diff --git a/graphify/extract.py b/graphify/extract.py
index 20e697e9e..b1a161fcf 100644
--- a/graphify/extract.py
+++ b/graphify/extract.py
@@ -82,6 +82,18 @@ def _file_stem(path: Path) -> str:
     return path.stem
 
 
+def _file_node_id(path: Path) -> str:
+    """Canonical file-level node ID matching the semantic subagent format (parent_dir_stem).
+
+    The semantic subagent (skill.md) uses ``{parent_dir}_{filename_without_ext}``, while
+    the AST extractor was using the full relative path including extension. This mismatch
+    split one file into two disconnected nodes (#1033). Using ``_file_stem`` as the base
+    produces ``script_pipeline_step`` instead of ``script_pipeline_step_py``, matching the
+    subagent format so Step-3C deduplication merges AST and semantic nodes for the same file.
+    """
+    return _make_id(_file_stem(path))
+
+
 _TSCONFIG_ALIAS_CACHE: dict[str, dict[str, str]] = {}
 _WORKSPACE_PACKAGE_CACHE: dict[str, dict[str, Path]] = {}
 _JS_CACHE_BYPASS_SUFFIXES = {".js", ".jsx", ".mjs", ".ts", ".tsx", ".vue", ".svelte"}
@@ -1086,7 +1098,7 @@ def _import_python(node, source: bytes, file_nid: str, stem: str, edges: list, s
                 for _ in range(dots - 1):
                     base = base.parent
                 rel = (module_name.replace(".", "/") + ".py") if module_name else "__init__.py"
-                tgt_nid = _make_id(str(base / rel))
+                tgt_nid = _file_node_id(base / rel)
             else:
                 tgt_nid = _make_id(raw)
             edges.append({
@@ -1112,7 +1124,7 @@ def _resolve_js_import_target(raw: str, str_path: str) -> "tuple[str, Path | Non
         return None
     resolved_path = _resolve_js_module_path(raw, Path(str_path).parent)
     if resolved_path is not None:
-        return _make_id(str(resolved_path)), resolved_path
+        return _file_node_id(resolved_path), resolved_path
     module_name = raw.split("/")[-1]
     if not module_name:
         return None
@@ -1330,7 +1342,7 @@ def _import_c(node, source: bytes, file_nid: str, stem: str, edges: list, str_pa
             if child.type != "system_lib_string":
                 resolved = _resolve_c_include_path(raw, str_path)
                 if resolved is not None:
-                    tgt_nid = _make_id(str(resolved))
+                    tgt_nid = _file_node_id(resolved)
                     edges.append({
                         "source": file_nid,
                         "target": tgt_nid,
@@ -1341,6 +1353,7 @@ def _import_c(node, source: bytes, file_nid: str, stem: str, edges: list, str_pa
                         "source_location": f"L{node.start_point[0] + 1}",
                         "weight": 1.0,
                     })
+
                     break
             module_name = raw.split("/")[-1].split(".")[0]
             if module_name:
@@ -2056,14 +2069,11 @@ def add_edge(src: str, tgt: str, relation: str, line: int,
 
     def ensure_named_node(name: str, line: int) -> str:
         nid = _make_id(stem, name)
-        if nid in seen_ids:
-            return nid
-        nid = _make_id(name)
         if nid not in seen_ids:
             add_node(nid, name, line)
         return nid
 
-    file_nid = _make_id(str(path))
+    file_nid = _file_node_id(path)
     add_node(file_nid, path.name, 1)
 
     def walk(node, parent_class_nid: str | None = None) -> None:
@@ -2114,16 +2124,14 @@ def walk(node, parent_class_nid: str | None = None) -> None:
                             base = _read_text(arg, source)
                             base_nid = _make_id(stem, base)
                             if base_nid not in seen_ids:
-                                base_nid = _make_id(base)
-                                if base_nid not in seen_ids:
-                                    nodes.append({
-                                        "id": base_nid,
-                                        "label": base,
-                                        "file_type": "code",
-                                        "source_file": "",
-                                        "source_location": "",
-                                    })
-                                    seen_ids.add(base_nid)
+                                nodes.append({
+                                    "id": base_nid,
+                                    "label": base,
+                                    "file_type": "code",
+                                    "source_file": "",
+                                    "source_location": "",
+                                })
+                                seen_ids.add(base_nid)
                             add_edge(class_nid, base_nid, "inherits", line)
 
             # Swift-specific: conformance / inheritance
@@ -2187,16 +2195,14 @@ def _php_emit_base(base_name: str, rel: str, at_line: int) -> None:
                         return
                     base_nid = _make_id(stem, base_name)
                     if base_nid not in seen_ids:
-                        base_nid = _make_id(base_name)
-                        if base_nid not in seen_ids:
-                            nodes.append({
-                                "id": base_nid,
-                                "label": base_name,
-                                "file_type": "code",
-                                "source_file": "",
-                                "source_location": "",
-                            })
-                            seen_ids.add(base_nid)
+                        nodes.append({
+                            "id": base_nid,
+                            "label": base_name,
+                            "file_type": "code",
+                            "source_file": "",
+                            "source_location": "",
+                        })
+                        seen_ids.add(base_nid)
                     add_edge(class_nid, base_nid, rel, at_line)
 
                 for child in node.children:
@@ -2253,16 +2259,14 @@ def _php_emit_base(base_name: str, rel: str, at_line: int) -> None:
                             continue
                         base_nid = _make_id(stem, base)
                         if base_nid not in seen_ids:
-                            base_nid = _make_id(base)
-                            if base_nid not in seen_ids:
-                                nodes.append({
-                                    "id": base_nid,
-                                    "label": base,
-                                    "file_type": "code",
-                                    "source_file": "",
-                                    "source_location": "",
-                                })
-                                seen_ids.add(base_nid)
+                            nodes.append({
+                                "id": base_nid,
+                                "label": base,
+                                "file_type": "code",
+                                "source_file": "",
+                                "source_location": "",
+                            })
+                            seen_ids.add(base_nid)
                         add_edge(class_nid, base_nid, relation, line)
                         for arg_child in user_type_node.children:
                             if arg_child.type != "type_arguments":
@@ -2301,16 +2305,14 @@ def _php_emit_base(base_name: str, rel: str, at_line: int) -> None:
                             continue
                         base_nid = _make_id(stem, base)
                         if base_nid not in seen_ids:
-                            base_nid = _make_id(base)
-                            if base_nid not in seen_ids:
-                                nodes.append({
-                                    "id": base_nid,
-                                    "label": base,
-                                    "file_type": "code",
-                                    "source_file": "",
-                                    "source_location": "",
-                                })
-                                seen_ids.add(base_nid)
+                            nodes.append({
+                                "id": base_nid,
+                                "label": base,
+                                "file_type": "code",
+                                "source_file": "",
+                                "source_location": "",
+                            })
+                            seen_ids.add(base_nid)
                         relation = _csharp_classify_base(base, csharp_interface_names)
                         add_edge(class_nid, base_nid, relation, line)
                         if sub.type == "generic_name":
@@ -2334,16 +2336,14 @@ def _emit_java_parent(base_name: str, rel: str, at_line: int) -> None:
                         return
                     base_nid = _make_id(stem, base_name)
                     if base_nid not in seen_ids:
-                        base_nid = _make_id(base_name)
-                        if base_nid not in seen_ids:
-                            nodes.append({
-                                "id": base_nid,
-                                "label": base_name,
-                                "file_type": "code",
-                                "source_file": "",
-                                "source_location": "",
-                            })
-                            seen_ids.add(base_nid)
+                        nodes.append({
+                            "id": base_nid,
+                            "label": base_name,
+                            "file_type": "code",
+                            "source_file": "",
+                            "source_location": "",
+                        })
+                        seen_ids.add(base_nid)
                     add_edge(class_nid, base_nid, rel, at_line)
 
                 sup = node.child_by_field_name("superclass")
@@ -2403,16 +2403,14 @@ def _emit_java_parent(base_name: str, rel: str, at_line: int) -> None:
                             continue
                         base_nid = _make_id(stem, base)
                         if base_nid not in seen_ids:
-                            base_nid = _make_id(base)
-                            if base_nid not in seen_ids:
-                                nodes.append({
-                                    "id": base_nid,
-                                    "label": base,
-                                    "file_type": "code",
-                                    "source_file": "",
-                                    "source_location": "",
-                                })
-                                seen_ids.add(base_nid)
+                            nodes.append({
+                                "id": base_nid,
+                                "label": base,
+                                "file_type": "code",
+                                "source_file": "",
+                                "source_location": "",
+                            })
+                            seen_ids.add(base_nid)
                         add_edge(class_nid, base_nid, "inherits", line)
 
             # Find body and recurse
@@ -3189,7 +3187,7 @@ def _extract_python_rationale(path: Path, result: dict) -> None:
     nodes = result["nodes"]
     edges = result["edges"]
     seen_ids = {n["id"] for n in nodes}
-    file_nid = _make_id(str(path))
+    file_nid = _file_node_id(path)
 
     def _get_docstring(body_node) -> tuple[str, int] | None:
         if not body_node:
@@ -3306,10 +3304,7 @@ def extract_svelte(path: Path) -> dict:
         import re as _re
         src = path.read_text(encoding="utf-8", errors="replace")
         existing_ids = {n["id"] for n in result.get("nodes", [])}
-        # Source file node ID must match the one _extract_generic creates:
-        # _make_id(str(path)) - single arg, no stem prefix. Otherwise the source
-        # endpoint is a phantom node and build_from_json drops the edge (#701).
-        file_node_id = _make_id(str(path))
+        file_node_id = _file_node_id(path)
         aliases = _load_tsconfig_aliases(path.parent)
         for m in _re.finditer(r"""import\(\s*['"]([^'"]+)['"]\s*\)""", src):
             raw = m.group(1)
@@ -3322,7 +3317,7 @@ def extract_svelte(path: Path) -> dict:
                 # imports of bare paths and .svelte.ts rune files land on real
                 # file nodes instead of phantom ids (#716).
                 resolved = _resolve_js_module_path(resolved)
-                node_id = _make_id(str(resolved))
+                node_id = _file_node_id(resolved)
                 stub_source_file = str(resolved)
             else:
                 # Check tsconfig.json path aliases (e.g. "$lib/" -> "src/lib/", "@/" -> "src/")
@@ -3336,7 +3331,7 @@ def extract_svelte(path: Path) -> dict:
                         break
                 if resolved_alias is not None:
                     resolved_alias = _resolve_js_module_path(resolved_alias)
-                    node_id = _make_id(str(resolved_alias))
+                    node_id = _file_node_id(resolved_alias)
                     stub_source_file = str(resolved_alias)
                 else:
                     # Bare/scoped import (node_modules) - use last segment;
@@ -3388,7 +3383,7 @@ def extract_svelte(path: Path) -> dict:
                         resolved = resolved.with_suffix(".ts")
                     elif resolved.suffix == ".jsx":
                         resolved = resolved.with_suffix(".tsx")
-                    node_id = _make_id(str(resolved))
+                    node_id = _file_node_id(resolved)
                     stub_source_file = str(resolved)
                 else:
                     resolved_alias = None
@@ -3398,7 +3393,7 @@ def extract_svelte(path: Path) -> dict:
                             resolved_alias = Path(os.path.normpath(Path(alias_base) / rest))
                             break
                     if resolved_alias is not None:
-                        node_id = _make_id(str(resolved_alias))
+                        node_id = _file_node_id(resolved_alias)
                         stub_source_file = str(resolved_alias)
                     else:
                         module_name = raw.split("/")[-1]
@@ -3447,7 +3442,7 @@ def extract_astro(path: Path) -> dict:
         import re as _re
         src = path.read_text(encoding="utf-8", errors="replace")
         existing_ids = {n["id"] for n in result.get("nodes", [])}
-        file_node_id = _make_id(str(path))
+        file_node_id = _file_node_id(path)
         aliases = _load_tsconfig_aliases(path.parent)
         # Dynamic imports anywhere in the file: `import('./X.astro')` is legal in
         # frontmatter setup code and inside expression slots.
@@ -3458,7 +3453,7 @@ def extract_astro(path: Path) -> dict:
             if raw.startswith("."):
                 resolved = Path(os.path.normpath(path.parent / raw))
                 resolved = _resolve_js_module_path(resolved)
-                node_id = _make_id(str(resolved))
+                node_id = _file_node_id(resolved)
                 stub_source_file = str(resolved)
             else:
                 resolved_alias = None
@@ -3469,7 +3464,7 @@ def extract_astro(path: Path) -> dict:
                         break
                 if resolved_alias is not None:
                     resolved_alias = _resolve_js_module_path(resolved_alias)
-                    node_id = _make_id(str(resolved_alias))
+                    node_id = _file_node_id(resolved_alias)
                     stub_source_file = str(resolved_alias)
                 else:
                     module_name = raw.split("/")[-1]
@@ -3524,7 +3519,7 @@ def extract_astro(path: Path) -> dict:
                         resolved = resolved.with_suffix(".ts")
                     elif resolved.suffix == ".jsx":
                         resolved = resolved.with_suffix(".tsx")
-                    node_id = _make_id(str(resolved))
+                    node_id = _file_node_id(resolved)
                     stub_source_file = str(resolved)
                 else:
                     resolved_alias = None
@@ -3534,7 +3529,7 @@ def extract_astro(path: Path) -> dict:
                             resolved_alias = Path(os.path.normpath(Path(alias_base) / rest))
                             break
                     if resolved_alias is not None:
-                        node_id = _make_id(str(resolved_alias))
+                        node_id = _file_node_id(resolved_alias)
                         stub_source_file = str(resolved_alias)
                     else:
                         module_name = raw.split("/")[-1]
@@ -3729,7 +3724,7 @@ def extract_blade(path: Path) -> dict:
     except OSError:
         return {"error": f"cannot read {path}"}
 
-    file_nid = _make_id(str(path))
+    file_nid = _file_node_id(path)
     nodes = [{"id": file_nid, "label": path.name, "file_type": "code",
               "source_file": str(path), "source_location": None}]
     edges = []
@@ -3777,7 +3772,7 @@ def extract_dart(path: Path) -> dict:
 
     # Use stem (not str(path)) for child IDs to keep them machine-independent.
     stem = _file_stem(path)
-    file_nid = _make_id(str(path))
+    file_nid = _file_node_id(path)
     nodes = [{"id": file_nid, "label": path.name, "file_type": "code",
               "source_file": str(path), "source_location": None}]
     edges = []
@@ -3859,7 +3854,7 @@ def add_edge(src: str, tgt: str, relation: str, line: int,
                       "confidence": confidence, "confidence_score": score,
                       "source_file": str_path, "source_location": f"L{line}", "weight": 1.0})
 
-    file_nid = _make_id(str(path))
+    file_nid = _file_node_id(path)
     add_node(file_nid, path.name, 1)
 
     def walk(node, module_nid: str | None = None) -> None:
@@ -4254,7 +4249,7 @@ def add_edge(src: str, tgt: str, relation: str, line: int,
             edge["context"] = context
         edges.append(edge)
 
-    file_nid = _make_id(str(path))
+    file_nid = _file_node_id(path)
     add_node(file_nid, path.name, 1)
 
     def _func_name_from_signature(sig_node) -> str | None:
@@ -4506,7 +4501,7 @@ def add_edge(src: str, tgt: str, relation: str, line: int,
             edge["context"] = context
         edges.append(edge)
 
-    file_nid = _make_id(str(path))
+    file_nid = _file_node_id(path)
     add_node(file_nid, path.name, 1)
 
     def _fortran_name(stmt_node) -> str | None:
@@ -4678,7 +4673,7 @@ def add_edge(src: str, tgt: str, relation: str, line: int,
             edge["context"] = context
         edges.append(edge)
 
-    file_nid = _make_id(str(path))
+    file_nid = _file_node_id(path)
     add_node(file_nid, path.name, 1)
 
     def ensure_named_node(name: str, line: int) -> str:
@@ -5018,7 +5013,7 @@ def add_edge(src: str, tgt: str, relation: str, line: int,
             edge["context"] = context
         edges.append(edge)
 
-    file_nid = _make_id(str(path))
+    file_nid = _file_node_id(path)
     add_node(file_nid, path.name, 1)
 
     def ensure_named_node(name: str, line: int) -> str:
@@ -5286,7 +5281,7 @@ def add_edge(src: str, tgt: str, relation: str, line: int,
             edge["context"] = context
         edges.append(edge)
 
-    file_nid = _make_id(str(path))
+    file_nid = _file_node_id(path)
     add_node(file_nid, path.name, 1)
 
     def _extract_import(node) -> None:
@@ -5456,7 +5451,7 @@ def add_edge(src: str, tgt: str, relation: str, line: int,
             edge["context"] = context
         edges.append(edge)
 
-    file_nid = _make_id(str(path))
+    file_nid = _file_node_id(path)
     add_node(file_nid, path.name, 1)
 
     _PS_SKIP = frozenset({
@@ -5809,7 +5804,7 @@ def _apply_symbol_resolution_facts(
         return
 
     path_by_resolved = {path.resolve(): path for path in paths}
-    source_file_id = {path.resolve(): _make_id(str(path)) for path in paths}
+    source_file_id = {path.resolve(): _file_node_id(path) for path in paths}
     symbol_nodes: dict[tuple[Path, str], str] = {}
     for node in nodes:
         source_path = _js_source_path(str(node.get("source_file", "")), root)
@@ -5900,7 +5895,7 @@ def add_edge(source: str, target: str, relation: str, context: str, line: int, s
         if source_id is not None:
             add_edge(
                 source_id,
-                _make_id(str(path_by_resolved.get(target_path, target_path))),
+                _file_node_id(path_by_resolved.get(target_path, target_path)),
                 "re_exports",
                 "export",
                 star_fact.line,
@@ -5924,7 +5919,7 @@ def add_edge(source: str, target: str, relation: str, context: str, line: int, s
             if source_id is not None:
                 add_edge(
                     source_id,
-                    _make_id(str(path_by_resolved.get(origin[0], origin[0]))),
+                    _file_node_id(path_by_resolved.get(origin[0], origin[0])),
                     "re_exports",
                     "export",
                     export_fact.line,
@@ -6908,7 +6903,7 @@ def _resolve_cross_file_java_imports(
     new_edges: list[dict] = []
     seen_pairs: set[tuple[str, str]] = set()
     for path in paths:
-        file_nid = _make_id(str(path))
+        file_nid = _file_node_id(path)
         try:
             source = path.read_bytes()
             tree = parser.parse(source)
@@ -6995,7 +6990,7 @@ def add_edge(src: str, tgt: str, relation: str, line: int,
             edge["context"] = context
         edges.append(edge)
 
-    file_nid = _make_id(str(path))
+    file_nid = _file_node_id(path)
     add_node(file_nid, path.name, 1)
 
     def _read(node) -> str:
@@ -7197,7 +7192,7 @@ def add_edge(src: str, tgt: str, relation: str, line: int,
             edge["context"] = context
         edges.append(edge)
 
-    file_nid = _make_id(str(path))
+    file_nid = _file_node_id(path)
     add_node(file_nid, path.name, 1)
 
     _IMPORT_KEYWORDS = frozenset({"alias", "import", "require", "use"})
@@ -7389,7 +7384,7 @@ def add_edge(src: str, tgt: str, relation: str, line: int,
                       "confidence": confidence, "source_file": str_path,
                       "source_location": f"L{line}", "weight": weight})
 
-    file_nid = _make_id(str(path))
+    file_nid = _file_node_id(path)
     add_node(file_nid, path.name, 1)
 
     # Track heading stack for nesting: [(level, nid), ...]
@@ -7510,7 +7505,7 @@ def _pascal_resolve_unit(from_path: Path, unit_name: str) -> str:
         unit_map: dict[str, str] = {}
         for ext in (".pas", ".pp", ".dpr", ".dpk", ".inc"):
             for f in root.rglob("*" + ext):
-                unit_map[f.stem.lower()] = _make_id(str(f))
+                unit_map[f.stem.lower()] = _file_node_id(f)
         _pascal_unit_cache[root_key] = unit_map
     return _pascal_unit_cache[root_key].get(unit_name.lower(), _make_id(unit_name))
 
@@ -7902,7 +7897,7 @@ def add_edge(
             edge["context"] = context
         edges.append(edge)
 
-    file_nid = _make_id(str(path))
+    file_nid = _file_node_id(path)
     add_node(file_nid, path.name, 1)
     module_nid = file_nid
 
@@ -8125,7 +8120,7 @@ def add_edge(
             edge["context"] = context
         edges.append(edge)
 
-    file_nid = _make_id(str(path))
+    file_nid = _file_node_id(path)
     add_node(file_nid, path.name, 1)
 
     obj_re = re.compile(r"^\s*object\s+\w+\s*:\s*(\w+)", re.IGNORECASE)
@@ -8225,7 +8220,7 @@ def add_edge(
             edge["context"] = context
         edges.append(edge)
 
-    file_nid = _make_id(str(path))
+    file_nid = _file_node_id(path)
     add_node(file_nid, path.name, 1)
 
     obj_re   = re.compile(r"^\s*object\s+\w+\s*:\s*(\w+)", re.IGNORECASE)
@@ -8337,7 +8332,7 @@ def add_edge(src: str, tgt: str, relation: str, context: str | None = None) -> N
             edge["context"] = context
         edges.append(edge)
 
-    file_nid = _make_id(str(path))
+    file_nid = _file_node_id(path)
     add_node(file_nid, path.name)
 
     name_elem = xml_root.find(".//Package/Name")
@@ -8436,7 +8431,7 @@ def add_edge(src: str, tgt: str, relation: str, line: int,
             edge["context"] = context
         edges.append(edge)
 
-    file_nid = _make_id(str(path))
+    file_nid = _file_node_id(path)
     # file_nid is fully path-derived and never produced by _make_id(stem, func_name),
     # so appending "__entry" guarantees a distinct ID from any function node.
     entry_nid = file_nid + "__entry"
@@ -8559,7 +8554,7 @@ def walk(node, parent_nid: str) -> None:
                             # like `source ../../etc/passwd` that traverse outside
                             # the project tree (B-1).
                             if resolved.exists():
-                                tgt_nid = _make_id(str(resolved))
+                                tgt_nid = _file_node_id(resolved)
                                 add_edge(file_nid, tgt_nid, "imports_from", line,
                                          context="import")
                         else:
@@ -8622,7 +8617,7 @@ def extract_sln(path: Path) -> dict:
     except OSError:
         return {"nodes": [], "edges": [], "error": f"cannot read {path}"}
 
-    file_nid = _make_id(str(path))
+    file_nid = _file_node_id(path)
     str_path = str(path)
     nodes: list[dict] = [{"id": file_nid, "label": path.name, "file_type": "code",
                           "source_file": str_path, "source_location": None}]
@@ -8709,7 +8704,7 @@ def extract_csproj(path: Path) -> dict:
     except ET.ParseError as e:
         return {"nodes": [], "edges": [], "error": f"XML parse error: {e}"}
 
-    file_nid = _make_id(str(path))
+    file_nid = _file_node_id(path)
     str_path = str(path)
     nodes: list[dict] = [{"id": file_nid, "label": path.name, "file_type": "code",
                           "source_file": str_path, "source_location": None}]
@@ -8810,7 +8805,7 @@ def extract_razor(path: Path) -> dict:
     except OSError:
         return {"nodes": [], "edges": [], "error": f"cannot read {path}"}
 
-    file_nid = _make_id(str(path))
+    file_nid = _file_node_id(path)
     str_path = str(path)
     nodes: list[dict] = [{"id": file_nid, "label": path.name, "file_type": "code",
                           "source_file": str_path, "source_location": None}]
@@ -8969,7 +8964,7 @@ def add_edge(src: str, tgt: str, relation: str, line: int,
             edge["context"] = context
         edges.append(edge)
 
-    file_nid = _make_id(str(path))
+    file_nid = _file_node_id(path)
     add_node(file_nid, path.name, 1)
 
     def _key_text(pair_node) -> str | None:
@@ -9105,7 +9100,7 @@ def add_edge(src: str, tgt: str, relation: str, line: int,
             edge["context"] = context
         edges.append(edge)
 
-    file_nid = _make_id(str(path))
+    file_nid = _file_node_id(path)
     add_node(file_nid, path.name, 1)
 
     def _type_path_text(node) -> str:
@@ -9146,7 +9141,7 @@ def walk(node, parent_type_path: "str | None" = None,
                 resolved = (path.parent / norm).resolve()
                 edge: dict = {
                     "source": file_nid,
-                    "target": _make_id(str(resolved)) if resolved.exists() else _make_id(norm),
+                    "target": _file_node_id(resolved) if resolved.exists() else _make_id(norm),
                     "relation": "imports_from" if resolved.exists() else "imports",
                     "context": "import",
                     "confidence": "EXTRACTED",
@@ -9344,7 +9339,7 @@ def extract_dmi(path: Path) -> dict:
 
     str_path = str(path)
     stem = _file_stem(path)
-    file_nid = _make_id(str(path))
+    file_nid = _file_node_id(path)
     nodes: list[dict] = [{"id": file_nid, "label": path.name, "file_type": "code",
                            "source_file": str_path, "source_location": "L1"}]
     edges: list[dict] = []
@@ -9443,7 +9438,7 @@ def extract_dmm(path: Path) -> dict:
         return {"nodes": [], "edges": [], "error": str(e)}
 
     str_path = str(path)
-    file_nid = _make_id(str(path))
+    file_nid = _file_node_id(path)
     nodes: list[dict] = [{"id": file_nid, "label": path.name, "file_type": "code",
                            "source_file": str_path, "source_location": "L1"}]
     edges: list[dict] = []
@@ -9516,7 +9511,7 @@ def extract_dmf(path: Path) -> dict:
 
     str_path = str(path)
     stem = _file_stem(path)
-    file_nid = _make_id(str(path))
+    file_nid = _file_node_id(path)
     nodes: list[dict] = [{"id": file_nid, "label": path.name, "file_type": "code",
                            "source_file": str_path, "source_location": "L1"}]
     edges: list[dict] = []
@@ -9911,17 +9906,20 @@ def extract(
 
     _augment_symbol_resolution_edges(paths, all_nodes, all_edges, root)
 
-    # Remap file node IDs from absolute-path-derived to project-relative so
-    # graph.json edge endpoints are stable across machines (#502)
+    # Remap legacy absolute-path-derived file node IDs to the canonical
+    # stem-based format so existing graph.json files from pre-v8.0.17 still
+    # merge correctly on re-extract (#502, #1033).
     id_remap: dict[str, str] = {}
     for path in paths:
-        old_id = _make_id(str(path))
+        canonical = _file_node_id(path)
         try:
-            new_id = _make_id(str(path.relative_to(root)))
+            rel = path.relative_to(root)
         except ValueError:
             continue
-        if old_id != new_id:
-            id_remap[old_id] = new_id
+        old_ids = {_make_id(str(path)), _make_id(str(rel))}
+        for old_id in old_ids:
+            if old_id != canonical:
+                id_remap[old_id] = canonical
     if id_remap:
         for n in all_nodes:
             if n.get("id") in id_remap:
@@ -10003,7 +10001,7 @@ def extract(
             sf_rel = sf_path.relative_to(root) if sf_path.is_absolute() else sf_path
         except ValueError:
             sf_rel = sf_path
-        nid_to_file_nid[n["id"]] = _make_id(str(sf_rel))
+        nid_to_file_nid[n["id"]] = _file_node_id(sf_rel)
 
     existing_pairs = {(e["source"], e["target"]) for e in all_edges}
     for rc in all_raw_calls:
diff --git a/tests/test_astro_extraction.py b/tests/test_astro_extraction.py
index c21e66c24..307bed6b6 100644
--- a/tests/test_astro_extraction.py
+++ b/tests/test_astro_extraction.py
@@ -13,7 +13,7 @@
 
 from graphify.detect import CODE_EXTENSIONS
 from graphify.extract import (
-    _make_id,
+    _file_node_id,
     extract_astro,
 )
 
@@ -57,8 +57,8 @@ def test_extract_astro_picks_up_frontmatter_static_imports(tmp_path):
 
     result = extract_astro(page)
     targets = _import_targets(result, relation="imports_from")
-    assert _make_id(str(layout)) in targets
-    assert _make_id(str(hero)) in targets
+    assert _file_node_id(layout) in targets
+    assert _file_node_id(hero) in targets
 
 
 def test_extract_astro_handles_dynamic_import_in_frontmatter(tmp_path):
@@ -75,7 +75,7 @@ def test_extract_astro_handles_dynamic_import_in_frontmatter(tmp_path):
 
     result = extract_astro(page)
     targets = _import_targets(result, relation="dynamic_import")
-    assert _make_id(str(other)) in targets
+    assert _file_node_id(other) in targets
 
 
 def test_extract_astro_picks_up_client_side_script_imports(tmp_path):
@@ -100,8 +100,8 @@ def test_extract_astro_picks_up_client_side_script_imports(tmp_path):
 
     result = extract_astro(page)
     targets = _import_targets(result, relation="imports_from")
-    assert _make_id(str(layout)) in targets
-    assert _make_id(str(hydrate)) in targets
+    assert _file_node_id(layout) in targets
+    assert _file_node_id(hydrate) in targets
 
 
 def test_extract_astro_no_frontmatter_does_not_crash(tmp_path):
@@ -140,4 +140,4 @@ def test_extract_astro_handles_tsconfig_path_alias(tmp_path):
 
     result = extract_astro(page)
     targets = _import_targets(result, relation="imports_from")
-    assert _make_id(str(hero)) in targets
+    assert _file_node_id(hero) in targets
diff --git a/tests/test_import_extension_resolution.py b/tests/test_import_extension_resolution.py
index 0d1222c0a..9a6d6ca34 100644
--- a/tests/test_import_extension_resolution.py
+++ b/tests/test_import_extension_resolution.py
@@ -11,10 +11,9 @@
 from pathlib import Path
 
 from graphify.extract import (
-    _make_id,
+    extract_js, extract_python, extract_svelte,
+    _make_id, _file_node_id,
     _resolve_js_module_path,
-    extract_js,
-    extract_svelte,
 )
 
 
@@ -185,7 +184,7 @@ def test_bare_path_import_resolves_in_ts_file(tmp_path):
     importer = _write(tmp_path / "page.ts",
                       "import type { GetNestedType } from './type-helpers'\n")
     result = extract_js(importer)
-    expected = _make_id(str(target))
+    expected = _file_node_id(target)
     assert expected in _import_targets(result), (
         f"Bare-path .ts import must resolve to target node id; "
         f"expected {expected}; got {_import_targets(result)}"
@@ -199,7 +198,7 @@ def test_directory_import_resolves_to_index_ts(tmp_path):
     importer = _write(tmp_path / "page.ts",
                       "import { enqueue } from './queue'\n")
     result = extract_js(importer)
-    expected = _make_id(str(target))
+    expected = _file_node_id(target)
     assert expected in _import_targets(result), (
         f"Directory import must resolve to ./queue/index.ts; "
         f"expected {expected}; got {_import_targets(result)}"
@@ -216,7 +215,7 @@ def test_dot_svelte_import_resolves_to_dot_svelte_ts(tmp_path):
     importer = _write(tmp_path / "page.ts",
                       "import { isMobile } from './is-mobile.svelte'\n")
     result = extract_js(importer)
-    expected = _make_id(str(target))
+    expected = _file_node_id(target)
     assert expected in _import_targets(result), (
         f".svelte → .svelte.ts resolution failed; "
         f"expected {expected}; got {_import_targets(result)}"
@@ -233,7 +232,7 @@ def test_explicit_ts_import_still_works(tmp_path):
     importer = _write(tmp_path / "page.ts",
                       "import { x } from './foo.ts'\n")
     result = extract_js(importer)
-    expected = _make_id(str(target))
+    expected = _file_node_id(target)
     assert expected in _import_targets(result), (
         f"Explicit .ts imports must still resolve; "
         f"expected {expected}; got {_import_targets(result)}"
@@ -247,7 +246,7 @@ def test_explicit_svelte_import_still_works(tmp_path):
     importer = _write(tmp_path / "page.ts",
                       "import Card from './Card.svelte'\n")
     result = extract_js(importer)
-    expected = _make_id(str(target))
+    expected = _file_node_id(target)
     assert expected in _import_targets(result), (
         f"Existing .svelte imports must resolve to the .svelte node, "
         f"not get redirected; expected {expected}; "
@@ -285,7 +284,7 @@ def test_alias_import_with_bare_path_resolves(tmp_path):
     importer = _write(importer_dir / "page.ts",
                       "import type { X } from '$lib/type-helpers'\n")
     result = extract_js(importer)
-    expected = _make_id(str(target))
+    expected = _file_node_id(target)
     assert expected in _import_targets(result), (
         f"Alias + bare-path resolution failed; "
         f"expected {expected}; got {_import_targets(result)}"
@@ -304,7 +303,7 @@ def test_type_only_import_with_bare_path_resolves(tmp_path):
     importer = _write(tmp_path / "page.ts",
                       "import type { GetNestedType } from './type-helpers'\n")
     result = extract_js(importer)
-    expected = _make_id(str(target))
+    expected = _file_node_id(target)
     assert expected in _import_targets(result), (
         f"Type-only import with bare path failed to resolve; "
         f"expected {expected}; got {_import_targets(result)}"
@@ -342,7 +341,7 @@ def test_alias_directory_import_resolves_to_index_ts(tmp_path):
     importer = _write(src / "routes" / "page.ts",
                       "import { enqueue } from '$lib/queue'\n")
     result = extract_js(importer)
-    expected = _make_id(str(target))
+    expected = _file_node_id(target)
     assert expected in _import_targets(result), (
         f"Alias + directory resolution failed; "
         f"expected {expected}; got {_import_targets(result)}"
@@ -428,7 +427,7 @@ def test_end_to_end_multi_dot_import_resolves(tmp_path):
     importer = _write(tmp_path / "page.ts",
                       "import { apply } from './tag-action.shared'\n")
     result = extract_js(importer)
-    expected = _make_id(str(target))
+    expected = _file_node_id(target)
     assert expected in _import_targets(result), (
         f"Multi-dot import failed end-to-end; "
         f"expected {expected}; got {_import_targets(result)}"
@@ -448,7 +447,7 @@ def test_resolve_chain_alias_and_extension_compose(tmp_path):
     importer = _write(src / "routes" / "page.ts",
                       "import { isMobile } from '$lib/hooks/is-mobile.svelte'\n")
     result = extract_js(importer)
-    expected = _make_id(str(target))
+    expected = _file_node_id(target)
     assert expected in _import_targets(result), (
         f"Alias + .svelte→.svelte.ts chain failed to compose; "
         f"expected {expected}; got {_import_targets(result)}"
@@ -473,7 +472,7 @@ def test_ts_dynamic_import_bare_path_resolves(tmp_path):
 }
 """)
     result = extract_js(importer)
-    expected = _make_id(str(target))
+    expected = _file_node_id(target)
     targets = {str(e.get("target") or "") for e in result["edges"]
                if e.get("relation") in ("imports", "imports_from")}
     assert expected in targets, (
@@ -498,7 +497,7 @@ def test_ts_dynamic_import_alias_with_bare_path_resolves(tmp_path):
 }
 """)
     result = extract_js(importer)
-    expected = _make_id(str(target))
+    expected = _file_node_id(target)
     targets = {str(e.get("target") or "") for e in result["edges"]
                if e.get("relation") in ("imports", "imports_from")}
     assert expected in targets, (
@@ -521,7 +520,7 @@ def test_dynamic_import_bare_path_resolves(tmp_path):
     result = extract_svelte(importer)
     dyn_targets = {str(e.get("target") or "") for e in result["edges"]
                    if e.get("relation") == "dynamic_import"}
-    expected = _make_id(str(target))
+    expected = _file_node_id(target)
     assert expected in dyn_targets, (
         f"dynamic_import of .svelte that's actually .svelte.ts must "
         f"resolve through the new resolver; "