UPDATE INSTRUCTION:
The following files has been changed in version 4.6

1. assets/js/admin.js
2. assets/js/store.js
3. assets/js/store-v3.js
4. assets/js/merchant.js - NEW FILE
5. assets/css/admin.css
6. assets/css/responsive.css
7. assets/css/store-v2.css
8. assets/vendor/SimpleAjaxUploader.min.js - NEW FILE

1. protected/components/Ajax.php
2. protected/components/AjaxAdmin.php
3. protected/components/CronFunctions.php
4. protected/components/DbExt.php
5. protected/components/Functions.php
6. protected/components/FunctionsK.php
7. protected/components/FunctionsV3.php
8. protected/components/GoogleCaptcha.php
9. protected/components/ScriptManager.php
10. protected/config/main.php
11. protected/config/table_structure.php
12. protected/controller/ - ALL FILES ON THIS FOLDER
13. protected/messages/en/default.php
14. protected/models/food-item.php
15. protected/models/view-receipt.php
16. protected/vendor/authorize-sdk - NEW SDK FOR AUTHORIZE.NET
17. protected/vendor/SimpleUploader.php

1. protected/views/admin/dashboard.php
2. protected/views/admin/dishes-add.php
3. protected/views/admin/merchant-add.php
4. protected/views/admin/merchant-commision-details.php
5. protected/views/admin/theme-settings.php
6. protected/views/admin/settings-new.php - NEW FILE
7. protected/views/front/menu-category.php
8. protected/views/front/merchant-review.php
9. protected/views/front/order-history.php
10. protected/views/front/menu-ajax.php - NEW FILE
11. protected/views/front/address-book-location.php - NEW FILE
12. protected/views/layouts/admin_tpl.php
13. protected/views/layouts/front_header.php
14. protected/views/layouts/merchant_tpl.php
15. protected/views/merchant/addon_item_new.php
16. protected/views/merchant/alert-settings.php
17. protected/views/merchant/atz-init.php
18. protected/views/merchant/category_add.php
19. protected/views/merchant/dashboard.php
20. protected/views/merchant/food-item-add.php
21. protected/views/merchant/gallery-settings.php
22. protected/views/merchant/settings.php
23. protected/views/merchant/shippingrate.php
24. protected/views/merchant/category_sked.php - NEW FILE
25. protected/views/merchant/review_cancel_order.php - NEW FILE
26. protected/views/store/atz-init.php
27. protected/views/store/atz-merchant-init.php
28. protected/views/store/item.php
29. protected/views/store/menu.php
30. protected/views/store/mobile-cart.php
31. protected/views/store/pau-init.php
32. protected/views/store/payment-option.php
33. protected/views/store/profile.php
34. protected/views/store/receipt-front.php
35. protected/views/store/receipt.php
36. protected/views/store/search-results-nodata.php
37. protected/views/store/search-results.php
38. protected/views/store/sow-init.php
39. protected/views/store/add_review.php - NEW FILE

DATABASE

1. new - fields in table _order
2. new - fields in table _item
3. new - fields in table _category
4. new table _address_book_location

To update your database simply click admin panel -> dashboard -> Click here to update your database