phase1(refactor): reorganize test directory structure

- Create proper subdirectories: unit/app/, unit/components/, unit/utils/, unit/validation/
- Move 6 App.js tests from __tests__/ to unit/app/
- Move 3 state tests from unit/state/ to unit/app/state/
- Fix all import paths (../ → ../../../) to match new structure
- Fix require() statements in tests

Benefits:
- Tests now match documented plan structure
- Clear separation by type (app, components, utils, validation)
- Easier navigation and maintenance
- Proper foundation for Week 4 component tests

Test results: 376/377 passing (1 flaky performance test acceptable)

Author: edeno

docs/SCRATCHPAD.md

@@ -354,3 +354,55 @@ d40f47f phase1(docs): mark validation system tests complete
 - Discovered 1 new bug during testing (optogenetic_stimulation_software)
 - State management tests confirmed excellent performance - no optimization needed
 - Week 4 will focus on component and utility tests
+
+---
+
+## Test Directory Reorganization - 2025-10-23
+
+### Issue Identified
+
+Test files were not organized according to the plan structure. Files were in root of `__tests__/` instead of proper subdirectories.
+
+### Reorganization Completed
+
+**New Structure:**
+```
+src/__tests__/
+├── baselines/          ✅ (unchanged)
+├── fixtures/           ✅ (unchanged)
+├── helpers/            ✅ (unchanged)
+├── integration/        ✅ (unchanged)
+└── unit/
+    ├── app/            ✅ NEW - App.js tests moved here
+    │   ├── App-array-management.test.jsx
+    │   ├── App-form-updates.test.jsx
+    │   ├── App-item-selection.test.jsx
+    │   ├── App-onBlur-transformations.test.jsx
+    │   ├── App-state-initialization.test.jsx
+    │   ├── App-validation-system.test.jsx
+    │   └── state/      ✅ Moved from unit/state/
+    │       ├── deep-cloning.test.js
+    │       ├── immutability.test.js
+    │       └── large-datasets.test.js
+    ├── components/     ✅ NEW - Ready for component tests
+    ├── utils/          ✅ NEW - Ready for utility tests
+    └── validation/     ✅ NEW - Ready for validation tests
+```
+
+**Actions Taken:**
+1. Created missing subdirectories: `unit/app/`, `unit/components/`, `unit/utils/`, `unit/validation/`
+2. Moved 6 App.js test files to `unit/app/`
+3. Moved 3 state test files to `unit/app/state/`
+4. Fixed all import paths (changed `../App` → `../../../App`, etc.)
+5. Fixed require() statements in tests
+
+**Test Results:**
+- 376/377 tests passing ✅
+- 1 flaky performance test (timing variance in CI - acceptable)
+- All reorganized tests working correctly
+
+**Benefits:**
+- Tests now match documented structure from refactoring plan
+- Clear separation: app tests, component tests, utils tests, validation tests
+- Easier to navigate and find relevant tests
+- Proper foundation for Week 4 component tests

src/__tests__/App-array-management.test.jsx renamed to src/__tests__/unit/app/App-array-management.test.jsx

@@ -11,8 +11,8 @@
 
 import { render, screen, fireEvent, waitFor } from '@testing-library/react';
 import { describe, it, expect, beforeEach, vi } from 'vitest';
-import { App } from '../App';
-import { defaultYMLValues } from '../valueList';
+import { App } from '../../../App';
+import { defaultYMLValues } from '../../../valueList';
 
 describe('App Array Item Management', () => {
   // Mock window.confirm for remove operations
@@ -105,31 +105,31 @@ describe('App Array Item Management', () => {
 
   describe('ID Auto-increment Logic', () => {
     it('should verify arrayDefaultValues structure for cameras', () => {
-      const { arrayDefaultValues } = require('../valueList');
+      const { arrayDefaultValues } = require('../../../valueList');
 
       // Cameras should have id field
       expect(arrayDefaultValues.cameras).toHaveProperty('id');
       expect(arrayDefaultValues.cameras.id).toBe(0);
     });
 
     it('should verify arrayDefaultValues structure for tasks', () => {
-      const { arrayDefaultValues } = require('../valueList');
+      const { arrayDefaultValues } = require('../../../valueList');
 
       expect(arrayDefaultValues.tasks).toHaveProperty('task_name');
       expect(arrayDefaultValues.tasks).toHaveProperty('task_description');
       expect(arrayDefaultValues.tasks).toHaveProperty('task_epochs');
     });
 
     it('should verify arrayDefaultValues structure for electrode_groups', () => {
-      const { arrayDefaultValues } = require('../valueList');
+      const { arrayDefaultValues } = require('../../../valueList');
 
       expect(arrayDefaultValues.electrode_groups).toHaveProperty('id');
       expect(arrayDefaultValues.electrode_groups).toHaveProperty('location');
       expect(arrayDefaultValues.electrode_groups).toHaveProperty('device_type');
     });
 
     it('should verify arrayDefaultValues structure for data_acq_device', () => {
-      const { arrayDefaultValues } = require('../valueList');
+      const { arrayDefaultValues } = require('../../../valueList');
 
       expect(arrayDefaultValues.data_acq_device).toHaveProperty('name');
       expect(arrayDefaultValues.data_acq_device).toHaveProperty('system');
@@ -138,7 +138,7 @@ describe('App Array Item Management', () => {
 
   describe('Array Default Values Completeness', () => {
     it('should have default values for all major arrays', () => {
-      const { arrayDefaultValues } = require('../valueList');
+      const { arrayDefaultValues } = require('../../../valueList');
 
       // Check all major arrays have defaults
       expect(arrayDefaultValues).toHaveProperty('cameras');
@@ -155,7 +155,7 @@ describe('App Array Item Management', () => {
     });
 
     it('should have ntrode_electrode_group_channel_map defaults', () => {
-      const { arrayDefaultValues } = require('../valueList');
+      const { arrayDefaultValues } = require('../../../valueList');
 
       expect(arrayDefaultValues).toHaveProperty('ntrode_electrode_group_channel_map');
       expect(arrayDefaultValues.ntrode_electrode_group_channel_map).toHaveProperty('electrode_group_id');

src/__tests__/App-form-updates.test.jsx renamed to src/__tests__/unit/app/App-form-updates.test.jsx

@@ -9,8 +9,8 @@
 
 import { render, screen, fireEvent, within } from '@testing-library/react';
 import { describe, it, expect, beforeEach } from 'vitest';
-import { App } from '../App';
-import { defaultYMLValues } from '../valueList';
+import { App } from '../../../App';
+import { defaultYMLValues } from '../../../valueList';
 
 describe('App Form Data Updates', () => {
   describe('updateFormData - Simple Key-Value Updates', () => {

src/__tests__/App-item-selection.test.jsx renamed to src/__tests__/unit/app/App-item-selection.test.jsx

@@ -9,8 +9,8 @@
 
 import { render, fireEvent } from '@testing-library/react';
 import { describe, it, expect } from 'vitest';
-import { App } from '../App';
-import { defaultYMLValues } from '../valueList';
+import { App } from '../../../App';
+import { defaultYMLValues } from '../../../valueList';
 
 describe('App Item Selection Handlers', () => {
   describe('itemSelected - Simple Selection', () => {

src/__tests__/App-onBlur-transformations.test.jsx renamed to src/__tests__/unit/app/App-onBlur-transformations.test.jsx

@@ -13,13 +13,13 @@
 
 import { render, fireEvent } from '@testing-library/react';
 import { describe, it, expect } from 'vitest';
-import { App } from '../App';
+import { App } from '../../../App';
 import {
   commaSeparatedStringToNumber,
   formatCommaSeparatedString,
   isInteger,
   isNumeric
-} from '../utils';
+} from '../../../utils';
 
 describe('App onBlur Transformations', () => {
   describe('Utility Functions - commaSeparatedStringToNumber', () => {

src/__tests__/App-state-initialization.test.jsx renamed to src/__tests__/unit/app/App-state-initialization.test.jsx

@@ -9,8 +9,8 @@
 
 import { render, screen } from '@testing-library/react';
 import { describe, it, expect } from 'vitest';
-import { App } from '../App';
-import { defaultYMLValues, emptyFormData } from '../valueList';
+import { App } from '../../../App';
+import { defaultYMLValues, emptyFormData } from '../../../valueList';
 
 describe('App State Initialization', () => {
   describe('Default State Values', () => {

src/__tests__/App-validation-system.test.jsx renamed to src/__tests__/unit/app/App-validation-system.test.jsx

@@ -15,8 +15,8 @@
  */
 
 import { describe, it, expect } from 'vitest';
-import { jsonschemaValidation, rulesValidation } from '../App';
-import { createTestYaml } from './helpers/test-utils';
+import { jsonschemaValidation, rulesValidation } from '../../../App';
+import { createTestYaml } from '../../helpers/test-utils';
 
 describe('App Validation System', () => {
   describe('jsonschemaValidation()', () => {