Fix alert type code-comment

Right now it was being recorded every time that the step was
executed. With this PR now it's only recorded when a malicious
package is found and we elevate the severity type to `critical`

src/codegate/pipeline/extract_snippets/output.py

@@ -5,7 +5,7 @@
 from litellm import ModelResponse
 from litellm.types.utils import Delta, StreamingChoices
 
-from codegate.pipeline.base import CodeSnippet, PipelineContext
+from codegate.pipeline.base import AlertSeverity, CodeSnippet, PipelineContext
 from codegate.pipeline.extract_snippets.extract_snippets import extract_snippets
 from codegate.pipeline.output import OutputPipelineContext, OutputPipelineStep
 from codegate.storage import StorageEngine
@@ -85,6 +85,11 @@ async def _snippet_comment(self, snippet: CodeSnippet, context: PipelineContext)
 archived packages: {libobjects_text}\n"
         comment += "\n### 🚨 Warnings\n" + "\n".join(warnings) + "\n"
 
+        # Add an alert to the context
+        context.add_alert(
+            self.name, trigger_string=comment, severity_category=AlertSeverity.CRITICAL
+        )
+
         return comment
 
     def _split_chunk_at_code_end(self, content: str) -> tuple[str, str]:
@@ -147,9 +152,6 @@ async def process_chunk(
                 chunks.append(self._create_chunk(chunk, after))
                 complete_comment += after
 
-            # Add an alert to the context
-            input_context.add_alert(self.name, trigger_string=complete_comment)
-
             return chunks
 
         # Pass through all other content that does not create a new snippet