chore: Merge runner config args with CLI overrides

[cdc-as81]

Summary

• Add runner support for reading base args and merged custom args from the args section of the JSON config file.
• Keep global properties loading compatible by excluding the reserved args section before applying global property config.
• Add run_with_merged_args and RunnerArgs for callers that want config/CLI-merged custom arguments.
• Fix logging precedence so explicit CLI logging flags override config-sourced logging fields as a group.

[github-actions]

Benchmark Results

Hyperfine

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
large_sir::baseline	3.2 ± 0.0	3.2	3.4	1.00
large_sir::baseline_households	3.3 ± 0.1	3.2	3.5	1.01 ± 0.03
large_sir::entities	7.3 ± 0.1	7.1	7.6	2.25 ± 0.05
large_sir::households	7.2 ± 0.1	6.9	7.4	2.21 ± 0.05

Criterion

Regressions (slower)

Group	Bench	Param	Change	CI Lower	CI Upper
indexing	query_people_single_indexed_property_entities		10.023%	9.672%	10.252%
sampling	sampling_single_unindexed_entities		8.473%	8.312%	8.651%
large_dataset	bench_query_population_indexed_property_entities		7.577%	5.798%	9.619%
indexing	query_people_indexed_multi-property_entities		7.454%	6.803%	8.088%
counts	multi_property_unindexed_entities		6.478%	4.821%	8.274%
sampling	sampling_multiple_unindexed_entities		5.080%	4.997%	5.160%
large_dataset	bench_filter_indexed_entity		4.563%	1.940%	7.325%
indexing	query_people_multiple_individually_indexed_properties_entities		3.529%	3.398%	3.655%
sample_entity	sample_entity_whole_population	10000	3.173%	2.444%	3.807%
sampling	sampling_multiple_l_reservoir_entities		1.988%	1.900%	2.075%
counts	index_after_adding_entities		1.940%	1.603%	2.317%
sample_entity	sample_entity_whole_population	1000	1.497%	1.080%	1.974%

Improvements (faster)

Group	Bench	Param	Change	CI Lower	CI Upper
counts	multi_property_indexed_entities		-44.261%	-44.433%	-44.068%
large_dataset	bench_match_entity		-23.618%	-24.410%	-22.670%
sample_entity	sample_entity_single_property_unindexed	1000	-17.265%	-17.566%	-16.940%
sample_entity	sample_entity_single_property_unindexed	10000	-12.987%	-13.844%	-12.174%
large_dataset	bench_query_population_derived_property_entities		-11.364%	-11.945%	-10.810%
sampling	sampling_single_known_length_entities		-5.911%	-6.683%	-5.075%
sampling	count_and_sampling_single_known_length_entities		-5.806%	-6.593%	-5.161%
examples	example-basic-infection		-4.560%	-5.302%	-3.839%
indexing	query_people_count_multiple_individually_indexed_properties_enti		-3.394%	-3.651%	-2.994%
sample_entity	sample_entity_single_property_indexed	1000	-2.786%	-3.414%	-2.093%
sampling	count_and_sampling_single_unindexed_concrete_plus_derived_entiti		-2.500%	-2.604%	-2.396%
sampling	sampling_single_unindexed_concrete_plus_derived_entities		-2.356%	-2.422%	-2.272%
sample_entity	sample_entity_single_property_indexed	100000	-2.272%	-3.038%	-1.521%

Unchanged / inconclusive (CI crosses 0%)

Group	Bench	Param	Change	CI Lower	CI Upper
counts	single_property_indexed_entities		-1.646%	-2.804%	-0.544%
sample_entity	sample_entity_single_property_indexed	10000	-1.631%	-2.518%	-0.717%
sample_entity	sample_entity_whole_population	100000	1.427%	0.831%	2.051%
indexing	with_query_results_indexed_multi-property_entities		-1.387%	-1.936%	-0.809%
sample_entity	sample_entity_multi_property_indexed	1000	-1.223%	-2.068%	-0.379%
sample_entity	sample_entity_multi_property_indexed	10000	-1.204%	-2.052%	-0.375%
algorithm_benches	algorithm_sampling_single_known_length		-1.190%	-3.709%	1.281%
large_dataset	bench_query_population_multi_indexed_entities		1.105%	0.677%	1.616%
counts	reindex_after_adding_more_entities		-1.089%	-1.832%	-0.315%
algorithm_benches	algorithm_sampling_single_l_reservoir		1.026%	0.204%	2.214%
indexing	query_people_count_indexed_multi-property_entities		-0.893%	-1.436%	-0.526%
sample_entity	sample_entity_multi_property_indexed	100000	-0.820%	-1.709%	-0.009%
large_dataset	bench_query_population_multi_unindexed_entities		0.719%	0.327%	1.142%
large_dataset	bench_filter_unindexed_entity		-0.675%	-3.749%	2.507%
algorithm_benches	algorithm_sampling_multiple_l_reservoir		-0.560%	-1.215%	0.095%
indexing	with_query_results_single_indexed_property_entities		0.507%	0.146%	0.861%
indexing	with_query_results_multiple_individually_indexed_properties_enti		-0.417%	-0.821%	0.222%
sample_entity	sample_entity_single_property_unindexed	100000	0.382%	-0.027%	0.720%
algorithm_benches	algorithm_sampling_multiple_known_length		-0.364%	-0.915%	0.208%
sampling	sampling_multiple_known_length_entities		-0.313%	-0.601%	-0.012%
sampling	sampling_single_l_reservoir_entities		0.312%	0.134%	0.480%
large_dataset	bench_query_population_property_entities		0.226%	-0.061%	0.555%
examples	example-births-deaths		-0.196%	-0.444%	0.092%
algorithm_benches	algorithm_sampling_single_rand_reservoir		-0.154%	-0.855%	0.466%
indexing	query_people_count_single_indexed_property_entities		0.097%	-0.662%	0.701%
counts	single_property_unindexed_entities		-0.073%	-0.807%	0.757%
counts	concrete_plus_derived_unindexed_entities		-0.060%	-0.692%	0.345%

Not Compared (no baseline yet)

Group	Bench	Reason
(none)