Merge remote-tracking branch 'origin/main' into feat-spec-approach

# Conflicts:
#	Agents/BusinessLogicExtractorAgent.cs
#	Agents/CSharpConverterAgent.cs
#	Agents/ChunkAwareCSharpConverter.cs
#	Agents/ChunkAwareJavaConverter.cs
#	Agents/CobolAnalyzerAgent.cs
#	Agents/DependencyMapperAgent.cs
#	Agents/JavaConverterAgent.cs
#	CobolToQuarkusMigration.csproj

Author: jkordick

doctor.sh

@@ -845,7 +845,7 @@ run_setup() {
 
     # Create local config from template
     echo -e "${BLUE}📁 Creating local configuration file...${NC}"
-    TEMPLATE_CONFIG="$REPO_ROOT/Config/ai-config.local.env.example"
+    TEMPLATE_CONFIG="$REPO_ROOT/Config/ai-config.local.env.template"
 
     if [ ! -f "$TEMPLATE_CONFIG" ]; then
         echo -e "${RED}❌ Example configuration file not found: $TEMPLATE_CONFIG${NC}"

todo.md

@@ -0,0 +1,18 @@
+have a look at outdated instructions
+
+have a look at demo script
+
+fix devcontainer
+
+try it with gpt 5 codex mini
+
+runtime logs to make sense of non-functionial requirements
+
+spec kit for every agent
+
+save agents prompts in prompt files to make them easier to edit and reuse
+
+ghcp sdk?
+
+run-chunked / chunked (aliases) (doctor commands) check again after merge
+Irrelevant / dead code. In the main() router, run-chunked and chunked are mapped to run_migration (the standard run), not to run_migration_chunked(). That means the entire run_migration_chunked() function (~200 lines) is dead code — never called. It also passes --chunked to dotnet, which is not a recognized CLI flag. Should be removed entirely.