fix: retract provisional package import edges

(cherry picked from commit 9a54565cb4)

tests/test_python_import_resolution.py

@@ -256,3 +256,103 @@ def test_python_parameter_return_and_generic_contexts(tmp_path: Path):
     assert ("process()", "Payload", "parameter_type") in pairs
     assert ("process()", "Result", "return_type") in pairs
     assert ("process_many()", "Payload", "generic_arg") in pairs
+
+
+def test_issue_3777_package_module_collision_phantom_cycle_absent(tmp_path: Path):
+    from graphify.analyze import find_import_cycles
+    from graphify.build import build_from_json
+
+    nettacker_py = _write(
+        tmp_path / "nettacker.py",
+        "from nettacker.main import run\n\ndef cli():\n    run()\n",
+    )
+    init_py = _write(tmp_path / "nettacker/__init__.py", "")
+    main_py = _write(
+        tmp_path / "nettacker/main.py",
+        "from nettacker.core.app import Nettacker\n\ndef run():\n    return Nettacker()\n",
+    )
+    app_py = _write(
+        tmp_path / "nettacker/core/app.py",
+        "from nettacker import logger\n\nclass Nettacker:\n    def start(self):\n        logger.log_info('start')\n",
+    )
+    logger_py = _write(
+        tmp_path / "nettacker/logger.py",
+        "def log_info(msg):\n    print(msg)\n",
+    )
+
+    result = extract(
+        [nettacker_py, init_py, main_py, app_py, logger_py],
+        cache_root=tmp_path,
+        root=tmp_path,
+    )
+
+    app_file = _node_id(result, "app.py", "nettacker/core/app.py")
+    logger_file = _node_id(result, "logger.py", "nettacker/logger.py")
+    nettacker_file = _node_id(result, "nettacker.py", "nettacker.py")
+
+    assert _has_edge(result, app_file, logger_file, "imports_from")
+    assert not _has_edge(result, app_file, nettacker_file, "imports_from")
+
+    graph = build_from_json(result)
+    assert find_import_cycles(graph) == []
+
+
+def test_issue_3777_nested_module_package_collision_resolves_to_submodule(tmp_path: Path):
+    from graphify.analyze import find_import_cycles
+    from graphify.build import build_from_json
+
+    runner_py = _write(
+        tmp_path / "pkg/runner.py",
+        "from pkg.runner.step import run\n\ndef start():\n    run()\n",
+    )
+    init_py = _write(tmp_path / "pkg/runner/__init__.py", "")
+    step_py = _write(
+        tmp_path / "pkg/runner/step.py",
+        "from pkg.runner import helper\n\ndef run():\n    helper.work()\n",
+    )
+    helper_py = _write(
+        tmp_path / "pkg/runner/helper.py",
+        "def work():\n    pass\n",
+    )
+
+    result = extract(
+        [runner_py, init_py, step_py, helper_py],
+        cache_root=tmp_path,
+        root=tmp_path,
+    )
+
+    step_file = _node_id(result, "step.py", "pkg/runner/step.py")
+    helper_file = _node_id(result, "helper.py", "pkg/runner/helper.py")
+    runner_file = _node_id(result, "runner.py", "pkg/runner.py")
+
+    assert _has_edge(result, step_file, helper_file, "imports_from")
+    assert not _has_edge(result, step_file, runner_file, "imports_from")
+
+    graph = build_from_json(result)
+    assert find_import_cycles(graph) == []
+
+
+def test_issue_3777_namespace_package_submodule_import(tmp_path: Path):
+    sub = _write(tmp_path / "ns/sub.py", "def helper():\n    pass\n")
+    consumer = _write(tmp_path / "ns/consumer.py", "from ns import sub\n")
+
+    result = extract([sub, consumer], cache_root=tmp_path, root=tmp_path)
+
+    consumer_file = _node_id(result, "consumer.py", "ns/consumer.py")
+    sub_file = _node_id(result, "sub.py", "ns/sub.py")
+
+    assert _has_edge(result, consumer_file, sub_file, "imports_from")
+
+
+def test_issue_3777_standalone_module_import_unaffected(tmp_path: Path):
+    standalone = _write(tmp_path / "standalone.py", "def fn():\n    return 42\n")
+    consumer = _write(tmp_path / "consumer.py", "from standalone import fn\n")
+
+    result = extract([standalone, consumer], cache_root=tmp_path, root=tmp_path)
+
+    consumer_file = _node_id(result, "consumer.py", "consumer.py")
+    standalone_file = _node_id(result, "standalone.py", "standalone.py")
+    fn_symbol = _node_id(result, "fn()", "standalone.py")
+
+    assert _has_edge(result, consumer_file, standalone_file, "imports_from")
+    assert _has_edge(result, consumer_file, fn_symbol, "imports")