fix(extract): create json_config reference target nodes (#1764)

extract_json emitted `imports` edges for package.json dependencies and
`extends`/`$ref` edges for tsconfig.json to target ids (`_make_id("ref", ...)`
/ `_make_id(key)`) that it never created as nodes. build_from_json drops edges
to unknown node ids silently (that case is filtered out of real_errors), so
dependency and extends structure vanished from the graph on two of the most
common files in any JS/TS repo, surfaced only by diagnose_extraction after the
fact.

The extractor now adds the referenced target as a `concept` node (external ref,
not a corpus file) before emitting each edge, so the edges survive build.
Regression test asserts no dangling endpoints, the concept nodes exist, and the
import/extends edges land on real targets with no self-loops.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

CHANGELOG.md

@@ -4,6 +4,8 @@ Full release notes with details on each version: [GitHub Releases](https://githu
 
 ## 0.9.12 (unreleased)
 
+- Fix: `json_config` no longer emits `imports`/`extends` edges to node IDs it never creates (#1764, thanks @oleksii-tumanov). `package.json` dependencies and `tsconfig.json` `extends`/`$ref` targets produced edges whose endpoint node was absent, so `build_from_json` silently dropped them (the "no matching node id" case is filtered out of real errors) — losing dependency/extends structure on two of the most common files in any JS/TS repo. The extractor now creates the referenced target as a `concept` node before adding the edge.
+
 - Fix: `graphify update` no longer deletes semantic hyperedges on every run (#1755, thanks @oleksii-tumanov). The AST-only rebuild treated every rebuilt corpus file as grounds to evict hyperedges anchored to it, but the AST pass never re-emits hyperedges, so doc-sourced hyperedges (exactly what semantic extraction produces) were permanently lost on the first `update` after a full build — even a no-op run. Hyperedge eviction is now scoped to genuinely deleted (or symlink-outside) sources, mirroring node/edge handling; replacement-by-id and dangling-member cleanup are unchanged.
 
 - Fix: Java member calls resolve against the receiver's declared type instead of a bare method-name match (#1696/#1697, thanks @oleksii-tumanov). `gw.charge()` where `gw: PaymentGateway` now binds to `PaymentGateway.charge`, not a same-named `AuditLog.charge` in another file. Explicit-type receivers and `this` are exact; current-class fields, method parameters, and explicitly-typed locals resolve via a method-scoped type table; a missing, ambiguous, inherited, or chained receiver is skipped rather than guessed (same god-node guard as the C#/Swift/Ruby resolvers). Fully-qualified and nested-type receivers are deferred (they need package/nesting-aware type identity).

graphify/extractors/json_config.py

@@ -90,10 +90,10 @@ def extract_json(path: Path) -> dict:
         "optionalDependencies", "bundleDependencies", "bundledDependencies",
     })
 
-    def add_node(nid: str, label: str, line: int) -> None:
+    def add_node(nid: str, label: str, line: int, file_type: str = "code") -> None:
         if nid and nid not in seen_ids:
             seen_ids.add(nid)
-            nodes.append({"id": nid, "label": label, "file_type": "code",
+            nodes.append({"id": nid, "label": label, "file_type": file_type,
                           "source_file": str_path, "source_location": f"L{line}"})
 
     def add_edge(src: str, tgt: str, relation: str, line: int,
@@ -165,6 +165,7 @@ def extract_json(path: Path) -> dict:
                         if ref:
                             ref_nid = _make_id("ref", ref)
                             if ref_nid:
+                                add_node(ref_nid, ref, line, file_type="concept")
                                 add_edge(key_nid, ref_nid, "extends", line, context="import")
 
             elif val.type == "string":
@@ -175,6 +176,7 @@ def extract_json(path: Path) -> dict:
                     # Namespace external refs to avoid ID collision with file nodes (J-4)
                     ref_nid = _make_id("ref", val_text)
                     if ref_nid:
+                        add_node(ref_nid, val_text, line, file_type="concept")
                         add_edge(file_nid, ref_nid, "extends", line, context="import")
 
                 elif key == "$ref" and val_text:
@@ -186,6 +188,7 @@ def extract_json(path: Path) -> dict:
                 elif parent_key in _DEP_KEYS and val_text:
                     dep_nid = _make_id(key)
                     if dep_nid:
+                        add_node(dep_nid, key, line, file_type="concept")
                         add_edge(key_nid, dep_nid, "imports", line, context="import")
 
     # Entry: find root document → object

tests/test_extract.py

@@ -6,6 +6,7 @@ from pathlib import Path
 
 import pytest
 
+from graphify.build import build_from_json
 from graphify.extract import extract_python, extract, collect_files, _make_id, extract_bash, extract_json, _DISPATCH
 
 FIXTURES = Path(__file__).parent / "fixtures"
@@ -1468,6 +1469,55 @@ def test_extract_json_extends_resolved():
     assert extends_edges[0].get("context") == "import"
 
 
+def test_extract_json_import_and_extends_targets_are_real_nodes(tmp_path):
+    package_json = tmp_path / "package.json"
+    package_json.write_text(json.dumps({
+        "name": "demo",
+        "dependencies": {"left-pad": "^1.3.0"},
+        "devDependencies": {"bats": "^1.11.0"},
+    }))
+    tsconfig = tmp_path / "tsconfig.json"
+    tsconfig.write_text(json.dumps({
+        "extends": "./tsconfig.base.json",
+        "compilerOptions": {"strict": True},
+    }))
+
+    results = [extract_json(package_json), extract_json(tsconfig)]
+    combined = {
+        "nodes": [node for result in results for node in result["nodes"]],
+        "edges": [edge for result in results for edge in result["edges"]],
+    }
+    node_ids = {node["id"] for node in combined["nodes"]}
+    dangling = [
+        edge for edge in combined["edges"]
+        if edge["source"] not in node_ids or edge["target"] not in node_ids
+    ]
+    assert dangling == []
+    assert {"left-pad", "bats", "./tsconfig.base.json"} <= {
+        node["label"] for node in combined["nodes"] if node["file_type"] == "concept"
+    }
+
+    extracted = extract([package_json, tsconfig], cache_root=tmp_path, parallel=False)
+    graph = build_from_json(extracted, directed=True)
+    import_targets = {
+        graph.nodes[data["_tgt"]]["label"]
+        for _, _, data in graph.edges(data=True)
+        if data.get("relation") == "imports"
+    }
+    extends_targets = {
+        graph.nodes[data["_tgt"]]["label"]
+        for _, _, data in graph.edges(data=True)
+        if data.get("relation") == "extends"
+    }
+    self_loops = [
+        data for _, _, data in graph.edges(data=True)
+        if data.get("relation") in {"imports", "extends"} and data["_src"] == data["_tgt"]
+    ]
+    assert self_loops == []
+    assert {"left-pad", "bats"} <= import_targets
+    assert extends_targets == {"./tsconfig.base.json"}
+
+
 def test_extract_json_large_file_skipped(tmp_path):
     big = tmp_path / "big.json"
     # Write a JSON file just over 1 MiB