Use .env or CLI for paths and options

Co-authored-by: Cursor <cursoragent@cursor.com>

capacitors_by_net_pair.py

@@ -4,8 +4,7 @@ Parse Protel PCB 2.8 ASCII (or Protel 99 SE PCB ASCII) and output capacitors
 by net pair: JSON with net pair as key, designator/value/package and total
 capacitance per net pair.
 
-Input/output paths are read from .env (INPUT_FILE, OUTPUT_FILE) if set;
-CLI arguments override them.
+All paths: use .env (INPUT_FILE, OUTPUT_FILE) or CLI; CLI overrides .env.
 
 Usage:
   python capacitors_by_net_pair.py [file.pcb] [-o output.json]

compare_protel_locations.py

@@ -3,7 +3,7 @@
 Load two Protel PCB 2.8 ASCII files and report which components have moved
 between them. Component position is taken as the centroid of pin coordinates.
 
-Input/output paths can be set in .env (FILE1, FILE2, COMPARE_OUTPUT); CLI overrides.
+All paths: use .env (FILE1, FILE2, COMPARE_OUTPUT) or CLI; CLI overrides .env.
 
 Usage:
   python3 compare_protel_locations.py file1.pcb file2.pcb [-o report.json]
@@ -101,6 +101,11 @@ def main() -> int:
         os.environ.get("COMPARE_OUTPUT", "").strip()
         or "output/compare_locations.json"
     )
+    default_threshold = os.environ.get("THRESHOLD", "").strip()
+    try:
+        default_threshold = float(default_threshold) if default_threshold else 1.0
+    except ValueError:
+        default_threshold = 1.0
 
     parser = argparse.ArgumentParser(
         description="Compare two Protel PCB ASCII files and list components that moved"
@@ -126,8 +131,8 @@ def main() -> int:
     parser.add_argument(
         "--threshold",
         type=float,
-        default=1.0,
-        help="Minimum position change to count as moved (default: 1.0)",
+        default=default_threshold,
+        help="Minimum position change to count as moved (default: THRESHOLD from .env or 1.0)",
     )
     args = parser.parse_args()