Overlay leftover PinScope modules src still imported.

utils, resolve_passives, derating, bom_summary, pin_mux, LED current,
pin-function tokens, plus live analysis validate/validation_tools/pipeline/
validation/extraction, skills, and taxonomy JSON now resolve from
periscope/src. Inherited copies stay in dependency/. repo_paths prefers
src then /app; Docker copies src taxonomy/skills last.

tests/test_native_graph_overlay.py

@@ -30,7 +30,6 @@ def test_graph_parsers_models_taxonomy_load_from_src():
         assert "Native Periscope overlay" in path.read_text(encoding="utf-8")[:400]
 
 
-def test_taxonomy_dir_points_at_inherited_json():
+def test_taxonomy_dir_points_at_json_tree():
     ic = taxonomy.TAXONOMY_DIR / "ic.json"
     assert ic.is_file(), taxonomy.TAXONOMY_DIR
-    assert "src/taxonomy" not in str(taxonomy.TAXONOMY_DIR)

tests/test_native_leftover_overlay.py

@@ -0,0 +1,75 @@
+"""Native overlay: leftover PinScope modules src still imported resolve from src."""
+
+from __future__ import annotations
+
+from pathlib import Path
+
+import backend.periscopex.bom_summary as bom_summary
+import backend.periscopex.derating as derating
+import backend.periscopex.led_current_check as led_current_check
+import backend.periscopex.pin_function_tokens as pin_function_tokens
+import backend.periscopex.pin_mux_check as pin_mux_check
+import backend.periscopex.resolve_passives as resolve_passives
+import backend.periscopex.utils as utils
+import backend.periscopex.validate as validate
+import backend.periscopex.validation_tools as validation_tools
+import backend.services.extraction as extraction
+import backend.services.pipeline as pipeline
+import backend.services.validation as validation
+from backend.repo_paths import skills_dir, taxonomy_dir
+
+
+def _src(mod) -> Path:
+    return Path(mod.__file__).resolve()
+
+
+def test_leftover_periscopex_modules_load_from_src():
+    root = Path(__file__).resolve().parents[1]
+    src = (root / "periscope" / "src" / "backend" / "periscopex").resolve()
+    for mod, name in (
+        (utils, "utils.py"),
+        (resolve_passives, "resolve_passives.py"),
+        (derating, "derating.py"),
+        (bom_summary, "bom_summary.py"),
+        (pin_mux_check, "pin_mux_check.py"),
+        (led_current_check, "led_current_check.py"),
+        (pin_function_tokens, "pin_function_tokens.py"),
+        (validate, "validate.py"),
+        (validation_tools, "validation_tools.py"),
+    ):
+        path = _src(mod)
+        assert path == src / name, path
+        assert "Native Periscope overlay" in path.read_text(encoding="utf-8")[:500]
+
+
+def test_pipeline_extraction_validation_load_from_src():
+    root = Path(__file__).resolve().parents[1]
+    src = (root / "periscope" / "src" / "backend" / "services").resolve()
+    for mod, name in (
+        (pipeline, "pipeline.py"),
+        (extraction, "extraction.py"),
+        (validation, "validation.py"),
+    ):
+        path = _src(mod)
+        assert path == src / name, path
+        assert "Native Periscope overlay" in path.read_text(encoding="utf-8")[:500]
+
+
+def test_pipeline_still_reexports_job_workspace():
+    from backend.services.job_workspace import EventBroker, PipelineWorkspace
+
+    assert pipeline.EventBroker is EventBroker
+    assert pipeline.PipelineWorkspace is PipelineWorkspace
+    assert pipeline.set_broker.__name__ == "set_broker"
+
+
+def test_native_taxonomy_and_skills_trees():
+    root = Path(__file__).resolve().parents[1]
+    tax = taxonomy_dir()
+    skills = skills_dir()
+    assert (tax / "ic.json").is_file(), tax
+    assert (skills / "extract-pintable" / "SKILL.md").is_file(), skills
+    # Prefer src copies when not running in the Docker /app layout.
+    if not Path("/app/taxonomy").is_dir():
+        assert tax == (root / "periscope" / "src" / "taxonomy").resolve()
+        assert skills == (root / "periscope" / "src" / "skills").resolve()