fix: preserve tested_by edges for Swift, Rust, Ruby, and PHP

.claude-plugin/plugin.json

@@ -1,7 +1,7 @@
 {
   "name": "understand-anything",
   "description": "AI-powered codebase understanding — analyze, visualize, and explain any project",
-  "version": "2.9.6",
+  "version": "2.9.7",
   "author": {
     "name": "Egonex"
   },

.copilot-plugin/plugin.json

@@ -1,7 +1,7 @@
 {
   "name": "understand-anything",
   "description": "AI-powered codebase understanding — analyze, visualize, and explain any project",
-  "version": "2.9.6",
+  "version": "2.9.7",
   "author": {
     "name": "Egonex"
   },

.cursor-plugin/plugin.json

@@ -2,7 +2,7 @@
   "name": "understand-anything",
   "displayName": "Understand Anything",
   "description": "AI-powered codebase understanding — analyze, visualize, and explain any project",
-  "version": "2.9.6",
+  "version": "2.9.7",
   "author": {
     "name": "Egonex"
   },

tests/skill/understand/test_merge_batch_graphs.py

@@ -147,6 +147,36 @@ def test_scala_test_files(self) -> None:
         self.assertTrue(mbg.is_test_path("src/test/scala/com/foo/BarTest.scala"))
         self.assertTrue(mbg.is_test_path("src/test/scala/com/foo/BarTests.scala"))
 
+    def test_swift_test_files(self) -> None:
+        for path in [
+            "Sources/App/AppTests.swift",
+            "Sources/App/AppTest.swift",
+            "Sources/App/AppSpec.swift",
+            "Tests/AppTests/AppTests.swift",
+            "Tests/AppTests/TestSupport.swift",
+        ]:
+            with self.subTest(path=path):
+                self.assertTrue(mbg.is_test_path(path), f"{path} should be a test")
+
+    def test_rust_test_files(self) -> None:
+        for path in ["src/parser_test.rs", "tests/parser.rs"]:
+            with self.subTest(path=path):
+                self.assertTrue(mbg.is_test_path(path), f"{path} should be a test")
+
+    def test_ruby_test_files(self) -> None:
+        for path in [
+            "test/user_test.rb",
+            "spec/user_spec.rb",
+            "spec/spec_helper.rb",
+        ]:
+            with self.subTest(path=path):
+                self.assertTrue(mbg.is_test_path(path), f"{path} should be a test")
+
+    def test_php_test_files(self) -> None:
+        for path in ["src/UserTest.php", "tests/Feature/User.php"]:
+            with self.subTest(path=path):
+                self.assertTrue(mbg.is_test_path(path), f"{path} should be a test")
+
     def test_csharp_test_files(self) -> None:
         self.assertTrue(mbg.is_test_path("Foo.Tests/BarTests.cs"))
         self.assertTrue(mbg.is_test_path("Foo.Tests/BarTest.cs"))
@@ -171,6 +201,10 @@ def test_production_files_rejected(self) -> None:
             "Foo.cs",
             "Bar.kt",
             "Bar.java",
+            "Sources/App/Contest.swift",
+            "src/contest.rs",
+            "lib/latest.rb",
+            "src/Contest.php",
         ]:
             with self.subTest(path=path):
                 self.assertFalse(mbg.is_test_path(path), f"{path} should be production")
@@ -393,6 +427,88 @@ def test_scala_multimodule_sbt_pairing_emits_forward_edge(self) -> None:
             "file:modules/core/src/test/scala/com/foo/BarSpec.scala",
         )
 
+    def test_swift_canonical_llm_edge_is_preserved(self) -> None:
+        # Regression for #646: a production → test edge must not be treated
+        # as production → production just because the test file is Swift.
+        nodes_by_id = {
+            "file:Sources/App/App.swift": _file_node("Sources/App/App.swift"),
+            "file:Sources/App/AppTests.swift": _file_node(
+                "Sources/App/AppTests.swift",
+            ),
+        }
+        edges: list[dict[str, Any]] = [
+            {
+                "source": "file:Sources/App/App.swift",
+                "target": "file:Sources/App/AppTests.swift",
+                "type": "tested_by",
+                "direction": "forward",
+                "weight": 0.5,
+                "description": "from LLM",
+            },
+        ]
+
+        added, dropped, tagged, swapped = mbg.link_tests(nodes_by_id, edges)
+
+        self.assertEqual((added, dropped, tagged, swapped), (0, 0, 1, 0))
+        self.assertEqual(len(edges), 1)
+        self.assertEqual(edges[0]["source"], "file:Sources/App/App.swift")
+        self.assertEqual(edges[0]["target"], "file:Sources/App/AppTests.swift")
+
+    def test_other_missing_language_patterns_preserve_canonical_edges(self) -> None:
+        cases = [
+            ("src/parser.rs", "tests/parser.rs"),
+            ("lib/user.rb", "spec/user_spec.rb"),
+            ("src/User.php", "tests/Feature/User.php"),
+        ]
+        for production_path, test_path in cases:
+            with self.subTest(test_path=test_path):
+                production_id = f"file:{production_path}"
+                test_id = f"file:{test_path}"
+                nodes_by_id = {
+                    production_id: _file_node(production_path),
+                    test_id: _file_node(test_path),
+                }
+                edges: list[dict[str, Any]] = [
+                    {
+                        "source": production_id,
+                        "target": test_id,
+                        "type": "tested_by",
+                        "direction": "forward",
+                        "weight": 0.5,
+                    },
+                ]
+
+                result = mbg.link_tests(nodes_by_id, edges)
+
+                self.assertEqual(result, (0, 0, 1, 0))
+                self.assertEqual(len(edges), 1)
+                self.assertEqual(edges[0]["source"], production_id)
+                self.assertEqual(edges[0]["target"], test_id)
+
+    def test_swift_inverted_llm_edge_is_swapped_and_tagged(self) -> None:
+        nodes_by_id = {
+            "file:Sources/App/App.swift": _file_node("Sources/App/App.swift"),
+            "file:Sources/App/AppTests.swift": _file_node(
+                "Sources/App/AppTests.swift",
+            ),
+        }
+        edges: list[dict[str, Any]] = [
+            {
+                "source": "file:Sources/App/AppTests.swift",
+                "target": "file:Sources/App/App.swift",
+                "type": "tested_by",
+                "direction": "forward",
+                "weight": 0.5,
+            },
+        ]
+
+        added, dropped, tagged, swapped = mbg.link_tests(nodes_by_id, edges)
+
+        self.assertEqual((added, dropped, tagged, swapped), (0, 0, 1, 1))
+        self.assertEqual(edges[0]["source"], "file:Sources/App/App.swift")
+        self.assertEqual(edges[0]["target"], "file:Sources/App/AppTests.swift")
+        self.assertIn("tested", nodes_by_id["file:Sources/App/App.swift"]["tags"])
+
     def test_no_production_counterpart_no_edge(self) -> None:
         nodes_by_id = {
             "file:src/foo.test.ts": _file_node("src/foo.test.ts"),
@@ -924,6 +1040,34 @@ def test_malformed_tags_is_replaced_not_crashed(self) -> None:
 class MergeIntegrationTests(unittest.TestCase):
     """Verify the linker is wired into merge_and_normalize correctly."""
 
+    def test_swift_canonical_edge_survives_full_merge(self) -> None:
+        production_path = "Sources/App/App.swift"
+        test_path = "Tests/AppTests/AppTests.swift"
+        batch = {
+            "nodes": [_file_node(production_path), _file_node(test_path)],
+            "edges": [
+                {
+                    "source": f"file:{production_path}",
+                    "target": f"file:{test_path}",
+                    "type": "tested_by",
+                    "direction": "forward",
+                    "weight": 0.5,
+                    "description": "LLM-emitted Swift coverage edge",
+                },
+            ],
+        }
+
+        assembled, _report = mbg.merge_and_normalize([batch])
+
+        tested_by_edges = [e for e in assembled["edges"] if e["type"] == "tested_by"]
+        self.assertEqual(len(tested_by_edges), 1)
+        self.assertEqual(tested_by_edges[0]["source"], f"file:{production_path}")
+        self.assertEqual(tested_by_edges[0]["target"], f"file:{test_path}")
+        production_node = next(
+            node for node in assembled["nodes"] if node["id"] == f"file:{production_path}"
+        )
+        self.assertIn("tested", production_node["tags"])
+
     def test_linker_runs_during_merge(self) -> None:
         batch = {
             "nodes": [

understand-anything-plugin/.claude-plugin/plugin.json

@@ -1,7 +1,7 @@
 {
   "name": "understand-anything",
   "description": "AI-powered codebase understanding — analyze, visualize, and explain any project",
-  "version": "2.9.6",
+  "version": "2.9.7",
   "author": {
     "name": "Egonex"
   },

understand-anything-plugin/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@understand-anything/skill",
-  "version": "2.9.6",
+  "version": "2.9.7",
   "type": "module",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",

understand-anything-plugin/packages/viewer/package.json

@@ -1,6 +1,6 @@
 {
   "name": "understand-anything-viewer",
-  "version": "2.9.6",
+  "version": "2.9.7",
   "description": "Standalone read-only viewer for Understand-Anything knowledge graphs — no Claude Code or LLM required.",
   "type": "module",
   "license": "MIT",

understand-anything-plugin/skills/understand/merge-batch-graphs.py

@@ -118,11 +118,24 @@ def resolve_ua_dir(root: Path) -> Path:
     ".kt": ((), ("Test", "Tests")),
     ".scala": ((), ("Spec", "Suite", "Test", "Tests")),
     ".cs": ((), ("Test", "Tests")),
+    ".swift": ((), ("Tests", "Test", "Spec")),
+    ".rs": (("test_",), ("_test",)),
+    ".rb": (("test_",), ("_test", "_spec")),
+    ".php": ((), ("Test",)),
     ".c": (("test_",), ("_test",)),
     ".cpp": (("test_",), ("_test",)),
     ".cc": (("test_",), ("_test",)),
 }
 
+# These language configs treat every source file below `tests/` as part of a
+# test target, even when the basename itself has no test marker.  JS/TS is
+# intentionally absent: files such as `__tests__/helpers.ts` remain helpers.
+_TEST_DIRECTORY_EXTENSIONS: frozenset[str] = frozenset({".swift", ".rs", ".php"})
+
+_EXACT_TEST_STEMS: dict[str, frozenset[str]] = {
+    ".rb": frozenset({"spec_helper"}),
+}
+
 
 # Mirrors packages/core/src/schema.ts so the dashboard validator has nothing
 # left to auto-correct for the `direction` field on merged graphs.
@@ -327,19 +340,29 @@ def _basename(path: str) -> str:
 
 
 def is_test_path(path: str) -> bool:
-    """Return True if `path` looks like a test file by basename convention.
+    """Return True if `path` looks like a test file by language convention.
 
-    Files inside `tests/`, `__tests__/`, `test/`, or `spec/` directories that
-    do NOT carry a recognized test extension are treated as helpers/fixtures
-    and classified as non-test (so `__tests__/helpers.ts` is not a test).
+    Most languages use basename markers. Swift, Rust, and PHP additionally
+    make `tests/` a test-source root. JS/TS files still require `.test` or
+    `.spec`, so `__tests__/helpers.ts` remains a non-test helper.
     """
     stem, ext = os.path.splitext(_basename(path))
+    ext = ext.lower()
 
     # JS/TS family: the test marker is an infix on the stem (foo.test.ts has
     # stem "foo.test", ext ".ts"), not a prefix/suffix on the stem itself.
     if ext in _JS_TS_TEST_EXTS:
         return stem.endswith(".test") or stem.endswith(".spec")
 
+    if ext in _TEST_DIRECTORY_EXTENSIONS and any(
+        segment.lower() == "tests" for segment in _path_segments(path)[:-1]
+    ):
+        return True
+
+    exact_stems = _EXACT_TEST_STEMS.get(ext)
+    if exact_stems is not None and stem in exact_stems:
+        return True
+
     patterns = _TEST_NAME_PATTERNS.get(ext)
     if patterns is None:
         return False