These are just the deprecation notice, you can successfully proceed for the next steps. If you are getting any error then you can write us. Also, specify your bagisto and bulk-upload version.
It is always recommended that never done any changes in the the package folder but if you are familiar with Laravel codes and upgrade then you can feel free to do this.
Take an example of the vendor folder, we never do any changes in the vendor folder instead we override this and publish our files.
So I recommend you to publish all the Bagisto content in one shot and then customize your theme in the resources/ folder. Always take a backup of the resources/ folder.
First, set up all your Vue dependencies in a custom module.
Second, adjust your webpack in your custom module.
Third, start developing your component.
Fourth, once done compile your package.
Fifth, publish your changes where you want. If you want to override the theme file then publish as per the theme path.
Yes, it will cause an issue, that's why I told you to have the compatibility at your end. Because you are removing the default things.
Suppose if other modules are using some methods of Velocity package then you need to take care of this and also update that method with your new modules.
For velocity layered navigation, you can include this file,
packages/Webkul/Velocity/src/Resources/views/shop/products/list/layered-navigation.blade.php
For default theme, you can include this file,
packages/Webkul/Shop/src/Resources/views/products/list/layered-navigation.blade.php
I am just sharing the file rest you need to customize as per your need.
Thank you very much for your reply !! It is very valuable.