fix: pass warnings through MCP handler to user

Fixed critical bug where warnings were generated by the diff engine
but not included in the MCP response, making them invisible to users.

Now warnings are properly passed through in all return paths:
- Success path (workflow updated)
- validateOnly path (dry run mode)
- Failure path (continueOnError mode)

This completes the fix for issue #360, ensuring users receive helpful
guidance when using sourceIndex instead of branch/case parameters.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

src/mcp/handlers-workflow-diff.ts

@@ -138,6 +138,7 @@ export async function handleUpdatePartialWorkflow(
           error: 'Failed to apply diff operations',
           details: {
             errors: diffResult.errors,
+            warnings: diffResult.warnings,
             operationsApplied: diffResult.operationsApplied,
             applied: diffResult.applied,
             failed: diffResult.failed
@@ -154,6 +155,9 @@ export async function handleUpdatePartialWorkflow(
         data: {
           valid: true,
           operationsToApply: input.operations.length
+        },
+        details: {
+          warnings: diffResult.warnings
         }
       };
     }
@@ -252,7 +256,8 @@ export async function handleUpdatePartialWorkflow(
           workflowName: updatedWorkflow.name,
           applied: diffResult.applied,
           failed: diffResult.failed,
-          errors: diffResult.errors
+          errors: diffResult.errors,
+          warnings: diffResult.warnings
         }
       };
     } catch (error) {