs_update flag if present
-            flag = out / "needs_update"
-            if flag.exists():
-                flag.unlink()
-
             if same_graph:
                 print("[graphify watch] No code-graph changes detected (--no-cluster); outputs left untouched.")
             else:
@@ -1894,9 +1889,6 @@ def _failed(f: str) -> bool:
                     )
                 except Exception:
                     pass
-                flag = out / "needs_update"
-                if flag.exists():
-                    flag.unlink()
                 html_action = _reconcile_graph_html(out, existing_graph_data)
                 if html_action == "rendered":
                     print(
@@ -2086,11 +2078,6 @@ def _failed(f: str) -> bool:
             except Exception as cf_err:
                 print(f"[graphify watch] callflow HTML update skipped: {cf_err}")
 
-        # clear stale needs_update flag if present
-        flag = out / "needs_update"
-        if flag.exists():
-            flag.unlink()
-
         if not no_change:
             print(f"[graphify watch] Rebuilt: {G.number_of_nodes()} nodes, "
                   f"{G.number_of_edges()} edges, {len(communities)} communities")
diff --git a/tests/test_watch.py b/tests/test_watch.py
index a189446b6..6f9dfac63 100644
--- a/tests/test_watch.py
+++ b/tests/test_watch.py
@@ -163,6 +163,32 @@ def test_check_update_does_not_clear_flag(tmp_path):
     assert flag.exists()
 
 
+@pytest.mark.parametrize(
+    ("no_cluster", "change_topology"),
+    [(True, False), (False, False), (False, True)],
+    ids=["no-cluster", "unchanged-topology", "clustered-rebuild"],
+)
+def test_code_rebuild_preserves_semantic_update_flag(
+    tmp_path, no_cluster, change_topology
+):
+    """An AST-only rebuild cannot clear pending semantic work (#3294)."""
+    source = tmp_path / "app.py"
+    source.write_text("def before(): pass\n", encoding="utf-8")
+    assert _rebuild_code(
+        tmp_path, no_cluster=no_cluster, acquire_lock=False
+    ) is True
+
+    flag = tmp_path / "graphify-out" / "needs_update"
+    flag.write_text("docs/PRD.md\n", encoding="utf-8")
+    if change_topology:
+        source.write_text("def after(): pass\n", encoding="utf-8")
+
+    assert _rebuild_code(
+        tmp_path, no_cluster=no_cluster, acquire_lock=False
+    ) is True
+    assert flag.read_text(encoding="utf-8") == "docs/PRD.md\n"
+
+
 def test_watch_raises_without_watchdog(tmp_path, monkeypatch):
     import builtins
     real_import = builtins.__import__