Merge pull request CodeGraphContext#1132 from CodeGraphContext/fix/e2e-security-followup

fix: preserve multiple IMPORTS edges per file and in bundle export

Author: Shashankss1205

CGC_E2E_BUG_REPORT.md

@@ -635,11 +635,6 @@ def _extract_edges(self, output_file: Path, repo_path: Optional[Path]) -> int:
                             else:
                                 to_id = str(id(target))
 
-                        edge_key = (str(from_id), str(rel_type), str(to_id))
-                        if edge_key in seen_edges:
-                            continue
-                        seen_edges.add(edge_key)
-                        
                         # Clean up absolute path prefix inside edge properties
                         if repo_path:
                             repo_str = str(repo_path.resolve())
@@ -652,6 +647,17 @@ def _extract_edges(self, output_file: Path, repo_path: Optional[Path]) -> int:
                                 elif val.startswith(repo_prefix):
                                     rel = val[len(repo_prefix):].lstrip('/\\')
                                     rel_props[key] = "./" + rel if rel else "."
+
+                        props_key = tuple(
+                            sorted(
+                                (k, json.dumps(v, sort_keys=True, default=str))
+                                for k, v in rel_props.items()
+                            )
+                        )
+                        edge_key = (str(from_id), str(rel_type), str(to_id), props_key)
+                        if edge_key in seen_edges:
+                            continue
+                        seen_edges.add(edge_key)
 
                         # Create edge representation
                         edge_dict = {

src/codegraphcontext/core/cgc_bundle.py

@@ -499,10 +499,9 @@ def add_file_to_graph(self, file_data: Dict, repo_name: str, imports_map: dict,
                     UNWIND $batch AS row
                     MATCH (f:File {path: $file_path})
                     MERGE (m:Module {name: row.module_name})
-                    MERGE (f)-[r:IMPORTS]->(m)
+                    MERGE (f)-[r:IMPORTS {line_number: row.line_number}]->(m)
                     SET r.imported_name = row.imported_name,
-                        r.alias = row.alias,
-                        r.line_number = row.line_number
+                        r.alias = row.alias
                 """, batch=js_imports, file_path=file_path_str)
 
             if other_imports:
@@ -513,9 +512,8 @@ def add_file_to_graph(self, file_data: Dict, repo_name: str, imports_map: dict,
                     MERGE (m:Module {name: row.name})
                     SET m.alias = row.alias,
                         m.full_import_name = coalesce(row.full_import_name, m.full_import_name)
-                    MERGE (f)-[r:IMPORTS]->(m)
-                    SET r.line_number = row.line_number,
-                        r.alias = row.alias
+                    MERGE (f)-[r:IMPORTS {line_number: row.line_number}]->(m)
+                    SET r.alias = row.alias
                 """, batch=other_imports, file_path=file_path_str)
 
             # ── Batch: Ruby Class INCLUDES Module ─────────────────────────────

src/codegraphcontext/tools/graph_builder.py

@@ -446,10 +446,9 @@ def add_file_to_graph(
                     UNWIND $batch AS row
                     MATCH (f:File {path: $file_path})
                     MERGE (m:Module {name: row.module_name})
-                    MERGE (f)-[r:IMPORTS]->(m)
+                    MERGE (f)-[r:IMPORTS {line_number: row.line_number}]->(m)
                     SET r.imported_name = row.imported_name,
-                        r.alias = row.alias,
-                        r.line_number = row.line_number
+                        r.alias = row.alias
                 """,
                     batch=js_imports,
                     file_path=file_path_str,
@@ -463,9 +462,8 @@ def add_file_to_graph(
                     MERGE (m:Module {name: row.name})
                     SET m.lang = coalesce(row.lang, m.lang),
                         m.full_import_name = coalesce(row.full_import_name, m.full_import_name)
-                    MERGE (f)-[r:IMPORTS]->(m)
-                    SET r.line_number = row.line_number,
-                        r.alias = coalesce(row.alias, ""),
+                    MERGE (f)-[r:IMPORTS {line_number: row.line_number}]->(m)
+                    SET r.alias = coalesce(row.alias, ""),
                         r.imported_name = row.imported_name,
                         r.full_import_name = row.full_import_name
                 """,

src/codegraphcontext/tools/indexing/persistence/writer.py

@@ -1,16 +1,16 @@
 {
   "cgc_version": "0.1.0",
-  "exported_at": "2026-06-07T16:25:53Z",
+  "exported_at": "2026-06-07T18:00:01Z",
   "format_version": "1.0.0",
   "repo": "sample_project",
   "repo_path": ".",
   "is_dependency": false,
-  "commit": "c6d693bc",
-  "branch": "main",
+  "commit": "f3f62d33",
+  "branch": "fix/e2e-security-followup",
   "generator": "PYv0.4.16",
   "name": "sample_project.cgc",
   "graph_metrics": {
     "total_nodes": 482,
-    "total_edges": 619
+    "total_edges": 621
   }
 }