Zend certified PHP/Magento developer

Files Missing after upgrade Magento 2.4.1 to 2.4.6-p3

I am trying to upgrade Magento 2.4.1 to 2.4.6

PHP version  7.4
Composer version 2.6.5 

Below steps I have followed to upgrade

1- cp composer.json composer.json.bak

2- composer require magento/composer-root-update-plugin=~2.0 --no-update

3- composer require magento/product-community-edition=2.4.5 --no-update

4- copied contents of “require-dev” from https://github.com/magento/magento2/blob/2.4.6-p3/composer.json
and placed in my root composer.json file

5- Changed PHP version to 8.2

6- composer update While running this command there were below prompts which I set y

7- Do you trust “magento/composer-root-update-plugin” to execute code and wish to enable it now? (writes “allow-plugins” to composer.json) [y,n,d,?] y

8- Do you trust “magento/composer-dependency-version-audit-plugin” to execute code and wish to enable it now? (writes “allow-plugins” to composer.json) [y,n,d,?] y

9- Do you trust “magento/inventory-composer-installer” to execute code and wish to enable it now? (writes “allow-plugins” to composer.json) [y,n,d,?] y

These all steps went smoothly without any errors.

But the weird thing is many files are missing like Magento and .htaccess files in the bin folder

also in app/etc and bootstrap.php also missing

HOwever before doing all above steps site is running properly and all files ere available.

How to fix these?