style: normalize with ruff and tidy logging/error handling

Apply ruff formatting/import-sorting across the tree and, in the touched
modules, replace bare/silent excepts with except Exception + logging and
route debug/error prints through module loggers. No behavior change.

Author: bx33661

pure_auto_codeql/agents/__init__.py

@@ -11,8 +11,8 @@
 - SinkVerificationAgent: Verifies identified Sink points using CodeQL queries
 - SourceVerificationAgent: Verifies identified Source points using CodeQL queries
 
-NOTE: The UnifiedSinkPathAgent and UnifiedSourceAnalysisAgent are the recommended agents 
-for all sink and source path analysis tasks. They support Java, Python, and C/C++ with 
+NOTE: The UnifiedSinkPathAgent and UnifiedSourceAnalysisAgent are the recommended agents
+for all sink and source path analysis tasks. They support Java, Python, and C/C++ with
 consistent logic and improved efficiency.
 """
 

pure_auto_codeql/agents/codeql_gen_agents/__init__.py

@@ -1,15 +1,15 @@
 """CodeQL generation agents package."""
 
-from pure_auto_codeql.agents.codeql_gen_agents.codeql_gen_agent import CodeQLGenAgent
 from pure_auto_codeql.agents.codeql_gen_agents.codeql_error_agent import CodeQLErrorAgent
 from pure_auto_codeql.agents.codeql_gen_agents.codeql_fix_inplace_agent import CodeQLFixInplaceAgent
-from pure_auto_codeql.agents.codeql_gen_agents.template_refinement_agent import TemplateRefinementAgent
+from pure_auto_codeql.agents.codeql_gen_agents.codeql_gen_agent import CodeQLGenAgent
 from pure_auto_codeql.agents.codeql_gen_agents.source_sink_fallback_agent import SourceSinkFallbackAgent
+from pure_auto_codeql.agents.codeql_gen_agents.template_refinement_agent import TemplateRefinementAgent
 
 __all__ = [
     'CodeQLGenAgent',
     'CodeQLErrorAgent',
     'CodeQLFixInplaceAgent',
     'TemplateRefinementAgent',
     'SourceSinkFallbackAgent',
-]
+]