diff --git a/graphify/skill-agents.md b/graphify/skill-agents.md
index 3f7fade81..126a76ca7 100644
--- a/graphify/skill-agents.md
+++ b/graphify/skill-agents.md
@@ -190,7 +190,10 @@ for f in detect.get('files', {}).get('code', []):
     code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
 
 if code_files:
-    result = extract(code_files, cache_root=Path('INPUT_PATH'))
+    # root= anchors node ids and source_file on the scan root; cache_root only says
+    # where graphify-out/cache lives. Pass both: without root= the anchor falls back
+    # to cache_root, so pointing the cache elsewhere would rename every node (#3727).
+    result = extract(code_files, cache_root=Path('INPUT_PATH'), root=Path('INPUT_PATH'))
     Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
     print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
 else:
diff --git a/graphify/skill-amp.md b/graphify/skill-amp.md
index 3f7fade81..126a76ca7 100644
--- a/graphify/skill-amp.md
+++ b/graphify/skill-amp.md
@@ -190,7 +190,10 @@ for f in detect.get('files', {}).get('code', []):
     code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
 
 if code_files:
-    result = extract(code_files, cache_root=Path('INPUT_PATH'))
+    # root= anchors node ids and source_file on the scan root; cache_root only says
+    # where graphify-out/cache lives. Pass both: without root= the anchor falls back
+    # to cache_root, so pointing the cache elsewhere would rename every node (#3727).
+    result = extract(code_files, cache_root=Path('INPUT_PATH'), root=Path('INPUT_PATH'))
     Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
     print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
 else:
diff --git a/graphify/skill-claw.md b/graphify/skill-claw.md
index 2eca2a295..72baabb55 100644
--- a/graphify/skill-claw.md
+++ b/graphify/skill-claw.md
@@ -190,7 +190,10 @@ for f in detect.get('files', {}).get('code', []):
     code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
 
 if code_files:
-    result = extract(code_files, cache_root=Path('INPUT_PATH'))
+    # root= anchors node ids and source_file on the scan root; cache_root only says
+    # where graphify-out/cache lives. Pass both: without root= the anchor falls back
+    # to cache_root, so pointing the cache elsewhere would rename every node (#3727).
+    result = extract(code_files, cache_root=Path('INPUT_PATH'), root=Path('INPUT_PATH'))
     Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
     print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
 else:
diff --git a/graphify/skill-codex.md b/graphify/skill-codex.md
index a126527fd..48c77384f 100644
--- a/graphify/skill-codex.md
+++ b/graphify/skill-codex.md
@@ -190,7 +190,10 @@ for f in detect.get('files', {}).get('code', []):
     code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
 
 if code_files:
-    result = extract(code_files, cache_root=Path('INPUT_PATH'))
+    # root= anchors node ids and source_file on the scan root; cache_root only says
+    # where graphify-out/cache lives. Pass both: without root= the anchor falls back
+    # to cache_root, so pointing the cache elsewhere would rename every node (#3727).
+    result = extract(code_files, cache_root=Path('INPUT_PATH'), root=Path('INPUT_PATH'))
     Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
     print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
 else:
diff --git a/graphify/skill-copilot.md b/graphify/skill-copilot.md
index 2eca2a295..72baabb55 100644
--- a/graphify/skill-copilot.md
+++ b/graphify/skill-copilot.md
@@ -190,7 +190,10 @@ for f in detect.get('files', {}).get('code', []):
     code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
 
 if code_files:
-    result = extract(code_files, cache_root=Path('INPUT_PATH'))
+    # root= anchors node ids and source_file on the scan root; cache_root only says
+    # where graphify-out/cache lives. Pass both: without root= the anchor falls back
+    # to cache_root, so pointing the cache elsewhere would rename every node (#3727).
+    result = extract(code_files, cache_root=Path('INPUT_PATH'), root=Path('INPUT_PATH'))
     Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
     print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
 else:
diff --git a/graphify/skill-droid.md b/graphify/skill-droid.md
index b1eeb4925..639bde513 100644
--- a/graphify/skill-droid.md
+++ b/graphify/skill-droid.md
@@ -190,7 +190,10 @@ for f in detect.get('files', {}).get('code', []):
     code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
 
 if code_files:
-    result = extract(code_files, cache_root=Path('INPUT_PATH'))
+    # root= anchors node ids and source_file on the scan root; cache_root only says
+    # where graphify-out/cache lives. Pass both: without root= the anchor falls back
+    # to cache_root, so pointing the cache elsewhere would rename every node (#3727).
+    result = extract(code_files, cache_root=Path('INPUT_PATH'), root=Path('INPUT_PATH'))
     Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
     print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
 else:
diff --git a/graphify/skill-kilo.md b/graphify/skill-kilo.md
index 387563de4..1797e2f27 100644
--- a/graphify/skill-kilo.md
+++ b/graphify/skill-kilo.md
@@ -190,7 +190,10 @@ for f in detect.get('files', {}).get('code', []):
     code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
 
 if code_files:
-    result = extract(code_files, cache_root=Path('INPUT_PATH'))
+    # root= anchors node ids and source_file on the scan root; cache_root only says
+    # where graphify-out/cache lives. Pass both: without root= the anchor falls back
+    # to cache_root, so pointing the cache elsewhere would rename every node (#3727).
+    result = extract(code_files, cache_root=Path('INPUT_PATH'), root=Path('INPUT_PATH'))
     Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
     print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
 else:
diff --git a/graphify/skill-kiro.md b/graphify/skill-kiro.md
index 2eca2a295..72baabb55 100644
--- a/graphify/skill-kiro.md
+++ b/graphify/skill-kiro.md
@@ -190,7 +190,10 @@ for f in detect.get('files', {}).get('code', []):
     code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
 
 if code_files:
-    result = extract(code_files, cache_root=Path('INPUT_PATH'))
+    # root= anchors node ids and source_file on the scan root; cache_root only says
+    # where graphify-out/cache lives. Pass both: without root= the anchor falls back
+    # to cache_root, so pointing the cache elsewhere would rename every node (#3727).
+    result = extract(code_files, cache_root=Path('INPUT_PATH'), root=Path('INPUT_PATH'))
     Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
     print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
 else:
diff --git a/graphify/skill-opencode.md b/graphify/skill-opencode.md
index 144378e65..98f2d8111 100644
--- a/graphify/skill-opencode.md
+++ b/graphify/skill-opencode.md
@@ -190,7 +190,10 @@ for f in detect.get('files', {}).get('code', []):
     code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
 
 if code_files:
-    result = extract(code_files, cache_root=Path('INPUT_PATH'))
+    # root= anchors node ids and source_file on the scan root; cache_root only says
+    # where graphify-out/cache lives. Pass both: without root= the anchor falls back
+    # to cache_root, so pointing the cache elsewhere would rename every node (#3727).
+    result = extract(code_files, cache_root=Path('INPUT_PATH'), root=Path('INPUT_PATH'))
     Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
     print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
 else:
diff --git a/graphify/skill-pi.md b/graphify/skill-pi.md
index 2eca2a295..72baabb55 100644
--- a/graphify/skill-pi.md
+++ b/graphify/skill-pi.md
@@ -190,7 +190,10 @@ for f in detect.get('files', {}).get('code', []):
     code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
 
 if code_files:
-    result = extract(code_files, cache_root=Path('INPUT_PATH'))
+    # root= anchors node ids and source_file on the scan root; cache_root only says
+    # where graphify-out/cache lives. Pass both: without root= the anchor falls back
+    # to cache_root, so pointing the cache elsewhere would rename every node (#3727).
+    result = extract(code_files, cache_root=Path('INPUT_PATH'), root=Path('INPUT_PATH'))
     Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
     print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
 else:
diff --git a/graphify/skill-trae.md b/graphify/skill-trae.md
index 36706e3d7..68ee4ca00 100644
--- a/graphify/skill-trae.md
+++ b/graphify/skill-trae.md
@@ -190,7 +190,10 @@ for f in detect.get('files', {}).get('code', []):
     code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
 
 if code_files:
-    result = extract(code_files, cache_root=Path('INPUT_PATH'))
+    # root= anchors node ids and source_file on the scan root; cache_root only says
+    # where graphify-out/cache lives. Pass both: without root= the anchor falls back
+    # to cache_root, so pointing the cache elsewhere would rename every node (#3727).
+    result = extract(code_files, cache_root=Path('INPUT_PATH'), root=Path('INPUT_PATH'))
     Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
     print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
 else:
diff --git a/graphify/skill-vscode.md b/graphify/skill-vscode.md
index 6191a4ca6..66d3bea85 100644
--- a/graphify/skill-vscode.md
+++ b/graphify/skill-vscode.md
@@ -190,7 +190,10 @@ for f in detect.get('files', {}).get('code', []):
     code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
 
 if code_files:
-    result = extract(code_files, cache_root=Path('INPUT_PATH'))
+    # root= anchors node ids and source_file on the scan root; cache_root only says
+    # where graphify-out/cache lives. Pass both: without root= the anchor falls back
+    # to cache_root, so pointing the cache elsewhere would rename every node (#3727).
+    result = extract(code_files, cache_root=Path('INPUT_PATH'), root=Path('INPUT_PATH'))
     Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
     print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
 else:
diff --git a/graphify/skill-windows.md b/graphify/skill-windows.md
index 456244a24..4ad034ba1 100644
--- a/graphify/skill-windows.md
+++ b/graphify/skill-windows.md
@@ -218,7 +218,10 @@ for f in detect.get('files', {}).get('code', []):
     code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
 
 if code_files:
-    result = extract(code_files, cache_root=Path('INPUT_PATH'))
+    # root= anchors node ids and source_file on the scan root; cache_root only says
+    # where graphify-out/cache lives. Pass both: without root= the anchor falls back
+    # to cache_root, so pointing the cache elsewhere would rename every node (#3727).
+    result = extract(code_files, cache_root=Path('INPUT_PATH'), root=Path('INPUT_PATH'))
     Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding="utf-8")
     print(f'AST: {len(result["nodes"])} nodes, {len(result["edges"])} edges')
 else:
diff --git a/graphify/skill.md b/graphify/skill.md
index 2eca2a295..72baabb55 100644
--- a/graphify/skill.md
+++ b/graphify/skill.md
@@ -190,7 +190,10 @@ for f in detect.get('files', {}).get('code', []):
     code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
 
 if code_files:
-    result = extract(code_files, cache_root=Path('INPUT_PATH'))
+    # root= anchors node ids and source_file on the scan root; cache_root only says
+    # where graphify-out/cache lives. Pass both: without root= the anchor falls back
+    # to cache_root, so pointing the cache elsewhere would rename every node (#3727).
+    result = extract(code_files, cache_root=Path('INPUT_PATH'), root=Path('INPUT_PATH'))
     Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
     print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
 else:
diff --git a/tests/test_skill_part_a_explicit_root.py b/tests/test_skill_part_a_explicit_root.py
new file mode 100644
index 000000000..381d1269d
--- /dev/null
+++ b/tests/test_skill_part_a_explicit_root.py
@@ -0,0 +1,78 @@
+"""Step 3 Part A passes root= to extract(), so the cache location never anchors ids (#3727).
+
+``extract(paths, cache_root=...)`` uses ``cache_root`` as the fallback anchor for
+``source_file`` and node ids when ``root`` is not given (#1941). Part A called it
+with ``cache_root`` alone. That is harmless while the cache sits in the scan root,
+but the two parameters look alike, and anyone adapting the block to a cache that
+lives elsewhere re-anchored every code node: same node count, every id renamed,
+and every cached edge into code left dangling. A node-count guard cannot see it.
+"""
+from __future__ import annotations
+
+import sys
+from pathlib import Path
+
+import pytest
+
+# tests/ -> repo root is one parent up; put it on the path so tools.skillgen
+# imports regardless of pytest's import mode.
+REPO_ROOT = Path(__file__).resolve().parent.parent
+if str(REPO_ROOT) not in sys.path:
+    sys.path.insert(0, str(REPO_ROOT))
+
+from graphify.extract import extract  # noqa: E402
+from tools.skillgen import gen  # noqa: E402
+
+_CALL = "extract(code_files, cache_root="
+
+
+def _split_hosts() -> list[gen.Platform]:
+    return [p for p in gen.load_platforms().values() if p.bucket != "monolith"]
+
+
+def _part_a_calls(platform: gen.Platform) -> list[str]:
+    body = gen.render(platform)[0].content
+    return [line.strip() for line in body.splitlines() if _CALL in line]
+
+
+def test_split_hosts_are_discovered():
+    """The parametrized guard below must not pass vacuously on an empty list."""
+    assert len(_split_hosts()) >= 10, [p.key for p in _split_hosts()]
+
+
+@pytest.mark.parametrize("platform", _split_hosts(), ids=lambda p: p.key)
+def test_part_a_passes_an_explicit_root(platform: gen.Platform):
+    calls = _part_a_calls(platform)
+    assert calls, f"[{platform.key}] Part A extract() call not found"
+    for call in calls:
+        assert "root=Path('INPUT_PATH')" in call.replace("cache_root=Path('INPUT_PATH')", ""), (
+            f"[{platform.key}] Part A calls extract() with cache_root but no root= (#3727): {call!r}"
+        )
+
+
+def test_relocating_only_the_cache_does_not_rename_part_a_nodes(tmp_path: Path):
+    """Run the shipped call twice, moving nothing but the cache: ids must not change."""
+    scan_root = tmp_path / "proj"
+    (scan_root / "pkg").mkdir(parents=True)
+    module = scan_root / "pkg" / "mod.py"
+    module.write_text("def hello():\n    return 1\n", encoding="utf-8")
+    elsewhere = tmp_path / "cache-elsewhere"
+    elsewhere.mkdir()
+
+    (call,) = _part_a_calls(gen.load_platforms()["claude"])
+    expression = call.removeprefix("result = ")
+    in_place = expression.replace("Path('INPUT_PATH')", f"Path({str(scan_root)!r})")
+    relocated = expression.replace(
+        "cache_root=Path('INPUT_PATH')", f"cache_root=Path({str(elsewhere)!r})"
+    ).replace("Path('INPUT_PATH')", f"Path({str(scan_root)!r})")
+    assert in_place != relocated
+
+    scope = {"extract": extract, "Path": Path, "code_files": [module]}
+    ids_in_place = sorted(n["id"] for n in eval(in_place, dict(scope))["nodes"])
+    ids_relocated = sorted(n["id"] for n in eval(relocated, dict(scope))["nodes"])
+
+    assert ids_in_place, "expected AST nodes for the module"
+    assert ids_relocated == ids_in_place, (
+        "moving only the cache renamed the code nodes: "
+        f"{ids_in_place} -> {ids_relocated}"
+    )
diff --git a/tools/skillgen/expected/graphify__skill-agents.md b/tools/skillgen/expected/graphify__skill-agents.md
index 3f7fade81..126a76ca7 100644
--- a/tools/skillgen/expected/graphify__skill-agents.md
+++ b/tools/skillgen/expected/graphify__skill-agents.md
@@ -190,7 +190,10 @@ for f in detect.get('files', {}).get('code', []):
     code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
 
 if code_files:
-    result = extract(code_files, cache_root=Path('INPUT_PATH'))
+    # root= anchors node ids and source_file on the scan root; cache_root only says
+    # where graphify-out/cache lives. Pass both: without root= the anchor falls back
+    # to cache_root, so pointing the cache elsewhere would rename every node (#3727).
+    result = extract(code_files, cache_root=Path('INPUT_PATH'), root=Path('INPUT_PATH'))
     Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
     print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
 else:
diff --git a/tools/skillgen/expected/graphify__skill-amp.md b/tools/skillgen/expected/graphify__skill-amp.md
index 3f7fade81..126a76ca7 100644
--- a/tools/skillgen/expected/graphify__skill-amp.md
+++ b/tools/skillgen/expected/graphify__skill-amp.md
@@ -190,7 +190,10 @@ for f in detect.get('files', {}).get('code', []):
     code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
 
 if code_files:
-    result = extract(code_files, cache_root=Path('INPUT_PATH'))
+    # root= anchors node ids and source_file on the scan root; cache_root only says
+    # where graphify-out/cache lives. Pass both: without root= the anchor falls back
+    # to cache_root, so pointing the cache elsewhere would rename every node (#3727).
+    result = extract(code_files, cache_root=Path('INPUT_PATH'), root=Path('INPUT_PATH'))
     Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
     print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
 else:
diff --git a/tools/skillgen/expected/graphify__skill-claw.md b/tools/skillgen/expected/graphify__skill-claw.md
index 2eca2a295..72baabb55 100644
--- a/tools/skillgen/expected/graphify__skill-claw.md
+++ b/tools/skillgen/expected/graphify__skill-claw.md
@@ -190,7 +190,10 @@ for f in detect.get('files', {}).get('code', []):
     code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
 
 if code_files:
-    result = extract(code_files, cache_root=Path('INPUT_PATH'))
+    # root= anchors node ids and source_file on the scan root; cache_root only says
+    # where graphify-out/cache lives. Pass both: without root= the anchor falls back
+    # to cache_root, so pointing the cache elsewhere would rename every node (#3727).
+    result = extract(code_files, cache_root=Path('INPUT_PATH'), root=Path('INPUT_PATH'))
     Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
     print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
 else:
diff --git a/tools/skillgen/expected/graphify__skill-codex.md b/tools/skillgen/expected/graphify__skill-codex.md
index a126527fd..48c77384f 100644
--- a/tools/skillgen/expected/graphify__skill-codex.md
+++ b/tools/skillgen/expected/graphify__skill-codex.md
@@ -190,7 +190,10 @@ for f in detect.get('files', {}).get('code', []):
     code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
 
 if code_files:
-    result = extract(code_files, cache_root=Path('INPUT_PATH'))
+    # root= anchors node ids and source_file on the scan root; cache_root only says
+    # where graphify-out/cache lives. Pass both: without root= the anchor falls back
+    # to cache_root, so pointing the cache elsewhere would rename every node (#3727).
+    result = extract(code_files, cache_root=Path('INPUT_PATH'), root=Path('INPUT_PATH'))
     Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
     print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
 else:
diff --git a/tools/skillgen/expected/graphify__skill-copilot.md b/tools/skillgen/expected/graphify__skill-copilot.md
index 2eca2a295..72baabb55 100644
--- a/tools/skillgen/expected/graphify__skill-copilot.md
+++ b/tools/skillgen/expected/graphify__skill-copilot.md
@@ -190,7 +190,10 @@ for f in detect.get('files', {}).get('code', []):
     code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
 
 if code_files:
-    result = extract(code_files, cache_root=Path('INPUT_PATH'))
+    # root= anchors node ids and source_file on the scan root; cache_root only says
+    # where graphify-out/cache lives. Pass both: without root= the anchor falls back
+    # to cache_root, so pointing the cache elsewhere would rename every node (#3727).
+    result = extract(code_files, cache_root=Path('INPUT_PATH'), root=Path('INPUT_PATH'))
     Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
     print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
 else:
diff --git a/tools/skillgen/expected/graphify__skill-droid.md b/tools/skillgen/expected/graphify__skill-droid.md
index b1eeb4925..639bde513 100644
--- a/tools/skillgen/expected/graphify__skill-droid.md
+++ b/tools/skillgen/expected/graphify__skill-droid.md
@@ -190,7 +190,10 @@ for f in detect.get('files', {}).get('code', []):
     code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
 
 if code_files:
-    result = extract(code_files, cache_root=Path('INPUT_PATH'))
+    # root= anchors node ids and source_file on the scan root; cache_root only says
+    # where graphify-out/cache lives. Pass both: without root= the anchor falls back
+    # to cache_root, so pointing the cache elsewhere would rename every node (#3727).
+    result = extract(code_files, cache_root=Path('INPUT_PATH'), root=Path('INPUT_PATH'))
     Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
     print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
 else:
diff --git a/tools/skillgen/expected/graphify__skill-kilo.md b/tools/skillgen/expected/graphify__skill-kilo.md
index 387563de4..1797e2f27 100644
--- a/tools/skillgen/expected/graphify__skill-kilo.md
+++ b/tools/skillgen/expected/graphify__skill-kilo.md
@@ -190,7 +190,10 @@ for f in detect.get('files', {}).get('code', []):
     code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
 
 if code_files:
-    result = extract(code_files, cache_root=Path('INPUT_PATH'))
+    # root= anchors node ids and source_file on the scan root; cache_root only says
+    # where graphify-out/cache lives. Pass both: without root= the anchor falls back
+    # to cache_root, so pointing the cache elsewhere would rename every node (#3727).
+    result = extract(code_files, cache_root=Path('INPUT_PATH'), root=Path('INPUT_PATH'))
     Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
     print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
 else:
diff --git a/tools/skillgen/expected/graphify__skill-kiro.md b/tools/skillgen/expected/graphify__skill-kiro.md
index 2eca2a295..72baabb55 100644
--- a/tools/skillgen/expected/graphify__skill-kiro.md
+++ b/tools/skillgen/expected/graphify__skill-kiro.md
@@ -190,7 +190,10 @@ for f in detect.get('files', {}).get('code', []):
     code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
 
 if code_files:
-    result = extract(code_files, cache_root=Path('INPUT_PATH'))
+    # root= anchors node ids and source_file on the scan root; cache_root only says
+    # where graphify-out/cache lives. Pass both: without root= the anchor falls back
+    # to cache_root, so pointing the cache elsewhere would rename every node (#3727).
+    result = extract(code_files, cache_root=Path('INPUT_PATH'), root=Path('INPUT_PATH'))
     Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
     print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
 else:
diff --git a/tools/skillgen/expected/graphify__skill-opencode.md b/tools/skillgen/expected/graphify__skill-opencode.md
index 144378e65..98f2d8111 100644
--- a/tools/skillgen/expected/graphify__skill-opencode.md
+++ b/tools/skillgen/expected/graphify__skill-opencode.md
@@ -190,7 +190,10 @@ for f in detect.get('files', {}).get('code', []):
     code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
 
 if code_files:
-    result = extract(code_files, cache_root=Path('INPUT_PATH'))
+    # root= anchors node ids and source_file on the scan root; cache_root only says
+    # where graphify-out/cache lives. Pass both: without root= the anchor falls back
+    # to cache_root, so pointing the cache elsewhere would rename every node (#3727).
+    result = extract(code_files, cache_root=Path('INPUT_PATH'), root=Path('INPUT_PATH'))
     Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
     print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
 else:
diff --git a/tools/skillgen/expected/graphify__skill-pi.md b/tools/skillgen/expected/graphify__skill-pi.md
index 2eca2a295..72baabb55 100644
--- a/tools/skillgen/expected/graphify__skill-pi.md
+++ b/tools/skillgen/expected/graphify__skill-pi.md
@@ -190,7 +190,10 @@ for f in detect.get('files', {}).get('code', []):
     code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
 
 if code_files:
-    result = extract(code_files, cache_root=Path('INPUT_PATH'))
+    # root= anchors node ids and source_file on the scan root; cache_root only says
+    # where graphify-out/cache lives. Pass both: without root= the anchor falls back
+    # to cache_root, so pointing the cache elsewhere would rename every node (#3727).
+    result = extract(code_files, cache_root=Path('INPUT_PATH'), root=Path('INPUT_PATH'))
     Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
     print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
 else:
diff --git a/tools/skillgen/expected/graphify__skill-trae.md b/tools/skillgen/expected/graphify__skill-trae.md
index 36706e3d7..68ee4ca00 100644
--- a/tools/skillgen/expected/graphify__skill-trae.md
+++ b/tools/skillgen/expected/graphify__skill-trae.md
@@ -190,7 +190,10 @@ for f in detect.get('files', {}).get('code', []):
     code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
 
 if code_files:
-    result = extract(code_files, cache_root=Path('INPUT_PATH'))
+    # root= anchors node ids and source_file on the scan root; cache_root only says
+    # where graphify-out/cache lives. Pass both: without root= the anchor falls back
+    # to cache_root, so pointing the cache elsewhere would rename every node (#3727).
+    result = extract(code_files, cache_root=Path('INPUT_PATH'), root=Path('INPUT_PATH'))
     Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
     print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
 else:
diff --git a/tools/skillgen/expected/graphify__skill-vscode.md b/tools/skillgen/expected/graphify__skill-vscode.md
index 6191a4ca6..66d3bea85 100644
--- a/tools/skillgen/expected/graphify__skill-vscode.md
+++ b/tools/skillgen/expected/graphify__skill-vscode.md
@@ -190,7 +190,10 @@ for f in detect.get('files', {}).get('code', []):
     code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
 
 if code_files:
-    result = extract(code_files, cache_root=Path('INPUT_PATH'))
+    # root= anchors node ids and source_file on the scan root; cache_root only says
+    # where graphify-out/cache lives. Pass both: without root= the anchor falls back
+    # to cache_root, so pointing the cache elsewhere would rename every node (#3727).
+    result = extract(code_files, cache_root=Path('INPUT_PATH'), root=Path('INPUT_PATH'))
     Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
     print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
 else:
diff --git a/tools/skillgen/expected/graphify__skill-windows.md b/tools/skillgen/expected/graphify__skill-windows.md
index 456244a24..4ad034ba1 100644
--- a/tools/skillgen/expected/graphify__skill-windows.md
+++ b/tools/skillgen/expected/graphify__skill-windows.md
@@ -218,7 +218,10 @@ for f in detect.get('files', {}).get('code', []):
     code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
 
 if code_files:
-    result = extract(code_files, cache_root=Path('INPUT_PATH'))
+    # root= anchors node ids and source_file on the scan root; cache_root only says
+    # where graphify-out/cache lives. Pass both: without root= the anchor falls back
+    # to cache_root, so pointing the cache elsewhere would rename every node (#3727).
+    result = extract(code_files, cache_root=Path('INPUT_PATH'), root=Path('INPUT_PATH'))
     Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding="utf-8")
     print(f'AST: {len(result["nodes"])} nodes, {len(result["edges"])} edges')
 else:
diff --git a/tools/skillgen/expected/graphify__skill.md b/tools/skillgen/expected/graphify__skill.md
index 2eca2a295..72baabb55 100644
--- a/tools/skillgen/expected/graphify__skill.md
+++ b/tools/skillgen/expected/graphify__skill.md
@@ -190,7 +190,10 @@ for f in detect.get('files', {}).get('code', []):
     code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
 
 if code_files:
-    result = extract(code_files, cache_root=Path('INPUT_PATH'))
+    # root= anchors node ids and source_file on the scan root; cache_root only says
+    # where graphify-out/cache lives. Pass both: without root= the anchor falls back
+    # to cache_root, so pointing the cache elsewhere would rename every node (#3727).
+    result = extract(code_files, cache_root=Path('INPUT_PATH'), root=Path('INPUT_PATH'))
     Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
     print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
 else:
diff --git a/tools/skillgen/fragments/core/core.md b/tools/skillgen/fragments/core/core.md
index c527a1256..4a30d95ed 100644
--- a/tools/skillgen/fragments/core/core.md
+++ b/tools/skillgen/fragments/core/core.md
@@ -143,7 +143,10 @@ for f in detect.get('files', {}).get('code', []):
     code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])
 
 if code_files:
-    result = extract(code_files, cache_root=Path('INPUT_PATH'))
+    # root= anchors node ids and source_file on the scan root; cache_root only says
+    # where graphify-out/cache lives. Pass both: without root= the anchor falls back
+    # to cache_root, so pointing the cache elsewhere would rename every node (#3727).
+    result = extract(code_files, cache_root=Path('INPUT_PATH'), root=Path('INPUT_PATH'))
     Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
     print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
 else: