fix: eliminate duplicate checkpoint entries and JSON-unsafe coercion

batch_runner: completed_prompts_set is already fully populated by the
time the aggregation loop runs (incremental updates happen at result
collection time), so the subsequent extend() call re-added every
completed prompt index a second time. Removed the redundant variable
and extend, and write sorted(completed_prompts_set) directly to the
final checkpoint instead.

model_tools: _coerce_number returned Python float('inf')/float('nan')
for inf/nan strings rather than the original string. json.dumps raises
ValueError for these values, so any tool call where the model emitted
"inf" or "nan" for a numeric parameter would crash at serialization.
Changed the guard to return the original string, matching the
function's documented "returns original string on failure" contract.

model_tools.py

@@ -464,9 +464,9 @@ def _coerce_number(value: str, integer_only: bool = False):
         f = float(value)
     except (ValueError, OverflowError):
         return value
-    # Guard against inf/nan before int() conversion
+    # Guard against inf/nan — not JSON-serializable, keep original string
     if f != f or f == float("inf") or f == float("-inf"):
-        return f
+        return value
     # If it looks like an integer (no fractional part), return int
     if f == int(f):
         return int(f)