lazy: repair fallout from store-infra resolve

The resolve brought over the pydantic ToolIndex and the incremental/twin
populate tests without adapting lazy-only surface: benchmarks.py still
called the deleted to_dict/from_dict, and the test config stubs lacked
the data-manager conf and biotools attributes the lazy populate path
reads. Convert benchmarks to model_dump/model_validate and consolidate
the two identical test stubs into one _populate_config helper carrying
the full attribute set.

Claude-Session: https://claude.ai/code/session_018L7ZmCv2ubKA3JNeSL8Pkr

lib/galaxy/tools/source_store/benchmarks.py

@@ -268,23 +268,23 @@ class ToolSourceBenchmarks:
         )
 
     def benchmark_index_serialization(self, iterations: int = 50) -> BenchmarkResult:
-        """Benchmark index to_dict serialization."""
+        """Benchmark index serialization to JSON-ready dicts."""
         index = self._build_sample_index(1000)
 
         return benchmark_function(
             "index_serialization",
-            lambda: index.to_dict(),
+            lambda: index.model_dump(mode="json"),
             iterations,
         )
 
     def benchmark_index_deserialization(self, iterations: int = 50) -> BenchmarkResult:
-        """Benchmark index from_dict deserialization."""
+        """Benchmark index deserialization from JSON-ready dicts."""
         index = self._build_sample_index(1000)
-        data = index.to_dict()
+        data = index.model_dump(mode="json")
 
         return benchmark_function(
             "index_deserialization",
-            lambda: ToolIndex.from_dict(data),
+            lambda: ToolIndex.model_validate(data),
             iterations,
         )