@@ -7655,22 +7655,36 @@ def _describe_syntax_error(rel: str, line: "int | None", kept: int) -> str:
 
     # #3946: a code file that parses CLEANLY (no parse_errors — distinct from
     # the #2551/#2599 case just above, where _syntax_error_files already
-    # explains the loss) but still yields only its own bare file node is
-    # usually a plain data literal the AST extractor has nothing to model
-    # (`const BANK = [...]`), not a code file with no symbols. Nothing
-    # reported this before; the file silently entered the graph as a bare,
+    # explains the loss) but yields NOTHING beyond its own bare file node often
+    # is a plain data literal the AST extractor has nothing to model
+    # (`const BANK = [...]`). It silently entered the graph as a bare,
     # zero-edge node, indistinguishable from a legitimately symbol-free file.
+    #
+    # Scope this to EXACTLY one node (the unconditional file node, engine.py):
+    # - `== 1`, not `<= 1`, so the 0-node domain stays owned by #1666 (zero
+    #   nodes / retry) and is not double-reported with contradictory advice;
+    # - skip `skipped` (#1224/#2879 intentional data declines, like #1666) and
+    #   no-extractor files (#1689 already reports those as unsupported code);
+    # - skip empty/whitespace-only files (an empty `__init__.py`, `py.typed`)
+    #   — there is nothing to model, so the warning would be pure noise.
+    # The message stays neutral ("no symbols"): a def-less script or thin
+    # module is symbol-less *code*, not necessarily data.
     _symbolless_files: list[tuple[str, int]] = []
     for i, _p in enumerate(paths):
         _res = per_file[i] or {}
-        if _res.get("parse_errors") or _res.get("error"):
+        if _res.get("parse_errors") or _res.get("error") or _res.get("skipped"):
             continue
-        if len(_res.get("nodes", [])) <= 1:
-            try:
-                _size = _p.stat().st_size
-            except OSError:
-                _size = 0
-            _symbolless_files.append((os.path.relpath(str(_p), str(root)).replace("\\", "/"), _size))
+        if _get_extractor(_p) is None:
+            continue
+        if len(_res.get("nodes", [])) != 1:
+            continue
+        try:
+            _size = _p.stat().st_size
+            if not _p.read_text(encoding="utf-8", errors="ignore").strip():
+                continue  # empty / whitespace-only: nothing to model, no signal
+        except OSError:
+            _size = 0
+        _symbolless_files.append((os.path.relpath(str(_p), str(root)).replace("\\", "/"), _size))
     if _symbolless_files:
         _total_bytes = sum(size for _, size in _symbolless_files)
         _total_mb = _total_bytes / (1024 * 1024)
@@ -7681,8 +7695,8 @@ def _describe_syntax_error(rel: str, line: "int | None", kept: int) -> str:
         )
         print(
             f"  warning: {len(_symbolless_files)} code file(s) yielded no symbols "
-            f"({_total_mb:.2f} MB); they may be data rather than code: "
-            f"{_shown_sl}{_more_sl}",
+            f"({_total_mb:.2f} MB) — a data file, or source this extractor models "
+            f"no symbols for: {_shown_sl}{_more_sl}",
             file=sys.stderr, flush=True,
         )
 
 
@@ -80,3 +80,66 @@ def test_the_citation_is_gone_from_the_source_not_just_one_path():
     assert "may be partially extracted: {_shown}{_more} (#2551)" not in text
     assert "no symbols extracted" in text
     assert "symbol(s) extracted" in text
+
+
+# ── #3946: a clean-parse file that yields nothing but its own file node ─────
+
+def _data_only_fixture(tmp_path):
+    """A plain data literal with no functions, classes or imports — the AST
+    extractor has nothing to model, but the file parses with zero errors, so
+    the syntax-error warning above must stay silent for it."""
+    f = tmp_path / "data.js"
+    f.write_text("module.exports = [{a: 1}, {b: 2}];\n", encoding="utf-8")
+    return f
+
+
+def test_symbolless_warning_names_the_file(tmp_path, capsys):
+    err = _run(tmp_path, [_data_only_fixture(tmp_path)], capsys)
+    assert "yielded no symbols" in err, err
+    assert "data.js" in err
+    # neutral wording: a symbol-less file may be data OR source the extractor
+    # models nothing for — do NOT assert it is "data rather than code".
+    assert "may be data rather than code" not in err
+
+
+def test_symbolless_warning_is_silent_for_an_empty_init(tmp_path, capsys):
+    """An empty __init__.py is symbol-less *code*, ubiquitous in Python
+    packages. It has nothing to model, so the warning must stay silent rather
+    than fire on essentially every package scan."""
+    pkg = tmp_path / "pkg"
+    pkg.mkdir()
+    (pkg / "__init__.py").write_text("", encoding="utf-8")
+    err = _run(tmp_path, [pkg / "__init__.py"], capsys)
+    assert "yielded no symbols" not in err
+
+
+def test_symbolless_warning_is_silent_for_a_whitespace_only_file(tmp_path, capsys):
+    f = tmp_path / "blank.py"
+    f.write_text("\n   \n\t\n", encoding="utf-8")
+    err = _run(tmp_path, [f], capsys)
+    # whitespace-only: nothing to model, so the strip-empty guard keeps it quiet
+    assert "yielded no symbols" not in err
+
+
+def test_symbolless_warning_does_not_fire_for_a_real_function(tmp_path, capsys):
+    f = tmp_path / "real.js"
+    f.write_text("function run() { return 1; }\n", encoding="utf-8")
+    err = _run(tmp_path, [f], capsys)
+    assert "yielded no symbols" not in err
+
+
+def test_symbolless_warning_does_not_overlap_the_syntax_error_warning(tmp_path, capsys):
+    """A file already explained by the partial-extraction warning (a genuine
+    parse error) must not ALSO be counted as a clean-parse data file."""
+    err = _run(tmp_path, [_partial_parse_fixture(tmp_path)], capsys)
+    assert "yielded no symbols" not in err
+
+
+def test_symbolless_warning_counts_total_size(tmp_path, capsys):
+    a = tmp_path / "a.js"
+    a.write_text("module.exports = [1, 2, 3];\n", encoding="utf-8")
+    b = tmp_path / "b.js"
+    b.write_text("export default [4, 5, 6];\n", encoding="utf-8")
+    err = _run(tmp_path, [a, b], capsys)
+    assert "2 code file(s) yielded no symbols" in err
+    assert "a.js" in err and "b.js" in err