Move manual helper scripts out of repo root

Author: senseibelbi

scripts/manual/README.md

@@ -0,0 +1,7 @@
+Manual helper scripts used for ad hoc local verification and debugging live outside the public package surface.
+
+- `start_epa_mcp.sh`: starts the local MCP server for manual testing.
+- `test_epa_mcp_curl.sh`, `test_mcp_http.sh`, `test_legacy_uri.sh`: shell-based smoke checks for the transport layer.
+- `epa_tool_runner.py`: JSON-RPC helper for direct `tools/call` execution against a local server.
+- `test_api.py`, `test_chlorpyrifos_analysis.py`: one-off API probing scripts kept for manual diagnosis.
+- `extract_api_structure.py`: captures a local CTX client method snapshot into ignored `artifacts/`.

epa_tool_runner.py scripts/manual/epa_tool_runner.pyepa_tool_runner.py renamed to scripts/manual/epa_tool_runner.py

@@ -59,8 +59,9 @@ def extract_class_methods(cls, instance=None):
     'search_toxprints': str(inspect.signature(ctx.search_toxprints))
 }
 
-# Save to an ignored local artifact path so ad hoc snapshots do not clutter the repo root.
-output_path = Path(__file__).resolve().parent / "artifacts" / "epa_comptox_api_structure.json"
+# Save to the repo-level ignored artifacts/ path so ad hoc snapshots stay out of the public tree.
+repo_root = Path(__file__).resolve().parents[2]
+output_path = repo_root / "artifacts" / "epa_comptox_api_structure.json"
 output_path.parent.mkdir(parents=True, exist_ok=True)
 
 with output_path.open("w") as f: