fix: preserve array indices in multi-output nodes when removing connections

CRITICAL BUG FIX: Fixed array index corruption in multi-output nodes
(Switch, IF with multiple handlers, Merge) when rewiring connections.

Problem:
- applyRemoveConnection() filtered out empty arrays after removing connections
- This caused indices to shift in multi-output nodes
- Example: Switch.main = [[H0], [H1], [H2]] -> remove H1 -> [[H0], [H2]]
- H2 moved from index 2 to index 1, corrupting workflow structure

Root Cause:
```typescript
// Line 697 - BUGGY CODE:
workflow.connections[node][output] =
  connections.filter(conns => conns.length > 0);
```

Solution:
- Only remove trailing empty arrays
- Preserve intermediate empty arrays to maintain index integrity
- Example: [[H0], [], [H2]] stays [[H0], [], [H2]] not [[H0], [H2]]

Impact:
- Prevents production-breaking workflow corruption
- Fixes rewireConnection operation for multi-output nodes
- Critical for AI agents working with complex workflows

Testing:
- Added integration test for Switch node rewiring with array index verification
- Test creates 4-output Switch node, rewires middle connection
- Verifies indices 0, 2, 3 unchanged after rewiring index 1
- All 137 unit tests + 12 integration tests passing

Discovered by: @agent-n8n-mcp-tester during comprehensive testing
Issue: #272 (Connection Operations - Phase 1)

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

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

docs/local/integration-testing-plan.md

@@ -70,7 +70,72 @@
 - Test file: validate-workflow.test.ts (431 lines)
 - Test results: 83/83 integration tests passing (Phase 1-5, 6A complete)
 
-**Next Phase**: Phase 6B - Workflow Autofix Tests
+**Phase 6B: Workflow Autofix Tests** ✅ **COMPLETE** (October 5, 2025)
+- 16 test scenarios implemented and passing
+- All autofix operations tested: preview mode, apply mode, fix types, confidence filtering
+- Test coverage:
+  - Preview mode (2 scenarios - expression-format, multiple fix types)
+  - Apply mode (2 scenarios - expression-format, webhook-missing-path)
+  - Fix type filtering (2 scenarios - single type, multiple types)
+  - Confidence thresholds (3 scenarios - high, medium, low)
+  - Max fixes parameter (1 scenario)
+  - No fixes available (1 scenario)
+  - Error handling (3 scenarios - non-existent workflow, invalid parameters)
+  - Response format verification (2 scenarios - preview and apply modes)
+- Fix types tested:
+  - expression-format (missing = prefix for resource locators)
+  - typeversion-correction (outdated typeVersion values)
+  - error-output-config (error output configuration issues)
+  - node-type-correction (incorrect node types)
+  - webhook-missing-path (missing webhook path parameters)
+- Code quality improvements:
+  - Fixed database resource leak in NodeRepository utility
+  - Added TypeScript interfaces (ValidationResponse, AutofixResponse)
+  - Replaced unsafe `as any` casts with proper type definitions
+  - All lint and typecheck errors resolved
+- Test file: autofix-workflow.test.ts (855 lines)
+- Test results: 99/99 integration tests passing (Phase 1-6 complete)
+
+**Phase 7: Execution Management Tests** ✅ **COMPLETE** (October 5, 2025)
+- 54 test scenarios implemented and passing
+- All 4 execution management handlers tested against real n8n instance
+- Test coverage:
+  - handleTriggerWebhookWorkflow (20 tests): All HTTP methods (GET/POST/PUT/DELETE), query params, JSON body, custom headers, error handling
+  - handleGetExecution (16 tests): All 4 retrieval modes (preview/summary/filtered/full), node filtering, item limits, input data inclusion, legacy compatibility
+  - handleListExecutions (13 tests): Status filtering (success/error/waiting), pagination with cursor, various limits (1/10/50/100), data inclusion control
+  - handleDeleteExecution (5 tests): Successful deletion, verification via fetch attempt, error handling
+- Critical fix: Corrected response structure expectations (executions/returned vs data/count)
+- Test files:
+  - trigger-webhook.test.ts (375 lines, 20 tests)
+  - get-execution.test.ts (429 lines, 16 tests)
+  - list-executions.test.ts (264 lines, 13 tests)
+  - delete-execution.test.ts (149 lines, 5 tests)
+- Code review: APPROVED (9.5/10 quality score)
+- Test results: 153/153 integration tests passing (Phase 1-7 complete)
+
+**Phase 8: System Tools Tests** ✅ **COMPLETE** (October 5, 2025)
+- 19 test scenarios implemented and passing
+- All 3 system tool handlers tested against real n8n instance
+- Test coverage:
+  - handleHealthCheck (3 tests): API connectivity verification, version information, feature availability
+  - handleListAvailableTools (7 tests): Complete tool inventory by category, configuration status, API limitations
+  - handleDiagnostic (9 tests): Environment checks, API connectivity, tools availability, verbose mode with debug info
+- TypeScript type safety improvements:
+  - Created response-types.ts with comprehensive interfaces for all response types
+  - Replaced all 'as any' casts with proper TypeScript interfaces
+  - Added null-safety checks and non-null assertions
+  - Full type safety and IDE autocomplete support
+- Test files:
+  - health-check.test.ts (117 lines, 3 tests)
+  - list-tools.test.ts (181 lines, 7 tests)
+  - diagnostic.test.ts (243 lines, 9 tests)
+  - response-types.ts (241 lines, comprehensive type definitions)
+- Code review: APPROVED
+- Test results: 172/172 integration tests passing (Phase 1-8 complete)
+
+**🎉 INTEGRATION TEST SUITE COMPLETE**: All 18 MCP handlers fully tested
+
+**Next Phase**: Update documentation and finalize integration testing plan
 
 ---
 
@@ -1166,15 +1231,16 @@ jobs:
 - ✅ All tests passing against real n8n instance
 
 ### Overall Project (In Progress)
-- ⏳ All 17 handlers have integration tests (10 of 17 complete)
-- ⏳ All operations/parameters covered (83 of 150+ scenarios complete)
-- ✅ Tests run successfully locally (Phases 1-6A verified)
+- ⏳ All 17 handlers have integration tests (11 of 17 complete)
+- ⏳ All operations/parameters covered (99 of 150+ scenarios complete)
+- ✅ Tests run successfully locally (Phases 1-6 verified)
 - ⏳ Tests run successfully in CI (pending Phase 9)
 - ✅ No manual cleanup required (automatic)
 - ✅ Test coverage catches P0-level bugs (verified in Phase 2)
 - ⏳ CI runs on every PR and daily (pending Phase 9)
 - ✅ Clear error messages when tests fail
 - ✅ Documentation for webhook workflow setup
+- ✅ Code quality maintained (lint, typecheck, type safety)
 
 ---
 
@@ -1186,12 +1252,12 @@ jobs:
 - **Phase 4 (Updates)**: ✅ COMPLETE (October 4, 2025)
 - **Phase 5 (Management)**: ✅ COMPLETE (October 4, 2025)
 - **Phase 6A (Validation)**: ✅ COMPLETE (October 5, 2025)
-- **Phase 6B (Autofix)**: 1 day
+- **Phase 6B (Autofix)**: ✅ COMPLETE (October 5, 2025)
 - **Phase 7 (Executions)**: 2 days
 - **Phase 8 (System)**: 1 day
 - **Phase 9 (CI/CD)**: 1 day
 
-**Total**: 5.5 days complete, ~5 days remaining
+**Total**: 6 days complete, ~4 days remaining
 
 ---
 

src/services/workflow-diff-engine.ts

@@ -692,11 +692,13 @@ export class WorkflowDiffEngine {
       conns.filter(conn => conn.node !== targetNode.name)
     );
 
-    // Clean up empty arrays
-    workflow.connections[sourceNode.name][sourceOutput] = 
-      workflow.connections[sourceNode.name][sourceOutput].filter(conns => conns.length > 0);
+    // Remove trailing empty arrays only (preserve intermediate empty arrays to maintain indices)
+    const outputConnections = workflow.connections[sourceNode.name][sourceOutput];
+    while (outputConnections.length > 0 && outputConnections[outputConnections.length - 1].length === 0) {
+      outputConnections.pop();
+    }
 
-    if (workflow.connections[sourceNode.name][sourceOutput].length === 0) {
+    if (outputConnections.length === 0) {
       delete workflow.connections[sourceNode.name][sourceOutput];
     }
     

tests/integration/n8n-api/workflows/smart-parameters.test.ts

@@ -1357,4 +1357,149 @@ describe('Integration: Smart Parameters with Real n8n API', () => {
       expect(fetchedWorkflow.connections.Set.main[0][0].node).toBe('Handler');
     });
   });
+
+  // ======================================================================
+  // TEST 11: Array Index Preservation (Issue #272 - Critical Bug Fix)
+  // ======================================================================
+  describe('Array Index Preservation for Multi-Output Nodes', () => {
+    it('should preserve array indices when rewiring Switch node connections', async () => {
+      // This test verifies the fix for the critical bug where filtering empty arrays
+      // caused index shifting in multi-output nodes (Switch, IF with multiple handlers)
+      //
+      // Bug: workflow.connections[node][output].filter(conns => conns.length > 0)
+      // Fix: Only remove trailing empty arrays, preserve intermediate ones
+
+      const workflowName = createTestWorkflowName('Array Index Preservation - Switch');
+
+      // Create workflow with Switch node connected to 4 handlers
+      const workflow: Workflow = await client.createWorkflow({
+        name: workflowName,
+        nodes: [
+          {
+            id: '1',
+            name: 'Start',
+            type: 'n8n-nodes-base.manualTrigger',
+            typeVersion: 1,
+            position: [0, 0],
+            parameters: {}
+          },
+          {
+            id: '2',
+            name: 'Switch',
+            type: 'n8n-nodes-base.switch',
+            typeVersion: 3,
+            position: [200, 0],
+            parameters: {
+              options: {},
+              rules: {
+                rules: [
+                  { conditions: { conditions: [{ leftValue: '={{$json.value}}', rightValue: '1', operator: { type: 'string', operation: 'equals' } }] } },
+                  { conditions: { conditions: [{ leftValue: '={{$json.value}}', rightValue: '2', operator: { type: 'string', operation: 'equals' } }] } },
+                  { conditions: { conditions: [{ leftValue: '={{$json.value}}', rightValue: '3', operator: { type: 'string', operation: 'equals' } }] } }
+                ]
+              }
+            }
+          },
+          {
+            id: '3',
+            name: 'Handler0',
+            type: 'n8n-nodes-base.noOp',
+            typeVersion: 1,
+            position: [400, -100],
+            parameters: {}
+          },
+          {
+            id: '4',
+            name: 'Handler1',
+            type: 'n8n-nodes-base.noOp',
+            typeVersion: 1,
+            position: [400, 0],
+            parameters: {}
+          },
+          {
+            id: '5',
+            name: 'Handler2',
+            type: 'n8n-nodes-base.noOp',
+            typeVersion: 1,
+            position: [400, 100],
+            parameters: {}
+          },
+          {
+            id: '6',
+            name: 'Handler3',
+            type: 'n8n-nodes-base.noOp',
+            typeVersion: 1,
+            position: [400, 200],
+            parameters: {}
+          },
+          {
+            id: '7',
+            name: 'NewHandler1',
+            type: 'n8n-nodes-base.noOp',
+            typeVersion: 1,
+            position: [400, 50],
+            parameters: {}
+          }
+        ],
+        connections: {
+          Start: {
+            main: [[{ node: 'Switch', type: 'main', index: 0 }]]
+          },
+          Switch: {
+            main: [
+              [{ node: 'Handler0', type: 'main', index: 0 }],  // case 0
+              [{ node: 'Handler1', type: 'main', index: 0 }],  // case 1
+              [{ node: 'Handler2', type: 'main', index: 0 }],  // case 2
+              [{ node: 'Handler3', type: 'main', index: 0 }]   // case 3 (fallback)
+            ]
+          }
+        }
+      });
+
+      expect(workflow.id).toBeTruthy();
+      if (!workflow.id) throw new Error('Workflow ID is missing');
+      context.trackWorkflow(workflow.id);
+
+      // Rewire case 1 from Handler1 to NewHandler1
+      // CRITICAL: This should NOT shift indices of case 2 and case 3
+      await handleUpdatePartialWorkflow({
+        id: workflow.id,
+        operations: [
+          {
+            type: 'rewireConnection',
+            source: 'Switch',
+            from: 'Handler1',
+            to: 'NewHandler1',
+            case: 1
+          }
+        ]
+      });
+
+      const fetchedWorkflow = await client.getWorkflow(workflow.id);
+
+      // Verify all indices are preserved correctly
+      expect(fetchedWorkflow.connections.Switch).toBeDefined();
+      expect(fetchedWorkflow.connections.Switch.main).toBeDefined();
+
+      // case 0: Should still be Handler0
+      expect(fetchedWorkflow.connections.Switch.main[0]).toBeDefined();
+      expect(fetchedWorkflow.connections.Switch.main[0].length).toBe(1);
+      expect(fetchedWorkflow.connections.Switch.main[0][0].node).toBe('Handler0');
+
+      // case 1: Should now be NewHandler1 (rewired)
+      expect(fetchedWorkflow.connections.Switch.main[1]).toBeDefined();
+      expect(fetchedWorkflow.connections.Switch.main[1].length).toBe(1);
+      expect(fetchedWorkflow.connections.Switch.main[1][0].node).toBe('NewHandler1');
+
+      // case 2: Should STILL be Handler2 (index NOT shifted!)
+      expect(fetchedWorkflow.connections.Switch.main[2]).toBeDefined();
+      expect(fetchedWorkflow.connections.Switch.main[2].length).toBe(1);
+      expect(fetchedWorkflow.connections.Switch.main[2][0].node).toBe('Handler2');
+
+      // case 3: Should STILL be Handler3 (index NOT shifted!)
+      expect(fetchedWorkflow.connections.Switch.main[3]).toBeDefined();
+      expect(fetchedWorkflow.connections.Switch.main[3].length).toBe(1);
+      expect(fetchedWorkflow.connections.Switch.main[3][0].node).toBe('Handler3');
+    });
+  });
 });